Nucleic acid tertiary structure
Encyclopedia
The tertiary structure of a nucleic acid
is its precise three-dimensional structure, as defined by the atomic coordinates. RNA
and DNA
molecules are capable of diverse functions ranging from molecular recognition to catalysis. Such functions require a precise three-dimensional tertiary structure. While such structures are diverse and seemingly complex, they are composed of recurring, easily recognizable tertiary structure motifs that serve as molecular building blocks. Some of the most common motifs for RNA and DNA tertiary structure are described below, but it is important to remember that this information is based on a limited number of solved structures. Many more tertiary structural motifs will be revealed as new RNA and DNA molecules are structurally characterized.
, B-DNA, and Z-DNA
. The "B" form described by James D. Watson
and Francis Crick
is believed to predominate in cells. James D. Watson
and Francis Crick
described this structure as a double helix with a radius of 10 Å
and pitch of 34 Å
, making one complete turn about its axis every 10 bp
of sequence. The double helix makes one complete turn about its axis every 10.4-10.5 base pairs in solution. This frequency of twist (known as the helical pitch) depends largely on stacking forces that each base exerts on its neighbours in the chain. Double-helical RNA adopts a conformation similar to the A-form structure.
Other conformations are possible; in fact, only the letters F, Q, U, V, and Y are now available to describe any new DNA structure that may appear in the future. However, most of these forms have been created synthetically and have not been observed in naturally occurring biological systems.
structural motif. Because interactions with the minor groove
are often mediated by the 2'-OH of the ribose
sugar, this RNA motif looks very different from its DNA
equivalent. The most common example of a minor loop triple is the A-minor motif, or the insertion of adenosine bases into the minor groove (see above). However, this motif is not restricted to adenosines, as other nucleobase
s have also been observed to interact with the RNA minor groove.
The minor groove presents a near-perfect complement for an inserted base. This allows for optimal van der Waals contacts
, extensive hydrogen bond
ing and hydrophobic
surface burial, and creates a highly energetically favorable interaction. Because minor groove triples are capable of stably packing a free loop and helix, they are key elements in the structure of large ribonucleotide
s, including the group I intron, the group II intron, and the ribosome
.
Although the major groove of standard A-form RNA is fairly narrow and therefore less available for triplex interaction than the minor groove, major groove triplex interactions can be observed in several RNA structures. These structures consist of several combinations of base pair
and Hoogsteen interactions. For example, the GGC triplex (GGC amino(N-2)-N-7, imino-carbonyl, carbonyl-amino(N-4); Watson-Crick) observed in the 50S ribosome
, composed of a Watson-Crick type G-C pair and an incoming G which forms a pseudo-Hoogsteen network of hydrogen bonding interactions between both bases involved in the canonical pairing. Other notable examples of major groove triplexes include (i) the catalytic core of the group II intron
shown in the figure at left (ii) a catalytically essential triple helix
observed in human telomerase RNA
and (iii) the SAM-II riboswitch.
Triple-stranded DNA
is also possible from Hoogsteen or reversed Hoogsteen hydrogen bonds
in the major groove of B-form DNA.
and DNA
can both also form quadruple helices. There are diverse structures of RNA base quadruplexes. Four consecutive guanine
residues can form a quadruplex in RNA by Hoogsteen
hydrogen bonds to form a “Hoogsteen ring” (See Figure). G-C and A-U pairs can also form base quadruplex with a combination of Watson-Crick
pairing and noncanonical pairing in the minor groove
.
The core of malachite green aptamer
is also a kind of base quadruplex with a different hydrogen bonding pattern (See Figure). The quadruplex can repeat several times consecutively, producing an immensely stable structure.
The unique structure of quadruplex regions in RNA may serve different functions in a biological system. Two important functions are the binding potential with ligand
s or proteins, and its ability to stabilize the whole tertiary structure
of DNA or RNA. The strong structure can inhibit or modulate transcription
and replication
, such as in the telomere
s of chromosomes and the UTR of mRNA. The base identity is important towards ligand binding. The G-quartet typically binds monovalent cations such as potassium, while other bases can bind numerous other ligands such as hypoxanthine in a U-U-C-U quadruplex.
Along with these functions, the G-quadruplex
in the mRNA around the ribosome binding regions could serve as a regulator of gene expression
in bacteria
. There may be more interesting structures and functions yet to be discovered in vivo
.
of tRNAPhe. More recently, coaxial stacking has been observed in higher order structures of many ribozymes, including many forms of the self-splicing group I
and group II introns. Common coaxial stacking motifs include the kissing loop interaction and the pseudoknot
. The stability of these interactions can be predicted by an adaptation of “Turner’s rules”.
In 1994, Walter and Turner determined the free energy contributions of nearest neighbor stacking interactions within a helix-helix interface by using a model system that created a helix-helix interface between a short oligomer
and a four-nucleotide
overhang at the end of a hairpin stem
. Their experiments confirmed that the thermodynamic contribution of base-stacking between two helical secondary structures closely mimics the thermodynamics of standard duplex formation (nearest neighbor interactions predict the thermodynamic stability of the resulting helix). The relative stability of nearest neighbor interactions can be used to predict favorable coaxial stacking based on known secondary structure. Walter and Turner found that, on average, prediction of RNA structure improved from 67% to 74% accuracy when coaxial stacking contributions were included. Theories of coaxial stacking can be tested using the technique of helical fusion. This approach was used by Murphy and Cech to confirm a coaxial stacking interaction between the P4 and P6 helices within the catalytic center of the Tetrahymena
group I intron.
Most well-studied RNA tertiary structures contain examples of coaxial stacking. Some prominent examples are tRNA-Phe, group I introns, group II introns, and ribosomal RNAs. Crystal structures of tRNA revealed the presence of two extended helices that result from coaxial stacking of the amino-acid acceptor stem with the T-arm, and stacking of the D- and anticodon-arms. These interactions within tRNA orient the anticodon stem perpendicularly to the amino-acid stem, leading to the functional L-shaped tertiary structure. In group I introns, the P4 and P6 helices were shown to coaxially stack using a combination of biochemical and crystallographic methods. The P456 crystal structure provided a detailed view of how coaxial stacking stabilizes the packing of RNA helices into tertiary structures. In the self-splicing group II intron from Oceanobacillus iheyensis, the IA and IB stems coaxially stack and contribute to the relative orientation of the constituent helices of a five-way junction. This orientation facilitates proper folding of the active site
of the functional ribozyme. The ribosome contains numerous examples of coaxial stacking, including stacked segments as long as 70 bp.
Two common motifs involving coaxial stacking are kissing loops and pseudoknots. In kissing loop interactions, the single-stranded loop regions of two hairpins interact through base pairing, forming a composite, coaxially stacked helix. Notably, this structure allows all of the nucleotides in each loop to participate in base-pairing and stacking interactions. This motif was visualized and studied using NMR analysis by Lee and Crothers. The pseudoknot motif occurs when a single stranded region of a hairpin loop basepairs with an upstream or downstream sequence within the same RNA strand. The two resulting duplex regions often stack upon one another, forming a stable coaxially stacked composite helix. One example of a pseudoknot motif is the highly stable Hepatitis Delta virus ribozyme, in which the backbone shows an overall double pseudoknot topology.
An effect similar to coaxial stacking has been observed in rationally designed
DNA structures. DNA origami
structures contain a large number of double helixes with exposed blunt ends. These structures were observed to stick together along the edges that contained these exposed blunt ends, due to the hydrophobic stacking interactions.
motif and a receptor motif located within an RNA duplex, creating a tertiary contact that stabilizes the global tertiary fold of an RNA
molecule. Tetraloops are also possible structures in DNA duplexes.
Stem-loops can vary greatly in size and sequence, but tetraloops of four nucleotides are very common and they usually belong to one of three categories, based on sequence. These three families are the CUYG, UNCG and GNRA (see figure on the right) tetraloops. In each of these tetraloop families, the second and third nucleotides form a turn in the RNA strand and a base-pair between the first and fourth nucleotides stabilizes the stemloop structure. It has been determined, in general, that the stability of the tetraloop depends on the composition of bases within the loop and on the composition of this "closing base pair". The GNRA family of tetraloops is the most commonly observed within Tetraloop-receptor interactions.
“Tetraloop receptor motifs” are long-range tertiary interactions consisting of hydrogen bonding between the bases in the tetraloop
to stemloop sequences in distal sections of the secondary RNA structure. In addition to hydrogen bonding, stacking interactions are an important component of these tertiary interactions. For example, in GNRA-tetraloop interactions, the second nucleotide of the tetraloop stacks directly on an A-platform motif (see above) within the receptor. The sequence of the tetraloop and its receptor often covary so that the same type of tertiary contact can be made with different isoforms of the tetraloop and its cognate receptor.
For example, the self-splicing group I intron relies on tetraloop receptor motifs for its structure and function. Specifically, the three adenine residues of the canonical GAAA motif stack on top of the receptor helix and form multiple stabilizing hydrogen bonds with the receptor. The first adenine of the GAAA sequence forms a triple base-pair with the receptor AU bases. The second adenine is stabilized by hydrogen bonds with the same uridine, as well as via its 2'-OH with the recptor and via interactions with the guanine of the GAAA tetraloop. The third adenine forms a triple base pair.
motif. It is formed by the insertion of an unpaired nucleoside
into the minor groove of an RNA duplex. As such it is an example of a minor groove triple. Although guanosine, cytosine and uridine can also form minor groove triple interactions, minor groove interactions by adenine are very common. In the case of adenine, the N1-C2-N3 edge of the inserting base forms hydrogen bonds with one or both of the 2’-OH’s of the duplex, as well as the bases of the duplex (see figure: A-minor interactions). The host duplex is often a G-C basepair.
A-minor motifs have been separated into four classes, types 0 to III, based upon the position of the inserting base relative to the two 2’-OH’s of the Watson-Crick base pair
. In type I and II A-minor motifs, N3 of adenine is inserted deeply within the minor groove of the duplex (see figure: A minor interactions - type II interaction), and there is good shape complementarity with the base pair. Unlike types 0 and III, type I and II interactions are specific for adenine due to hydrogen bonding interactions. In the type III interaction, both the O2' and N3 of the inserting base are associated less closely with the minor groove of the duplex. Type 0 and III motifs are weaker and non-specific because they are mediated by interactions with a single 2’-OH (see figure: A-minor Interactions - type 0 and type III interactions).
The A-minor motif is among the most common RNA structural motifs in the ribosome, where it contributes to the binding of tRNA to the 23S subunit. They most often stabilize RNA duplex interactions in loops and helices, such as in the core of group II introns.
An interesting example of A-minor is its role in anticodon recognition. The ribosome must discriminate between correct and incorrect codon-anticodon pairs. It does so, in part, through the insertion of adenine bases into the minor groove. Incorrect codon-anticodon pairs will present distorted helical geometry, which will prevent the A-minor interaction from stabilizing the binding, and increase the dissociation rate of the incorrect tRNA.
tertiary structural element in which two RNA chains are held together by hydrogen bonding interactions involving the 2’OH of ribose
sugars on different strands. The 2'OH can behave as both hydrogen bond donor and acceptor, which allows formation of bifurcated hydrogen bonds with another 2’ OH.
Numerous forms of ribose zipper have been reported, but a common type involves four hydrogen bonds between 2'-OH groups of two adjacent sugars. Ribose zippers commonly occur in arrays that stabilize interactions between separate RNA strands. Ribose zippers are often observed as Stem-loop
interactions with very low sequence specificity. However, in the small and large ribosomal subunits, there exists a propensity for ribose zippers of the CC/AA sequence- two cytosine
s on the first chain paired to two adenine
s on the second chain.
s are often folded, stable molecules with three-dimensional shapes rather than floppy, linear strands. Cations are essential for thermodynamic stabilization of RNA tertiary structures. Metal cations that bind RNA can be monovalent, divalent or trivalent. Potassium
(K+) is a common monovalent ion that binds RNA. A common divalent ion that binds RNA is magnesium
(Mg2+). Other ions including sodium
(Na+), calcium
(Ca2+) and manganese
(Mn2+) have been found to bind RNA in vivo and in vitro. Multivalent organic cations such as spermidine or spermine are also found in cells and these make important contributions to RNA folding. Trivalent ions such as cobalt hexamine or lanthanide ions such as terbium
(Tb3+) are useful experimental tools for studying metal binding to RNA.
A metal ion can interact with RNA in multiple ways. An ion can associate diffusely with the RNA backbone, shielding otherwise unfavorable electrostatic interactions. This charge screening is often fulfilled by monovalent ions. Site-bound ions stabilize specific elements of RNA tertiary structure. Site-bound interactions can be further subdivided into two categories depending on whether water mediates the metal binding. “Outer sphere” interactions are mediated by water molecules that surround the metal ion. For example, magnesium hexahydrate interacts with and stabilizes specific RNA tertiary structure motifs via interactions with guanosine
in the major groove. Conversely, “inner sphere” interactions are directly mediated by the metal ion. RNA often folds in multiple stages and these steps can be stabilized by different types of cations. In the early stages, RNA forms secondary structure
s stabilized through the binding of monovalent cations, divalent cations and polyanionic amines in order to neutralize the polyanionic backbone. The later stages of this process involve the formation of RNA tertiary structure, which is stabilized almost largely through the binding of divalent ions such as magnesium with possible contributions from potassium binding.
Metal-binding sites are often localized in the deep and narrow major groove of the RNA duplex, coordinating to the Hoogsteen
edges of purine
s. In particular, metal cations
stabilize sites of backbone twisting where tight packing of phosphate
s results in a region of dense negative charge. There are several metal ion-binding motifs in RNA duplexes that have been identified in crystal structures. For instance, in the P4-P6 domain of the Tetrahymena thermophila group I intron
, several ion-binding sites consist of tandem G-U wobble pairs
and tandem G-A mismatches
, in which divalent
cations interact with the Hoogsteen edge of guanosine via O6 and N7. Another ion-binding motif in the Tetrahymena group I intron is the A-A platform motif, in which consecutive adenosines in the same strand of RNA form a non-canonical pseudobase pair. Unlike the tandem G-U motif, the A-A platform motif binds preferentially to monovalent cations. In many of these motifs, absence of the monovalent or divalent cations results in either greater flexibility or loss of tertiary structure.
Divalent metal ions, especially magnesium
, have been found to be important for the structure of DNA junctions such as the Holliday junction
intermediate in genetic recombination
. The magnesium ion shields the negatively-charged phosphate groups in the junction and allows them to be positioned closer together, allowing a stacked conformation rather than an unstacked conformation. Magnesium is vital in stabilizing these kinds of junctions in artificially designed
structures used in DNA nanotechnology
, such as the double crossover motif.
In the mid 1960's, the role of tRNA in protein synthesis was being intensively studied. In 1965, Holley et al. purified and sequenced the first tRNA molecule, initially proposing that it adopted a cloverleaf structure, based largely on the ability of certain regions of the molecule to form stem loop structures. The isolation of tRNA proved to be the first major windfall in RNA structural biology. In 1971, Kim et al. achieved another breakthrough, producing crystals of yeast tRNAPHE that diffracted to 2-3 Ångström resolutions by using spermine, a naturally occurring polyamine, which bound to and stabilized the tRNA.
For a considerable time following the first tRNA structures, the field of RNA structure did not dramatically advance. The ability to study an RNA structure depended upon the potential to isolate the RNA target. This proved limiting to the field for many years, in part owing to the fact that other known targets - i.e. the ribosome - were significantly more difficult to isolate and crystallize. As such, for some twenty years following the original publication of the tRNAPHE structure, the structures of only a handful of other RNA targets were solved, with almost all of these belonging to the transfer RNA family.
This unfortunate lack of scope would eventually be overcome largely because of two major advancements in nucleic acid research: the identification of ribozymes, and the ability to produce them via in vitro transcription. Subsequent to Tom Cech's publication implicating the Tetrahymena group I intron as an autocatalytic ribozyme, and Sidney Altman's report of catalysis by ribonuclease P RNA, several other catalytic RNAs were identified in the late 1980s, including the hammerhead ribozyme. In 1994, McKay et al. published the structure of a 'hammerhead RNA-DNA ribozyme-inhibitor complex' at 2.6 Ångström resolution, in which the autocatalytic activity of the ribozyme was disrupted via binding to a DNA substrate. In addition to the advances being made in global structure determination via crystallography, the early 1990s also saw the implementation of NMR as a powerful technique in RNA structural biology. Investigations such as this enabled a more precise characterization of the base pairing and base stacking interactions which stabilized the global folds of large RNA molecules.
The resurgence of RNA structural biology in the mid-1990s has caused a veritable explosion in the field of nucleic acid structural research. Since the publication of the hammerhead and P4-6 structures, numerous major contributions to the field have been made. Some of the most noteworthy examples include the structures of the Group I and Group II introns, and the Ribosome. It should be noted that the first three structures were produced using in vitro transcription, and that NMR has played a role in investigating partial components of all four structures - testaments to the indispensability of both techniques for RNA research. Most recently, the 2009 Nobel Prize in Chemistry was awarded to Ada Yonath, Venkatraman Ramakrishnan, and Thomas Steitz for their structural work on the ribosome, demonstrating the prominent role RNA structural biology has taken in modern molecular biology.
Nucleic acid
Nucleic acids are biological molecules essential for life, and include DNA and RNA . Together with proteins, nucleic acids make up the most important macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information...
is its precise three-dimensional structure, as defined by the atomic coordinates. RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
and DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
molecules are capable of diverse functions ranging from molecular recognition to catalysis. Such functions require a precise three-dimensional tertiary structure. While such structures are diverse and seemingly complex, they are composed of recurring, easily recognizable tertiary structure motifs that serve as molecular building blocks. Some of the most common motifs for RNA and DNA tertiary structure are described below, but it is important to remember that this information is based on a limited number of solved structures. Many more tertiary structural motifs will be revealed as new RNA and DNA molecules are structurally characterized.
Helical structures
Double helix
The double helix is the dominant tertiary structure for biological DNA, and is also a possible structure for RNA. Three DNA conformations are believed to be found in nature, A-DNAA-DNA
A-DNA is one of the many possible double helical structures of DNA. A-DNA is thought to be one of three biologically active double helical structures along with B- and Z-DNA. It is a right-handed double helix fairly similar to the more common and well-known B-DNA form, but with a shorter more...
, B-DNA, and Z-DNA
Z-DNA
Z-DNA is one of the many possible double helical structures of DNA. It is a left-handed double helical structure in which the double helix winds to the left in a zig-zag pattern...
. The "B" form described by James D. Watson
James D. Watson
James Dewey Watson is an American molecular biologist, geneticist, and zoologist, best known as one of the co-discoverers of the structure of DNA in 1953 with Francis Crick...
and Francis Crick
Francis Crick
Francis Harry Compton Crick OM FRS was an English molecular biologist, biophysicist, and neuroscientist, and most noted for being one of two co-discoverers of the structure of the DNA molecule in 1953, together with James D. Watson...
is believed to predominate in cells. James D. Watson
James D. Watson
James Dewey Watson is an American molecular biologist, geneticist, and zoologist, best known as one of the co-discoverers of the structure of DNA in 1953 with Francis Crick...
and Francis Crick
Francis Crick
Francis Harry Compton Crick OM FRS was an English molecular biologist, biophysicist, and neuroscientist, and most noted for being one of two co-discoverers of the structure of the DNA molecule in 1953, together with James D. Watson...
described this structure as a double helix with a radius of 10 Å
Ångström
The angstrom or ångström, is a unit of length equal to 1/10,000,000,000 of a meter . Its symbol is the Swedish letter Å....
and pitch of 34 Å
Ångström
The angstrom or ångström, is a unit of length equal to 1/10,000,000,000 of a meter . Its symbol is the Swedish letter Å....
, making one complete turn about its axis every 10 bp
Base pair
In molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...
of sequence. The double helix makes one complete turn about its axis every 10.4-10.5 base pairs in solution. This frequency of twist (known as the helical pitch) depends largely on stacking forces that each base exerts on its neighbours in the chain. Double-helical RNA adopts a conformation similar to the A-form structure.
Other conformations are possible; in fact, only the letters F, Q, U, V, and Y are now available to describe any new DNA structure that may appear in the future. However, most of these forms have been created synthetically and have not been observed in naturally occurring biological systems.
Major and minor groove triplexes
The minor groove triple is a ubiquitous RNARNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
structural motif. Because interactions with the minor groove
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
are often mediated by the 2'-OH of the ribose
Ribose
Ribose is an organic compound with the formula C5H10O5; specifically, a monosaccharide with linear form H––4–H, which has all the hydroxyl groups on the same side in the Fischer projection....
sugar, this RNA motif looks very different from its DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
equivalent. The most common example of a minor loop triple is the A-minor motif, or the insertion of adenosine bases into the minor groove (see above). However, this motif is not restricted to adenosines, as other nucleobase
Nucleobase
Nucleobases are a group of nitrogen-based molecules that are required to form nucleotides, the basic building blocks of DNA and RNA. Nucleobases provide the molecular structure necessary for the hydrogen bonding of complementary DNA and RNA strands, and are key components in the formation of stable...
s have also been observed to interact with the RNA minor groove.
The minor groove presents a near-perfect complement for an inserted base. This allows for optimal van der Waals contacts
Van der Waals force
In physical chemistry, the van der Waals force , named after Dutch scientist Johannes Diderik van der Waals, is the sum of the attractive or repulsive forces between molecules other than those due to covalent bonds or to the electrostatic interaction of ions with one another or with neutral...
, extensive hydrogen bond
Hydrogen bond
A hydrogen bond is the attractive interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen or fluorine, that comes from another molecule or chemical group. The hydrogen must be covalently bonded to another electronegative atom to create the bond...
ing and hydrophobic
Hydrophobic effect
The hydrophobic effect is the observed tendency of nonpolar substances to aggregate in aqueous solution and exclude water molecules. The name, literally meaning "water-fearing," describes the segregation and apparent repulsion between water and nonpolar substances...
surface burial, and creates a highly energetically favorable interaction. Because minor groove triples are capable of stably packing a free loop and helix, they are key elements in the structure of large ribonucleotide
Ribonucleotide
A ribonucleotide or ribotide is a nucleotide in which a purine or pyrimidine base is linked to a ribose molecule and exactly one phosphate group. In living organisms the most common bases for ribonucleotides are adenine , guanine , cytosine , or uracil ....
s, including the group I intron, the group II intron, and the ribosome
Ribosome
A ribosome is a component of cells that assembles the twenty specific amino acid molecules to form the particular protein molecule determined by the nucleotide sequence of an RNA molecule....
.
Although the major groove of standard A-form RNA is fairly narrow and therefore less available for triplex interaction than the minor groove, major groove triplex interactions can be observed in several RNA structures. These structures consist of several combinations of base pair
Base pair
In molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...
and Hoogsteen interactions. For example, the GGC triplex (GGC amino(N-2)-N-7, imino-carbonyl, carbonyl-amino(N-4); Watson-Crick) observed in the 50S ribosome
50S
50S is the larger subunit of the 70S ribosome of prokaryotes. It is the site of inhibition for antibiotics such as macrolides, chloramphenicol, clindamycin, and the pleuromutilins. It includes the subunits 5S and 23S.-Structure:...
, composed of a Watson-Crick type G-C pair and an incoming G which forms a pseudo-Hoogsteen network of hydrogen bonding interactions between both bases involved in the canonical pairing. Other notable examples of major groove triplexes include (i) the catalytic core of the group II intron
Group II intron
Group II introns are a large class of self-catalytic ribozymes as well as mobile genetic element found within the genes of all three domains of life. Ribozyme activity can occur under high-salt conditions in vitro. However, assistance from proteins is required for in vivo splicing...
shown in the figure at left (ii) a catalytically essential triple helix
Triple helix
In geometry, a triple helix is a set of three congruent geometrical helices with the same axis, differing by a translation along the axis. Structures in the form of a triple helix include:* collagen helix...
observed in human telomerase RNA
Telomerase RNA component
Telomerase RNA component, also known as TERC, is an RNA gene found in eukaryotes, that is a component of telomerase used to extend telomeres. Telomerase RNAs differ greatly in sequence and structure between vertebrates, ciliates and yeasts, but they share a 5' pseudoknot structure close to the...
and (iii) the SAM-II riboswitch.
Triple-stranded DNA
Triple-stranded DNA
A triple-stranded DNA is a structure of DNA in which three oligonucleotides wind around each other and form a triple helix. In this structure, one strand binds to a B-form DNA double helix through Hoogsteen or reversed Hoogsteen hydrogen bonds....
is also possible from Hoogsteen or reversed Hoogsteen hydrogen bonds
Hoogsteen base pair
A Hoogsteen base pair is a variation of base-pairing in nucleic acids such as the A•T pair. In this manner, two nucleobases on each strand can be held together by hydrogen bonds in the major groove...
in the major groove of B-form DNA.
Quadruplexes
Besides double helices and the above-mentioned triplexes, RNARNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
and DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
can both also form quadruple helices. There are diverse structures of RNA base quadruplexes. Four consecutive guanine
Guanine
Guanine is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine . In DNA, guanine is paired with cytosine. With the formula C5H5N5O, guanine is a derivative of purine, consisting of a fused pyrimidine-imidazole ring system with...
residues can form a quadruplex in RNA by Hoogsteen
Hoogsteen base pair
A Hoogsteen base pair is a variation of base-pairing in nucleic acids such as the A•T pair. In this manner, two nucleobases on each strand can be held together by hydrogen bonds in the major groove...
hydrogen bonds to form a “Hoogsteen ring” (See Figure). G-C and A-U pairs can also form base quadruplex with a combination of Watson-Crick
Base pair
In molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...
pairing and noncanonical pairing in the minor groove
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
.
The core of malachite green aptamer
Aptamer
Aptamers are oligonucleic acid or peptide molecules that bind to a specific target molecule. Aptamers are usually created by selecting them from a large random sequence pool, but natural aptamers also exist in riboswitches. Aptamers can be used for both basic research and clinical purposes as...
is also a kind of base quadruplex with a different hydrogen bonding pattern (See Figure). The quadruplex can repeat several times consecutively, producing an immensely stable structure.
The unique structure of quadruplex regions in RNA may serve different functions in a biological system. Two important functions are the binding potential with ligand
Ligand
In coordination chemistry, a ligand is an ion or molecule that binds to a central metal atom to form a coordination complex. The bonding between metal and ligand generally involves formal donation of one or more of the ligand's electron pairs. The nature of metal-ligand bonding can range from...
s or proteins, and its ability to stabilize the whole tertiary structure
Tertiary structure
In biochemistry and molecular biology, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.-Relationship to primary structure:...
of DNA or RNA. The strong structure can inhibit or modulate transcription
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
and replication
DNA replication
DNA replication is a biological process that occurs in all living organisms and copies their DNA; it is the basis for biological inheritance. The process starts with one double-stranded DNA molecule and produces two identical copies of the molecule...
, such as in the telomere
Telomere
A telomere is a region of repetitive DNA sequences at the end of a chromosome, which protects the end of the chromosome from deterioration or from fusion with neighboring chromosomes. Its name is derived from the Greek nouns telos "end" and merοs "part"...
s of chromosomes and the UTR of mRNA. The base identity is important towards ligand binding. The G-quartet typically binds monovalent cations such as potassium, while other bases can bind numerous other ligands such as hypoxanthine in a U-U-C-U quadruplex.
Along with these functions, the G-quadruplex
G-quadruplex
In molecular biology, G-quadruplexes are nucleic acid sequences that are rich in guanine and are capable of forming a four-stranded structure...
in the mRNA around the ribosome binding regions could serve as a regulator of gene expression
Gene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
in bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
. There may be more interesting structures and functions yet to be discovered in vivo
In vivo
In vivo is experimentation using a whole, living organism as opposed to a partial or dead organism, or an in vitro controlled environment. Animal testing and clinical trials are two forms of in vivo research...
.
Coaxial stacking
Coaxial stacking, otherwise known as helical stacking, is a major determinant of higher order RNA tertiary structure. Coaxial stacking occurs when two RNA duplexes form a contiguous helix, which is stabilized by base stacking at the interface of the two helices. Coaxial stacking was noted in the crystal structureCrystal structure
In mineralogy and crystallography, crystal structure is a unique arrangement of atoms or molecules in a crystalline liquid or solid. A crystal structure is composed of a pattern, a set of atoms arranged in a particular way, and a lattice exhibiting long-range order and symmetry...
of tRNAPhe. More recently, coaxial stacking has been observed in higher order structures of many ribozymes, including many forms of the self-splicing group I
Group I catalytic intron
Group I introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of nine paired regions...
and group II introns. Common coaxial stacking motifs include the kissing loop interaction and the pseudoknot
Pseudoknot
A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow mosaic virus in 1982...
. The stability of these interactions can be predicted by an adaptation of “Turner’s rules”.
In 1994, Walter and Turner determined the free energy contributions of nearest neighbor stacking interactions within a helix-helix interface by using a model system that created a helix-helix interface between a short oligomer
Oligomer
In chemistry, an oligomer is a molecule that consists of a few monomer units , in contrast to a polymer that, at least in principle, consists of an unlimited number of monomers. Dimers, trimers, and tetramers are oligomers. Many oils are oligomeric, such as liquid paraffin...
and a four-nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
overhang at the end of a hairpin stem
Stem-loop
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions,...
. Their experiments confirmed that the thermodynamic contribution of base-stacking between two helical secondary structures closely mimics the thermodynamics of standard duplex formation (nearest neighbor interactions predict the thermodynamic stability of the resulting helix). The relative stability of nearest neighbor interactions can be used to predict favorable coaxial stacking based on known secondary structure. Walter and Turner found that, on average, prediction of RNA structure improved from 67% to 74% accuracy when coaxial stacking contributions were included. Theories of coaxial stacking can be tested using the technique of helical fusion. This approach was used by Murphy and Cech to confirm a coaxial stacking interaction between the P4 and P6 helices within the catalytic center of the Tetrahymena
Tetrahymena
Tetrahymena are free-living ciliate protozoa that can also switch from commensalistic to pathogenic modes of survival. They are common in fresh-water. Tetrahymena species used as model organisms in biomedical research are T. thermophila and T. pyriformis.- T...
group I intron.
Most well-studied RNA tertiary structures contain examples of coaxial stacking. Some prominent examples are tRNA-Phe, group I introns, group II introns, and ribosomal RNAs. Crystal structures of tRNA revealed the presence of two extended helices that result from coaxial stacking of the amino-acid acceptor stem with the T-arm, and stacking of the D- and anticodon-arms. These interactions within tRNA orient the anticodon stem perpendicularly to the amino-acid stem, leading to the functional L-shaped tertiary structure. In group I introns, the P4 and P6 helices were shown to coaxially stack using a combination of biochemical and crystallographic methods. The P456 crystal structure provided a detailed view of how coaxial stacking stabilizes the packing of RNA helices into tertiary structures. In the self-splicing group II intron from Oceanobacillus iheyensis, the IA and IB stems coaxially stack and contribute to the relative orientation of the constituent helices of a five-way junction. This orientation facilitates proper folding of the active site
Active site
In biology the active site is part of an enzyme where substrates bind and undergo a chemical reaction. The majority of enzymes are proteins but RNA enzymes called ribozymes also exist. The active site of an enzyme is usually found in a cleft or pocket that is lined by amino acid residues that...
of the functional ribozyme. The ribosome contains numerous examples of coaxial stacking, including stacked segments as long as 70 bp.
Two common motifs involving coaxial stacking are kissing loops and pseudoknots. In kissing loop interactions, the single-stranded loop regions of two hairpins interact through base pairing, forming a composite, coaxially stacked helix. Notably, this structure allows all of the nucleotides in each loop to participate in base-pairing and stacking interactions. This motif was visualized and studied using NMR analysis by Lee and Crothers. The pseudoknot motif occurs when a single stranded region of a hairpin loop basepairs with an upstream or downstream sequence within the same RNA strand. The two resulting duplex regions often stack upon one another, forming a stable coaxially stacked composite helix. One example of a pseudoknot motif is the highly stable Hepatitis Delta virus ribozyme, in which the backbone shows an overall double pseudoknot topology.
An effect similar to coaxial stacking has been observed in rationally designed
Nucleic acid design
Nucleic acid design is the process of generating a set of nucleic acid base sequences that will associate into a desired conformation. Nucleic acid design is central to the fields of DNA nanotechnology and DNA computing...
DNA structures. DNA origami
DNA origami
DNA origami is the nanoscale folding of DNA to create arbitrary two and three dimensional shapes at the nanoscale. The specificity of the interactions between complementary base pairs make DNA a useful construction material through design of its base sequences...
structures contain a large number of double helixes with exposed blunt ends. These structures were observed to stick together along the edges that contained these exposed blunt ends, due to the hydrophobic stacking interactions.
Tetraloop-receptor interactions
Tetraloop-receptor interactions combine base-pairing and stacking interactions between the loop nucleotides of a tetraloopTetraloop
Tetraloops are a type of four-base hairpin loop motifs in RNA secondary structure that cap many double helices. Three types of tetraloops are common in ribosomal RNA: GNRA, UNCG and CUUG. The GNRA tetraloop has a guanine-adenine base-pair where the guanine is 5' to the helix and the adenine is 3'...
motif and a receptor motif located within an RNA duplex, creating a tertiary contact that stabilizes the global tertiary fold of an RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
molecule. Tetraloops are also possible structures in DNA duplexes.
Stem-loops can vary greatly in size and sequence, but tetraloops of four nucleotides are very common and they usually belong to one of three categories, based on sequence. These three families are the CUYG, UNCG and GNRA (see figure on the right) tetraloops. In each of these tetraloop families, the second and third nucleotides form a turn in the RNA strand and a base-pair between the first and fourth nucleotides stabilizes the stemloop structure. It has been determined, in general, that the stability of the tetraloop depends on the composition of bases within the loop and on the composition of this "closing base pair". The GNRA family of tetraloops is the most commonly observed within Tetraloop-receptor interactions.
“Tetraloop receptor motifs” are long-range tertiary interactions consisting of hydrogen bonding between the bases in the tetraloop
Tetraloop
Tetraloops are a type of four-base hairpin loop motifs in RNA secondary structure that cap many double helices. Three types of tetraloops are common in ribosomal RNA: GNRA, UNCG and CUUG. The GNRA tetraloop has a guanine-adenine base-pair where the guanine is 5' to the helix and the adenine is 3'...
to stemloop sequences in distal sections of the secondary RNA structure. In addition to hydrogen bonding, stacking interactions are an important component of these tertiary interactions. For example, in GNRA-tetraloop interactions, the second nucleotide of the tetraloop stacks directly on an A-platform motif (see above) within the receptor. The sequence of the tetraloop and its receptor often covary so that the same type of tertiary contact can be made with different isoforms of the tetraloop and its cognate receptor.
For example, the self-splicing group I intron relies on tetraloop receptor motifs for its structure and function. Specifically, the three adenine residues of the canonical GAAA motif stack on top of the receptor helix and form multiple stabilizing hydrogen bonds with the receptor. The first adenine of the GAAA sequence forms a triple base-pair with the receptor AU bases. The second adenine is stabilized by hydrogen bonds with the same uridine, as well as via its 2'-OH with the recptor and via interactions with the guanine of the GAAA tetraloop. The third adenine forms a triple base pair.
A-minor motif
The A-minor motif is a ubiquitous RNA tertiary structuralTertiary structure
In biochemistry and molecular biology, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.-Relationship to primary structure:...
motif. It is formed by the insertion of an unpaired nucleoside
Nucleoside
Nucleosides are glycosylamines consisting of a nucleobase bound to a ribose or deoxyribose sugar via a beta-glycosidic linkage...
into the minor groove of an RNA duplex. As such it is an example of a minor groove triple. Although guanosine, cytosine and uridine can also form minor groove triple interactions, minor groove interactions by adenine are very common. In the case of adenine, the N1-C2-N3 edge of the inserting base forms hydrogen bonds with one or both of the 2’-OH’s of the duplex, as well as the bases of the duplex (see figure: A-minor interactions). The host duplex is often a G-C basepair.
A-minor motifs have been separated into four classes, types 0 to III, based upon the position of the inserting base relative to the two 2’-OH’s of the Watson-Crick base pair
Base pair
In molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...
. In type I and II A-minor motifs, N3 of adenine is inserted deeply within the minor groove of the duplex (see figure: A minor interactions - type II interaction), and there is good shape complementarity with the base pair. Unlike types 0 and III, type I and II interactions are specific for adenine due to hydrogen bonding interactions. In the type III interaction, both the O2' and N3 of the inserting base are associated less closely with the minor groove of the duplex. Type 0 and III motifs are weaker and non-specific because they are mediated by interactions with a single 2’-OH (see figure: A-minor Interactions - type 0 and type III interactions).
The A-minor motif is among the most common RNA structural motifs in the ribosome, where it contributes to the binding of tRNA to the 23S subunit. They most often stabilize RNA duplex interactions in loops and helices, such as in the core of group II introns.
An interesting example of A-minor is its role in anticodon recognition. The ribosome must discriminate between correct and incorrect codon-anticodon pairs. It does so, in part, through the insertion of adenine bases into the minor groove. Incorrect codon-anticodon pairs will present distorted helical geometry, which will prevent the A-minor interaction from stabilizing the binding, and increase the dissociation rate of the incorrect tRNA.
Ribose zipper
The ribose zipper is an RNARNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
tertiary structural element in which two RNA chains are held together by hydrogen bonding interactions involving the 2’OH of ribose
Ribose
Ribose is an organic compound with the formula C5H10O5; specifically, a monosaccharide with linear form H––4–H, which has all the hydroxyl groups on the same side in the Fischer projection....
sugars on different strands. The 2'OH can behave as both hydrogen bond donor and acceptor, which allows formation of bifurcated hydrogen bonds with another 2’ OH.
Numerous forms of ribose zipper have been reported, but a common type involves four hydrogen bonds between 2'-OH groups of two adjacent sugars. Ribose zippers commonly occur in arrays that stabilize interactions between separate RNA strands. Ribose zippers are often observed as Stem-loop
Stem-loop
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions,...
interactions with very low sequence specificity. However, in the small and large ribosomal subunits, there exists a propensity for ribose zippers of the CC/AA sequence- two cytosine
Cytosine
Cytosine is one of the four main bases found in DNA and RNA, along with adenine, guanine, and thymine . It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached . The nucleoside of cytosine is cytidine...
s on the first chain paired to two adenine
Adenine
Adenine is a nucleobase with a variety of roles in biochemistry including cellular respiration, in the form of both the energy-rich adenosine triphosphate and the cofactors nicotinamide adenine dinucleotide and flavin adenine dinucleotide , and protein synthesis, as a chemical component of DNA...
s on the second chain.
Role of metal ions
Functional RNARNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
s are often folded, stable molecules with three-dimensional shapes rather than floppy, linear strands. Cations are essential for thermodynamic stabilization of RNA tertiary structures. Metal cations that bind RNA can be monovalent, divalent or trivalent. Potassium
Potassium
Potassium is the chemical element with the symbol K and atomic number 19. Elemental potassium is a soft silvery-white alkali metal that oxidizes rapidly in air and is very reactive with water, generating sufficient heat to ignite the hydrogen emitted in the reaction.Potassium and sodium are...
(K+) is a common monovalent ion that binds RNA. A common divalent ion that binds RNA is magnesium
Magnesium
Magnesium is a chemical element with the symbol Mg, atomic number 12, and common oxidation number +2. It is an alkaline earth metal and the eighth most abundant element in the Earth's crust and ninth in the known universe as a whole...
(Mg2+). Other ions including sodium
Sodium
Sodium is a chemical element with the symbol Na and atomic number 11. It is a soft, silvery-white, highly reactive metal and is a member of the alkali metals; its only stable isotope is 23Na. It is an abundant element that exists in numerous minerals, most commonly as sodium chloride...
(Na+), calcium
Calcium
Calcium is the chemical element with the symbol Ca and atomic number 20. It has an atomic mass of 40.078 amu. Calcium is a soft gray alkaline earth metal, and is the fifth-most-abundant element by mass in the Earth's crust...
(Ca2+) and manganese
Manganese
Manganese is a chemical element, designated by the symbol Mn. It has the atomic number 25. It is found as a free element in nature , and in many minerals...
(Mn2+) have been found to bind RNA in vivo and in vitro. Multivalent organic cations such as spermidine or spermine are also found in cells and these make important contributions to RNA folding. Trivalent ions such as cobalt hexamine or lanthanide ions such as terbium
Terbium
Terbium is a chemical element with the symbol Tb and atomic number 65. It is a silvery-white rare earth metal that is malleable, ductile and soft enough to be cut with a knife...
(Tb3+) are useful experimental tools for studying metal binding to RNA.
A metal ion can interact with RNA in multiple ways. An ion can associate diffusely with the RNA backbone, shielding otherwise unfavorable electrostatic interactions. This charge screening is often fulfilled by monovalent ions. Site-bound ions stabilize specific elements of RNA tertiary structure. Site-bound interactions can be further subdivided into two categories depending on whether water mediates the metal binding. “Outer sphere” interactions are mediated by water molecules that surround the metal ion. For example, magnesium hexahydrate interacts with and stabilizes specific RNA tertiary structure motifs via interactions with guanosine
Guanosine
Guanosine is a purine nucleoside comprising guanine attached to a ribose ring via a β-N9-glycosidic bond. Guanosine can be phosphorylated to become guanosine monophosphate , cyclic guanosine monophosphate , guanosine diphosphate , and guanosine triphosphate...
in the major groove. Conversely, “inner sphere” interactions are directly mediated by the metal ion. RNA often folds in multiple stages and these steps can be stabilized by different types of cations. In the early stages, RNA forms secondary structure
Nucleic acid secondary structure
The secondary structure of a nucleic acid molecule refers to the basepairing interactions within a single molecule or set of interacting molecules, and can be represented as a list of bases which are paired in a nucleic acid molecule....
s stabilized through the binding of monovalent cations, divalent cations and polyanionic amines in order to neutralize the polyanionic backbone. The later stages of this process involve the formation of RNA tertiary structure, which is stabilized almost largely through the binding of divalent ions such as magnesium with possible contributions from potassium binding.
Metal-binding sites are often localized in the deep and narrow major groove of the RNA duplex, coordinating to the Hoogsteen
Hoogsteen base pair
A Hoogsteen base pair is a variation of base-pairing in nucleic acids such as the A•T pair. In this manner, two nucleobases on each strand can be held together by hydrogen bonds in the major groove...
edges of purine
Purine
A purine is a heterocyclic aromatic organic compound, consisting of a pyrimidine ring fused to an imidazole ring. Purines, including substituted purines and their tautomers, are the most widely distributed kind of nitrogen-containing heterocycle in nature....
s. In particular, metal cations
Ion
An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge. The name was given by physicist Michael Faraday for the substances that allow a current to pass between electrodes in a...
stabilize sites of backbone twisting where tight packing of phosphate
Phosphate
A phosphate, an inorganic chemical, is a salt of phosphoric acid. In organic chemistry, a phosphate, or organophosphate, is an ester of phosphoric acid. Organic phosphates are important in biochemistry and biogeochemistry or ecology. Inorganic phosphates are mined to obtain phosphorus for use in...
s results in a region of dense negative charge. There are several metal ion-binding motifs in RNA duplexes that have been identified in crystal structures. For instance, in the P4-P6 domain of the Tetrahymena thermophila group I intron
Group I catalytic intron
Group I introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of nine paired regions...
, several ion-binding sites consist of tandem G-U wobble pairs
Wobble base pair
In molecular biology, a wobble base pair is a non-Watson-Crick base pairing between two nucleotides in RNA molecules. The four main wobble base pairs are guanine-uracil, inosine-uracil, inosine-adenine, and inosine-cytosine . The thermodynamic stability of a wobble base pair is comparable to that...
and tandem G-A mismatches
Base pair
In molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...
, in which divalent
Valence (chemistry)
In chemistry, valence, also known as valency or valence number, is a measure of the number of bonds formed by an atom of a given element. "Valence" can be defined as the number of valence bonds...
cations interact with the Hoogsteen edge of guanosine via O6 and N7. Another ion-binding motif in the Tetrahymena group I intron is the A-A platform motif, in which consecutive adenosines in the same strand of RNA form a non-canonical pseudobase pair. Unlike the tandem G-U motif, the A-A platform motif binds preferentially to monovalent cations. In many of these motifs, absence of the monovalent or divalent cations results in either greater flexibility or loss of tertiary structure.
Divalent metal ions, especially magnesium
Magnesium in biology
Magnesium is an essential element in biological systems. Magnesium occurs typically as the Mg2+ ion. It is an essential mineral nutrient for life and is present in every cell type in every organism. For example, ATP , the main source of energy in cells, must be bound to a magnesium ion in order to...
, have been found to be important for the structure of DNA junctions such as the Holliday junction
Holliday junction
A Holliday junction is a mobile junction between four strands of DNA. The structure is named after Robin Holliday, who proposed it in 1964 to account for a particular type of exchange of genetic information he observed in yeast known as homologous recombination...
intermediate in genetic recombination
Genetic recombination
Genetic recombination is a process by which a molecule of nucleic acid is broken and then joined to a different one. Recombination can occur between similar molecules of DNA, as in homologous recombination, or dissimilar molecules, as in non-homologous end joining. Recombination is a common method...
. The magnesium ion shields the negatively-charged phosphate groups in the junction and allows them to be positioned closer together, allowing a stacked conformation rather than an unstacked conformation. Magnesium is vital in stabilizing these kinds of junctions in artificially designed
Nucleic acid design
Nucleic acid design is the process of generating a set of nucleic acid base sequences that will associate into a desired conformation. Nucleic acid design is central to the fields of DNA nanotechnology and DNA computing...
structures used in DNA nanotechnology
DNA nanotechnology
DNA nanotechnology is a branch of nanotechnology which uses the molecular recognition properties of DNA and other nucleic acids to create designed, artificial structures out of DNA for technological purposes. In this field, DNA is used as a structural material rather than as a carrier of genetic...
, such as the double crossover motif.
History
The earliest work in RNA structural biology coincided, more or less, with the work being done on DNA in the early 1950s. In their seminal 1953 paper, Watson and Crick suggested that van der Waals crowding by the 2`OH group of ribose would preclude RNA from adopting a double helical structure identical to the model they proposed - what we now know as B-form DNA. This provoked questions about the three dimensional structure of RNA: could this molecule form some type of helical structure, and if so, how?In the mid 1960's, the role of tRNA in protein synthesis was being intensively studied. In 1965, Holley et al. purified and sequenced the first tRNA molecule, initially proposing that it adopted a cloverleaf structure, based largely on the ability of certain regions of the molecule to form stem loop structures. The isolation of tRNA proved to be the first major windfall in RNA structural biology. In 1971, Kim et al. achieved another breakthrough, producing crystals of yeast tRNAPHE that diffracted to 2-3 Ångström resolutions by using spermine, a naturally occurring polyamine, which bound to and stabilized the tRNA.
For a considerable time following the first tRNA structures, the field of RNA structure did not dramatically advance. The ability to study an RNA structure depended upon the potential to isolate the RNA target. This proved limiting to the field for many years, in part owing to the fact that other known targets - i.e. the ribosome - were significantly more difficult to isolate and crystallize. As such, for some twenty years following the original publication of the tRNAPHE structure, the structures of only a handful of other RNA targets were solved, with almost all of these belonging to the transfer RNA family.
This unfortunate lack of scope would eventually be overcome largely because of two major advancements in nucleic acid research: the identification of ribozymes, and the ability to produce them via in vitro transcription. Subsequent to Tom Cech's publication implicating the Tetrahymena group I intron as an autocatalytic ribozyme, and Sidney Altman's report of catalysis by ribonuclease P RNA, several other catalytic RNAs were identified in the late 1980s, including the hammerhead ribozyme. In 1994, McKay et al. published the structure of a 'hammerhead RNA-DNA ribozyme-inhibitor complex' at 2.6 Ångström resolution, in which the autocatalytic activity of the ribozyme was disrupted via binding to a DNA substrate. In addition to the advances being made in global structure determination via crystallography, the early 1990s also saw the implementation of NMR as a powerful technique in RNA structural biology. Investigations such as this enabled a more precise characterization of the base pairing and base stacking interactions which stabilized the global folds of large RNA molecules.
The resurgence of RNA structural biology in the mid-1990s has caused a veritable explosion in the field of nucleic acid structural research. Since the publication of the hammerhead and P4-6 structures, numerous major contributions to the field have been made. Some of the most noteworthy examples include the structures of the Group I and Group II introns, and the Ribosome. It should be noted that the first three structures were produced using in vitro transcription, and that NMR has played a role in investigating partial components of all four structures - testaments to the indispensability of both techniques for RNA research. Most recently, the 2009 Nobel Prize in Chemistry was awarded to Ada Yonath, Venkatraman Ramakrishnan, and Thomas Steitz for their structural work on the ribosome, demonstrating the prominent role RNA structural biology has taken in modern molecular biology.
See also
- Stem-loopStem-loopStem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions,...
- PseudoknotPseudoknotA pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow mosaic virus in 1982...
- Secondary structure predictionSecondary structure predictionSecondary structure prediction is a set of techniques in bioinformatics that aim to predict the secondary structures of proteins and nucleic acid sequences based only on knowledge of their primary structure...
- Base pairBase pairIn molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...
- Wobble base pairWobble base pairIn molecular biology, a wobble base pair is a non-Watson-Crick base pairing between two nucleotides in RNA molecules. The four main wobble base pairs are guanine-uracil, inosine-uracil, inosine-adenine, and inosine-cytosine . The thermodynamic stability of a wobble base pair is comparable to that...
- Hoogsteen base pairHoogsteen base pairA Hoogsteen base pair is a variation of base-pairing in nucleic acids such as the A•T pair. In this manner, two nucleobases on each strand can be held together by hydrogen bonds in the major groove...
- RiboswitchRiboswitchIn molecular biology, a riboswitch is a part of an mRNA molecule that can directly bind a small target molecule, and whose binding of the target affects the gene's activity. Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, in response to the...
- RibozymeRibozymeA ribozyme is an RNA molecule with a well defined tertiary structure that enables it to catalyze a chemical reaction. Ribozyme means ribonucleic acid enzyme. It may also be called an RNA enzyme or catalytic RNA. Many natural ribozymes catalyze either the hydrolysis of one of their own...
- Hammerhead ribozymeHammerhead ribozymeHammerhead RNAs are RNAs that self-cleave via a small conserved secondary structural motif termed a hammerhead because of its shape. Most hammerhead RNAs are subsets of two classes of plant pathogenic RNAs: the satellite RNAs of RNA viruses and the viroids. The self-cleavage reactions, first...
- Group I catalytic intronGroup I catalytic intronGroup I introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of nine paired regions...
- Group II intronGroup II intronGroup II introns are a large class of self-catalytic ribozymes as well as mobile genetic element found within the genes of all three domains of life. Ribozyme activity can occur under high-salt conditions in vitro. However, assistance from proteins is required for in vivo splicing...
- tRNA
- G-quadruplexG-quadruplexIn molecular biology, G-quadruplexes are nucleic acid sequences that are rich in guanine and are capable of forming a four-stranded structure...
- TetraloopTetraloopTetraloops are a type of four-base hairpin loop motifs in RNA secondary structure that cap many double helices. Three types of tetraloops are common in ribosomal RNA: GNRA, UNCG and CUUG. The GNRA tetraloop has a guanine-adenine base-pair where the guanine is 5' to the helix and the adenine is 3'...