Hoogsteen base pair
Encyclopedia
A Hoogsteen base pair is a variation of base-pairing in nucleic acid
s such as the A•T pair. In this manner, two nucleobase
s on each strand can be held together by hydrogen bond
s in the major groove. A Hoogsteen base pair applies the N7 position of the purine
base (as a hydrogen bond
acceptor) and C6 amino group (as a donor), which bind the Watson-Crick (N3–N4) face of the pyrimidine
base.
. The angle between the two glycosylic bonds (ca. 80° in the A• T pair) is larger and the C1′–C1′ distance (ca. 860 pm or 8.6 Å) is smaller than in the regular geometry. In some cases, called reversed Hoogsteen base pairs, one base is rotated 180° with respect to the other.
, and form triple-stranded helices
such as (poly(dA)•2poly(dT)) and (poly(rC)•2poly(rC)). It can be also seen in three-dimensional structures of transfer RNA
.
es (G4-DNA and G4-RNA) at least in vitro. It needs four triplets of G, separated by short spacers. This permits assembly of planar quartets which are composed of stacked associations of hoogsteen bonded guanines.
Hoogsteen triple helix
base pairs are indicated by a "*" or a ":" (example: C•G*G+, T•A*T, C•G*G, or T•A*A).
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...
s such as the A•T pair. In this manner, two 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 on each strand can be held together by 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...
s in the major groove. A Hoogsteen base pair applies the N7 position of the 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....
base (as a 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...
acceptor) and C6 amino group (as a donor), which bind the Watson-Crick (N3–N4) face of the pyrimidine
Pyrimidine
Pyrimidine is a heterocyclic aromatic organic compound similar to benzene and pyridine, containing two nitrogen atoms at positions 1 and 3 of the six-member ring...
base.
History
This term is named for Karst Hoogsteen, who, in 1963, first recognized the potential for these unusual pairings (quoted from Lehninger Principles of Biochemistry by David Nelson and Michael Cox, 4th edition, published in 2005 by Freeman).Chemical properties
Hoogsteen pairs have quite different properties from Watson-Crick base pairsBase 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...
. The angle between the two glycosylic bonds (ca. 80° in the A• T pair) is larger and the C1′–C1′ distance (ca. 860 pm or 8.6 Å) is smaller than in the regular geometry. In some cases, called reversed Hoogsteen base pairs, one base is rotated 180° with respect to the other.
Triplex structures
This non-Watson-Crick base-pairing allows the third strands to wind around the duplexes, which are assembled in the Watson-Crick patternBase 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 form triple-stranded helices
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....
such as (poly(dA)•2poly(dT)) and (poly(rC)•2poly(rC)). It can be also seen in three-dimensional structures of transfer RNA
Transfer RNA
Transfer RNA is an adaptor molecule composed of RNA, typically 73 to 93 nucleotides in length, that is used in biology to bridge the three-letter genetic code in messenger RNA with the twenty-letter code of amino acids in proteins. The role of tRNA as an adaptor is best understood by...
.
Quadruplex structures
It also allows formation of secondary structures of single stranded DNA and RNA G-rich called G-quadruplexG-quadruplex
In molecular biology, G-quadruplexes are nucleic acid sequences that are rich in guanine and are capable of forming a four-stranded structure...
es (G4-DNA and G4-RNA) at least in vitro. It needs four triplets of G, separated by short spacers. This permits assembly of planar quartets which are composed of stacked associations of hoogsteen bonded guanines.
Triple helix base pairing
Watson and Crick base pairs are indicated by a "•", "-", or a "." (example: A•T, or poly(rC)•2poly(rC)).Hoogsteen 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...
base pairs are indicated by a "*" or a ":" (example: C•G*G+, T•A*T, C•G*G, or T•A*A).
See also
- 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...
- 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...
- RNA Tertiary Structure