Palindromic sequence
Encyclopedia
A palindromic sequence is a nucleic acid
sequence (DNA
or RNA
) that is the same whether read 5' (five-prime) to 3' (three prime) on one strand or 5' to 3' on the complementary strand
with which it forms a double helix.
The meaning of palindrome
in the context of genetics
is slightly different from the definition used for words and sentences. Since a double helix is formed by two paired strands of nucleotides that run in opposite directions in the 5'-to-3' sense
, and the nucleotides always pair in the same way (Adenine
(A) with Thymine
(T) for DNA, with Uracil
(U) for RNA; Cytosine
(C) with Guanine
(G)), a (single-stranded) nucleotide sequence is said to be a palindrome if it is equal to its reverse complement. For example, the DNA sequence ACCTAGGT is palindromic because its nucleotide-by-nucleotide complement
is TGGATCCA, and reversing the order of the nucleotides in the complement gives the original sequence.
A palindromic nucleotide sequence can form a hairpin
. Palindromic DNA motifs
are found in most genome
s or sets of gene
tic instructions. Palindromic motifs are made by the order of the nucleotide
s that specify the complex chemicals (protein
s) which, as a result of those genetic
instructions, the cell
is to produce. They have been specially researched in bacteria
l chromosomes and in the so-called Bacterial Interspersed Mosaic Elements (BIMEs) scattered over them. Recently a research genome sequencing project discovered that many of the bases on the Y chromosome
are arranged as palindromes. A palindrome structure allows the Y chromosome to repair itself by bending over at the middle if one side is damaged.
Palindromes also appear to be found frequently in proteins, but their role in the protein function is not clearly known. It is recently suggested that the prevalence existence of palindromes in peptides might be related to the prevalence of low-complexity regions in proteins, as palindromes are frequently associated with low-complexity sequences. Their prevalence might be also related to an alpha helical formation propensity of these sequences, or in formation of protein/protein complexes.
. Because a DNA sequence is double stranded, we read the base pair
s, not just the bases on one strand to determine a palindrome. Many restriction endonucleases (restriction enzymes) recognize specific palindromic sequences and cut them. The restriction enzyme EcoR1 recognizes the following palindromic sequence:
5'- G A A T T C -3'
3'- C T T A A G -5'
The top strand reads 5'-GAATTC-3', while the bottom strand reads 3'-CTTAAG-5'. If you flip the DNA strand over, the sequences are exactly the same ( 5'GAATTC-3' and 3'-CTTAAG-5'). Here are more restriction enzymes and the palindromic sequences which they recognize:
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...
sequence (DNA
DNA sequence
The sequence or primary structure of a nucleic acid is the composition of atoms that make up the nucleic acid and the chemical bonds that bond those atoms. Because nucleic acids, such as DNA and RNA, are unbranched polymers, this specification is equivalent to specifying the sequence of...
or RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
) that is the same whether read 5' (five-prime) to 3' (three prime) on one strand or 5' to 3' on the complementary strand
Complementarity (molecular biology)
In molecular biology, complementarity is a property of double-stranded nucleic acids such as DNA, as well as DNA:RNA duplexes. Each strand is complementary to the other in that the base pairs between them are non-covalently connected via two or three hydrogen bonds...
with which it forms a double helix.
The meaning of palindrome
Palindrome
A palindrome is a word, phrase, number, or other sequence of units that can be read the same way in either direction, with general allowances for adjustments to punctuation and word dividers....
in the context of genetics
Genetics
Genetics , a discipline of biology, is the science of genes, heredity, and variation in living organisms....
is slightly different from the definition used for words and sentences. Since a double helix is formed by two paired strands of nucleotides that run in opposite directions in the 5'-to-3' sense
Directionality (molecular biology)
Directionality, in molecular biology and biochemistry, is the end-to-end chemical orientation of a single strand of nucleic acid. The chemical convention of naming carbon atoms in the nucleotide sugar-ring numerically gives rise to a 5′-end and a 3′-end...
, and the nucleotides always pair in the same way (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...
(A) with Thymine
Thymine
Thymine is one of the four nucleobases in the nucleic acid of DNA that are represented by the letters G–C–A–T. The others are adenine, guanine, and cytosine. Thymine is also known as 5-methyluracil, a pyrimidine nucleobase. As the name suggests, thymine may be derived by methylation of uracil at...
(T) for DNA, with Uracil
Uracil
Uracil is one of the four nucleobases in the nucleic acid of RNA that are represented by the letters A, G, C and U. The others are adenine, cytosine, and guanine. In RNA, uracil binds to adenine via two hydrogen bonds. In DNA, the uracil nucleobase is replaced by thymine.Uracil is a common and...
(U) for RNA; 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...
(C) with 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...
(G)), a (single-stranded) nucleotide sequence is said to be a palindrome if it is equal to its reverse complement. For example, the DNA sequence ACCTAGGT is palindromic because its nucleotide-by-nucleotide complement
Complementarity (molecular biology)
In molecular biology, complementarity is a property of double-stranded nucleic acids such as DNA, as well as DNA:RNA duplexes. Each strand is complementary to the other in that the base pairs between them are non-covalently connected via two or three hydrogen bonds...
is TGGATCCA, and reversing the order of the nucleotides in the complement gives the original sequence.
A palindromic nucleotide sequence can form a hairpin
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,...
. Palindromic DNA motifs
Sequence motif
In genetics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance...
are found in most genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
s or sets of gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
tic instructions. Palindromic motifs are made by the order of the 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...
s that specify the complex chemicals (protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s) which, as a result of those genetic
Genetics
Genetics , a discipline of biology, is the science of genes, heredity, and variation in living organisms....
instructions, the cell
Cell (biology)
The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....
is to produce. They have been specially researched 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...
l chromosomes and in the so-called Bacterial Interspersed Mosaic Elements (BIMEs) scattered over them. Recently a research genome sequencing project discovered that many of the bases on the Y chromosome
Y chromosome
The Y chromosome is one of the two sex-determining chromosomes in most mammals, including humans. In mammals, it contains the gene SRY, which triggers testis development if present. The human Y chromosome is composed of about 60 million base pairs...
are arranged as palindromes. A palindrome structure allows the Y chromosome to repair itself by bending over at the middle if one side is damaged.
Palindromes also appear to be found frequently in proteins, but their role in the protein function is not clearly known. It is recently suggested that the prevalence existence of palindromes in peptides might be related to the prevalence of low-complexity regions in proteins, as palindromes are frequently associated with low-complexity sequences. Their prevalence might be also related to an alpha helical formation propensity of these sequences, or in formation of protein/protein complexes.
Restriction Enzyme Sites
Palindromic sequences play an important role in molecular biologyMolecular biology
Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...
. Because a DNA sequence is double stranded, we read the 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...
s, not just the bases on one strand to determine a palindrome. Many restriction endonucleases (restriction enzymes) recognize specific palindromic sequences and cut them. The restriction enzyme EcoR1 recognizes the following palindromic sequence:
5'- G A A T T C -3'
3'- C T T A A G -5'
The top strand reads 5'-GAATTC-3', while the bottom strand reads 3'-CTTAAG-5'. If you flip the DNA strand over, the sequences are exactly the same ( 5'GAATTC-3' and 3'-CTTAAG-5'). Here are more restriction enzymes and the palindromic sequences which they recognize:
| Enzyme | Source | Recognition Sequence | Cut |
|---|---|---|---|
| EcoR1 | Escherichia coli Escherichia coli Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls... |
5'GAATTC 3'CTTAAG |
5'---G AATTC---3' 3'---CTTAA G---5' |
| BamH1 | Bacillus amyloliquefaciens Bacillus amyloliquefaciens Bacillus amyloliquefaciens is a species of bacteria that is the source of the BamH1 restriction enzyme. It also synthesizes a natural antibiotic protein barnase, a widely studied ribonuclease that forms a famously tight complex with its intracellular inhibitor barstar.-Discovery and name:B... |
5'GGATCC 3'CCTAGG |
5'---G GATCC---3' 3'---CCTAG G---5' |
| Taq1 | Thermus aquaticus Thermus aquaticus Thermus aquaticus is a species of bacterium that can tolerate high temperatures, one of several thermophilic bacteria that belong to the Deinococcus-Thermus group... |
5'TCGA 3'AGCT |
5'---T CGA---3' 3'---AGC T---5' |
| Alu1* | Arthrobacter luteus | 5'AGCT 3'TCGA |
5'---AG CT---3' 3'---TC GA---5' |
| * = blunt ends | |||