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In
molecular biology, two
nucleotides on opposite complementarity (molecular biology)
DNA or RNA strands that are connected via
hydrogen bonds are called a
base pair (often abbreviated bp). In the canonical
Watson-Crick base pairing, adenine (A) forms a base pair with
thymine (T), as does
guanine (G) with cytosine (C) in DNA. In RNA,
thymine is replaced by
uracil (U). Non-Watson-Crick base pairing with alternate hydrogen bonding patterns also occur, especially in RNA; common such patterns are Hoogsteen base pairs.
Base pairing is also the mechanism by which codons on messenger RNA molecules are recognized by anticodons on
transfer RNA during protein
translation (genetics). Some DNA- or RNA-binding enzymes can recognize specific base pairing patterns that identify particular regulatory regions of genes.
The size of an individual gene or an organism's entire
genome is often measured in base pairs because DNA is usually double-stranded. Hence, the number of total base pairs is equal to the number of
nucleotides in one of the strands (with the exception of non-coding single-stranded regions of telomeres. The human genome is estimated to be about 3 billion base pairs long and to contain 20,000-25,000 distinct genes.
Examples
The following DNA sequences illustrate six-base-pair double-stranded patterns. By convention, the top strand is written from the 5' end to the
3' end; thus the bottom strand is written 3' to 5'.
A base-paired DNA sequence:
ATCGAT
TAGCTA
The corresponding base-paired RNA sequence, in which uracil is substituted for thymine:
AUCGAU
UAGCUA
==Length measurements==The following abbreviations are commonly used to describe the length of a DNA/RNA molecule:
- bp = base pair(s)
- kb (= kbp) = kilo base pairs = 1,000 bp
- Mb = mega base pairs = 1,000,000 bp
- Gb = giga base pairs = 1,000,000,000 bp
In case of single stranded DNA/RNA we talk about
nucleotides, abbreviated nt (or knt, Mnt, Gnt), rather than base pairs, as they are not paired.For distinction between units of computer storage and bases kbp, Mbp, Gbp etc may be used for disambiguation.
Hydrogen bonding and stability
ss
Hydrogen bond is the chemical mechanism that underlies the base-pairing rules described above. Appropriate geometrical correspondence of hydrogen bond donors and acceptors allows only the "right" pairs to form stably. The GC base pair has three hydrogen bonds, whereas the AT base pair has only two; as a consequence, the GC pair is more stable.
The larger nucleic acids, adenine and guanine, are members of a class of doubly-ringed chemical structures called
purines; the smaller nucleic acids, cytosine and thymine (and uracil), are members of a class of singly-ringed chemical structures called pyrimidines. Purines are only complementary with pyrimidines: pyrimidine-pyrimidine pairings are energetically unfavorable because the molecules are too far apart for hydrogen bonding to be established; purine-purine pairings are energetically unfavorable because the molecules are too close, leading to electrostatic repulsion. The only other possible pairings are GT and AC; these pairings are mismatches because the pattern of hydrogen donors and acceptors do not correspond. (It should be noted that the GU pairing, with two hydrogen bonds, does occur fairly often in RNA but rarely in
DNA.)
Paired DNA and RNA molecules are comparatively stable at room temperature but the two nucleotide strands will separate above a
melting point that is determined by the length of the molecules, the extent of mispairing (if any), and the GC content. Higher GC content results in higher melting temperatures; it is therefore unsurprising that the genomes of extremophile organisms such as
Thermus thermophilus are particularly GC-rich. Conversely, regions of a genome that need to separate frequently - for example, the promoter regions for often-transcription (genetics) genes - are comparatively GC-poor (for example, see TATA box). GC content and melting temperature must also be taken into account when designing primer (molecular biology) for
PCR reactions.
Base stacking
Base stacking (chemistry) interactions between the
pi bond of the bases' aromatic rings also contribute to stability, and again GC stacking interactions with adjacent bases tend to be more favorable. (Note, though, that a GC stacking interaction with the next base pair is geometrically different from a CG interaction.) Base stacking effects are especially important in the secondary structure of RNA; for example, RNA stem-loop structures are stabilized by base stacking in the loop region.
Base analogs and intercalators
Chemical analogs of nucleotides can take the place of proper nucleotides and establish non-canonical base-pairing, leading to errors (mostly
point mutations) in
DNA replication and Transcription (genetics). One common mutagenic base analog is
5-bromouracil, which resembles thymine but can base-pair to guanine in its
enol form.
Other chemicals, known as
DNA intercalation, fit into the gap between adjacent bases on a single strand and induce frameshift mutations by "masquerading" as a base, causing the DNA replication machinery to skip or insert additional nucleotides at the intercalated site. Most intercalators are large aromatic compounds and are known or suspected
carcinogens. Examples include
ethidium bromide and acridine.
See also
External links
- DAN - webserver version of the EMBOSS tool for calculating melting temperatures
Cited references
General references
- Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R. (2004). Molecular Biology of the Gene. 5th ed. Pearson Benjamin Cummings: CSHL Press. See esp. ch. 6 and 9.
In
molecular biology, two nucleotides on opposite complementarity (molecular biology)
DNA or
RNA strands that are connected via
hydrogen bonds are called a
base pair (often abbreviated bp). In the canonical
Watson-Crick base pairing,
adenine (A) forms a base pair with
thymine (T), as does guanine (G) with
cytosine (C) in DNA. In RNA,
thymine is replaced by uracil (U). Non-Watson-Crick base pairing with alternate hydrogen bonding patterns also occur, especially in RNA; common such patterns are
Hoogsteen base pairs.
Base pairing is also the mechanism by which
codons on messenger RNA molecules are recognized by
anticodons on
transfer RNA during protein translation (genetics). Some DNA- or RNA-binding enzymes can recognize specific base pairing patterns that identify particular regulatory regions of genes.
The size of an individual gene or an organism's entire genome is often measured in base pairs because DNA is usually double-stranded. Hence, the number of total base pairs is equal to the number of nucleotides in one of the strands (with the exception of non-coding single-stranded regions of telomeres. The
human genome is estimated to be about 3 billion base pairs long and to contain 20,000-25,000 distinct genes.
Examples
The following DNA sequences illustrate six-base-pair double-stranded patterns. By convention, the top strand is written from the 5' end to the 3' end; thus the bottom strand is written 3' to 5'.
A base-paired DNA sequence:
ATCGAT
TAGCTA
The corresponding base-paired RNA sequence, in which uracil is substituted for thymine:
AUCGAU
UAGCUA
==Length measurements==The following abbreviations are commonly used to describe the length of a DNA/RNA molecule:
- bp = base pair(s)
- kb (= kbp) = kilo base pairs = 1,000 bp
- Mb = mega base pairs = 1,000,000 bp
- Gb = giga base pairs = 1,000,000,000 bp
In case of single stranded DNA/RNA we talk about nucleotides, abbreviated nt (or knt, Mnt, Gnt), rather than base pairs, as they are not paired.For distinction between units of computer storage and bases kbp, Mbp, Gbp etc may be used for disambiguation.
Hydrogen bonding and stability
ss
Hydrogen bond is the chemical mechanism that underlies the base-pairing rules described above. Appropriate geometrical correspondence of hydrogen bond donors and acceptors allows only the "right" pairs to form stably. The GC base pair has three hydrogen bonds, whereas the AT base pair has only two; as a consequence, the GC pair is more stable.
The larger nucleic acids, adenine and guanine, are members of a class of doubly-ringed chemical structures called purines; the smaller nucleic acids, cytosine and thymine (and uracil), are members of a class of singly-ringed chemical structures called pyrimidines. Purines are only complementary with pyrimidines: pyrimidine-pyrimidine pairings are energetically unfavorable because the molecules are too far apart for hydrogen bonding to be established; purine-purine pairings are energetically unfavorable because the molecules are too close, leading to electrostatic repulsion. The only other possible pairings are GT and AC; these pairings are mismatches because the pattern of hydrogen donors and acceptors do not correspond. (It should be noted that the GU pairing, with two hydrogen bonds, does occur fairly often in
RNA but rarely in
DNA.)
Paired DNA and RNA molecules are comparatively stable at room temperature but the two nucleotide strands will separate above a
melting point that is determined by the length of the molecules, the extent of mispairing (if any), and the GC content. Higher GC content results in higher melting temperatures; it is therefore unsurprising that the genomes of extremophile organisms such as
Thermus thermophilus are particularly GC-rich. Conversely, regions of a genome that need to separate frequently - for example, the promoter regions for often-transcription (genetics) genes - are comparatively GC-poor (for example, see TATA box). GC content and melting temperature must also be taken into account when designing
primer (molecular biology) for PCR reactions.
Base stacking
Base
stacking (chemistry) interactions between the
pi bond of the bases' aromatic rings also contribute to stability, and again GC stacking interactions with adjacent bases tend to be more favorable. (Note, though, that a GC stacking interaction with the next base pair is geometrically different from a CG interaction.) Base stacking effects are especially important in the secondary structure of RNA; for example, RNA
stem-loop structures are stabilized by base stacking in the loop region.
Base analogs and intercalators
Chemical analogs of nucleotides can take the place of proper nucleotides and establish non-canonical base-pairing, leading to errors (mostly point mutations) in DNA replication and
Transcription (genetics). One common mutagenic base analog is 5-bromouracil, which resembles thymine but can base-pair to guanine in its
enol form.
Other chemicals, known as
DNA intercalation, fit into the gap between adjacent bases on a single strand and induce
frameshift mutations by "masquerading" as a base, causing the DNA replication machinery to skip or insert additional nucleotides at the intercalated site. Most intercalators are large
aromatic compounds and are known or suspected
carcinogens. Examples include ethidium bromide and acridine.
See also
External links
- DAN - webserver version of the EMBOSS tool for calculating melting temperatures
Cited references
General references
- Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R. (2004). Molecular Biology of the Gene. 5th ed. Pearson Benjamin Cummings: CSHL Press. See esp. ch. 6 and 9.
Base pair - Wikipedia, the free encyclopedia
In molecular biology, two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds are called a base pair (often abbreviated bp).
Wobble base pair - Wikipedia, the free encyclopedia
A wobble base pair is a G-U and I-U / I-A / I-C pair fundamental in RNA secondary structure. Its thermodynamic stability is comparable to that of the Watson-Crick base pair.
Definition: base pair from Online Medical Dictionary
The Online Medical Dictionary is a searchable dictionary of definitions from medicine, science and technology.
Tutorial on DNA Structure - Three basepairs
Three base pairs are shown in stick form to highlight the bonds with the van der Waals radius shown as dots. You should be able to see that each base pair is related by 36 o.
base pair - Hutchinson encyclopedia article about base pair
Hutchinson encyclopedia article about base pair. base pair. Information about base pair in the Hutchinson encyclopedia. base pairs, number of base pairs
genome.gov | Talking Glossary: "base pair"
Easy-to-use, talking glossary of genetic terms, produced by the National Human Genome Research Institute.
Base Pair
Look up a description of Base Pair in the NHGRI Talking Glossary. Download an Adobe Acrobat (.pdf) version of the image for full page 8-1/2" by 11" printing for handouts or ...
Genome Glossary
A nitrogenous base, one member of the base pair AT (adenine-thymine). See also: base pair, nucleotide. Affected relative pair Individuals related by blood, each of whom is affected ...
base pair
In biochemistry, the linkage of two base (purine or pyrimidine) molecules that join the complementary strands of DNA
Base Pairing
Base Pairing The rules of base pairing (or nucleotide pairing) are: A with T: the purine adenine (A) always pairs with the pyrimidine thymine (T) C with G: the pyrimidine cytosine ...
