Base pair



 

In molecular biology, two Hoogsteen base pairs.

Base pairing is also the mechanism by which codons on messenger RNA molecules are recognized by anticodons on translation. 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 telomeres. The haploid human genome (23 chromosomes) is estimated to be about 3 billion base pairs long and to contain 20,000-25,000 distinct genes.[1]

Examples

The following DNA sequences illustrate pair double-stranded patterns. By convention, the top strand is written from 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

   

Hydrogen bonding 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 DNA.)

Paired DNA and RNA molecules are comparatively stable at room temperature but the two nucleotide strands will separate above a TATA box). GC content and melting temperature must also be taken into account when designing primers for PCR reactions.

Base stacking

Base stem-loop structures are stabilized by base stacking in the loop region.

Further information: pi stacking

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 enol form.

Other chemicals, known as DNA intercalators, 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 acridine.

See also

Cited references

  1. ^ International Human Genome Sequencing Consortium (2004). "Finishing the euchromatic sequence of the human genome.". Nature 431 (7011): 931-45. PMID 15496913. [1]

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.
 
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