In genetics, two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds are called a base pair (often abbreviated bp). As DNA is usually double-stranded, the number of base pairs in the dsDNA strand equals the number of nucleotides in one of the strands. In DNA, adenine and thymine, as well as guanine and cytosine, can be a base pair. In RNA, thymine is replaced by uracil.

The following abbreviations are commonly used to describe the length of a DNA/RNA molecule:

• kbp = kilo base pairs = 1,000 bp
• Mbp = mega base pairs = 1,000,000 bp
• Gbp = 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.

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 unfavourable because the molecules are too far apart for hydrogen bonding to be established; purine-purine pairings are energetically unfavourable 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.

As hydrogen bonds are not very strong, the two nucleotides will separate on temparatures higher than 94C.

Chemical analogs of nucleotides can take the place of proper nucleotides and establish non-canonical base-pairing, leading to errors in DNA replication and DNA transcription. Some analogs are carcinogens; others are chemotherapy drugs.

Intramolecular base pairs

RNA can form intramolecular base pairs. These form a loop and a chain off the main RNA.

See also

• Nucleobase
• Wobble base pair

References

• Diagram by Martin Chaplin, released under GFDL. Link to original (http://www.sbu.ac.uk/water/nucleic.html) (contains information about the role of water in DNA structure formation and stabilization).

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