Base pair

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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). In DNA, adenine (A) forms a base pair with thymine (T), as does guanine (G) with cytosine (C). In RNA, thymine is replaced by uracil (U). As DNA is usually double-stranded, the number of base pairs given for a particular DNA strand is the number of nucleotides in one of the strands. Thus, the following examples of base-paired nucleotide sequence are said to be six base-pairs long:

A base-paired DNA sequence:

ATCGAT
TAGCTA

The corresponding base-paired RNA sequence:

AUCGAU
UAGCUA

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

bp = base pair(s)
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.

Thymine and adenine bond together through two hydrogen bonds, while cytosine and guanine bond together through three hydrogen bonds.

As hydrogen bonds are not very strong, the two nucleotide strands will separate on temperatures higher than 94 °C.

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.

Guanine and cytosine form 3 hydrogen bonds while adenine and thymine form only 2 hydrogen bonds. Consequently A-T pairs are less stable.

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