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Unit consisting of two nucleobases bound to each other by hydrogen bonds

A base pair (bp) is a fundamental unit of double stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, "Watson–Crick" (or "Watson–Crick–Franklin") base pairs (guanine–cytosine and adenine–thymine) allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. The complementary nature of this based paired structure provides a redundant copy of the genetic information encoded within each strand of DNA. The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA and RNA polymerase transcribes DNA into RNA. Many DNA binding proteins can recognize specific base pairing patterns that identify particular regulatory regions of genes. Intramolecular base pairs can occur within single stranded nucleic acids. This is particularly important in RNA molecules (e. g., transfer RNA), where Watson–Crick base pairs (guanine–cytosine and adenine–uracil) permit the formation of short double stranded helices, and a wide variety of non–Watson–Crick interactions (e. g., G–U or A–A) allow RNAs to fold into a vast range of specific three dimensional structures. In addition, base pairing between transfer RNA (tRNA) and messenger RNA (mRNA) forms the basis for the molecular recognition events that result in the nucleotide sequence of mRNA becoming translated into the amino acid sequence of proteins via the genetic code. 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 haploid human genome (23 chromosomes) is estimated to be about 3.2 billion bases long and to contain 20,000–25,000 distinct protein coding genes. A kilobase (kb) is a unit of measurement in molecular biology equal to 1000 base pairs of DNA or RNA. The total number of DNA base pairs on Earth is estimated at 5.0 with a weight of 50 billion tonnes. In comparison, the total mass of the biosphere has been estimated to be as much as 4 TtC (trillion tons of carbon).

Top, a G. C base pair with three hydrogen bonds. Bottom, an A. T base pair with two hydrogen bonds. Non covalent hydrogen bonds between the bases are shown as dashed lines. The wiggly lines stand for the connection to the pentose sugar and point in the direction of the minor groove. Hydrogen bonding is the chemical interaction 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. DNA with high GC content is more stable than DNA with low GC content. Crucially, however, stacking interactions are primarily responsible for stabilising the double helical structure; Watson Crick base pairing's contribution to global structural stability is minimal, but its role in the specificity underlying complementarity is, by contrast, of maximal importance as this underlies the template dependent processes of the central dogma (e. g. DNA replication). The bigger nucleobases, adenine and guanine, are members of a class of double ringed chemical structures called purines; the smaller nucleobases, cytosine and thymine (and uracil), are members of a class of single ringed chemical structures called pyrimidines. Purines are complementary only 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 overlap repulsion. Purine–pyrimidine base pairing of AT or GC or UA (in RNA) results in proper duplex structure. The only other purine–pyrimidine pairings would be AC and GT and UG (in RNA); these pairings are mismatches because the patterns of hydrogen donors and acceptors do not correspond. The GU pairing, with two hydrogen bonds, does occur fairly often in RNA (see wobble base pair). 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. On the converse, regions of a genome that need to separate frequently — for example, the promoter regions for often transcribed genes — are comparatively GC poor (for example, see TATA box). GC content and melting temperature must also be taken into account when designing primers for PCR reactions.

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 DNA transcription. This is due to their isosteric chemistry. 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 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 polyaromatic compounds and are known or suspected carcinogens. Examples include ethidium bromide and acridine.

Mismatched base pairs can be generated by errors of DNA replication and as intermediates during homologous recombination. The process of mismatch repair ordinarily must recognize and correctly repair a small number of base mispairs within a long sequence of normal DNA base pairs. To repair mismatches formed during DNA replication, several distinctive repair processes have evolved to distinguish between the template strand and the newly formed strand so that only the newly inserted incorrect nucleotide is removed (in order to avoid generating a mutation). The proteins employed in mismatch repair during DNA replication, and the clinical significance of defects in this process are described in the article DNA mismatch repair. The process of mispair correction during recombination is described in the article gene conversion.