In molecular biology, two nucleotides on opposite complementary DNA strands that are connected by hydrogen bonds are called a base pair (often abbreviated bp).
In DNA pairing, adenine (A) forms a base pair with thymine (T), to form an A/T base pair. Guanine (G) pairs with cytosine (C) in DNA, to form a G/C base pair.
Base pairing plays an essential role for DNA reduplication, for transcription and translation in the course of protein biosynthesis as well as for manifold arrangements of the secondary and tertiary structure of nucleic acids.
A base pair is formed by hydrogen bonding between two nucleobases. In this process, one of the purine bases guanine or adenine is joined to one of the pyrimidine bases cytosine, thymine or uracil to form a pair. In the complementary base pairings between two strand segments of nucleic acids, guanine pairs with cytosine and adenine pairs with thymine or with uracil. This can result in the following pairings:
DNA/DNA
DNA/RNA
RNA/RNA
As early as 1949, the Austrian biochemist Erwin Chargaff established with the Chargaff rules that in DNA the number of bases adenine (A) and thymine (T) is always present in the ratio 1 : 1, likewise the ratio of the bases guanine (G) and cytosine (C) is 1 : 1. In contrast, the quantity ratio A : G or C : T varies greatly (Chargaff's rules).
From this, James D. Watson and Francis Harry Compton Crick concluded that A-T and G-C each form complementary base pairs.
In tRNA and rRNA, base pairing also occurs when the nucleotide strand forms loops, resulting in complementary base sequences facing each other. Since in RNA only uracil is incorporated instead of thymine, the pairings are A-U and G-C.
Unusual pairings occur mainly in tRNAs and in triple helices. Although they follow the Watson-Crick scheme, they form other hydrogen bonds: Examples include reverse Watson-Crick pairings, Hoogsteen pairings (named after Karst Hoogsteen, born 1923), and reverse Hoogsteen pairings
As early as the late 20th century, several studies showed evidence for the existence of non-Watson-Crick base pairs with Watson-Crick-like geometry in the interaction of tRNA and mRNA when they contain pseudouridine(Ψ) or inosine(I).
In this representation, the tRNA residue is always located at position 34, the mRNA counterpart at position +3. For the A-Ψ binding, these values differ and are marked accordingly.
"■" indicates the use of the Hoogsteen site (cis), "⬤" that of the Watson-Crick site (cis). A mediation of base pairing by water is indicated by a "W" in the pairing. A "~" indicates the need for a tautomeric base. "*" indicates modified bases.
| Non-Watson-Crick base pairs with Watson-Crick-like geometry | ||
| tRNA residue | mRNA residue | Type of base pairing |
| Ψsyn | A | ■―⬤ |
| Gsyn | G | ■W⬤ |
| Gsyn | A+ | ■―⬤ |
| Gsyn | A+ | ■―⬤ |
| G | Gsyn | ■~⬤ |
| G | Gsyn | ⬤W■ |
| G | Asyn | ⬤―■ |
| I | Asyn | ⬤―■ |
| I | Gsyn | ⬤~■ |
| I | Gsyn | ⬤W■ |
| Ψ | A | Watson-Crick |
| U* | G | Watson-Crick (U~C) |
| C* | A | Watson-Crick (C~A) |
| A (36) | Ψ (+1) | Watson-Crick |
| A (36) | Ψsyn (+1) | ⬤―■ |
For the U⬤-■A and C⬤-■G bonds to be formed, C must either be in the imino form or protonated.
→ Main article: Wobble hypothesis
The term refers to the Wobble hypothesis of Francis Crick (1966). Wobble pairings are the non-Watson Crick pairings G-U or G-T and A-C:
In synthetic biology, nucleic acids with synthetic bases, among other things, are generated and studied, sometimes also with the aim of pairing these bases. One example is Hachimoji DNA.
