Base Pairing in DNA: Unusual Patterns


Watson–Crick base pairs comprise just two of 44 reasonable base pairing geometries involving the four common deoxyribonucleotides (dA, dC, dG, dT) in either their neutral or protonated forms. Most of the 42 non‐Watson–Crick base pairs have been observed experimentally in DNA. Although these unusual base pairs are difficult to detect in vivo, unusual base pairing may be significant for the biological functions of DNA.

Keywords: mutation; transversion; transition; telomere; I‐motif; Hoogsteen

Figure 1.

(a) The two Watson–Crick base pairs. Base pairs are indicated by numbers in square brackets in the text. The numbering for all four deoxynucleotides is indicated above the base pairs with hydrogen bond donor and acceptor sites in bold type. Hydrogen bonds are indicated by dashed lines. The torsion angle about the glycosidic bond, χ, adopts an anti orientation in the Watson–Crick base pairs and is indicated by an arrow for the purine deoxynucleotide in each Watson–Crick base pair. (b) Computer‐generated model structures of the Watson–Crick base pairs.

Figure 2.

Non‐Watson–Crick dA–dT and dG–dC (dG–dC+) base pairs. Base pairs consisting of chemically reasonable structures that have not yet been observed experimentally in DNA are indicated by [∗] in Figures , , , .

Figure 3.

Structures of possible transition mismatched base pairs involving dG with dT and dA with dC. Transition mismatched base pairs involving either protonated dA or protonated dC are also included.

Figure 4.

Structures of possible transversion mismatched base pairs involving two purines (dA–dA, dA–dG and dG–dG). Transversion mismatched base pairs involving protonated dA are also included.

Figure 5.

Structures of possible transversion mismatched base pairs involving two pyrimidines (dT–dT, dT–dC and dC–dC). Transversion mismatched base pairs involving protonated dC are also included.



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Yang XL, Sugiyama H, Ikeda S, Saito I and Wang AH (1998) Structural studies of a stable parallel‐stranded DNA duplex incorporating isoguanine: cytosine and isocytosine: guanine basepairs by nuclear magnetic resonance spectroscopy. Biophysical Journal 75: 1163–1171.

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Gmeiner, William H, and Walberer, Bernhard J(Apr 2001) Base Pairing in DNA: Unusual Patterns. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1038/npg.els.0003127]