Base Pairing in DNA: Unusual Patterns

Abstract

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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References

Boulard Y, Cognet JA, Gabarro‐Arpa J et al. (1992) The pH dependent configurations of the C.A mispair in DNA. Nucleic Acids Research 20: 1933–1941.

Boulard Y, Cognet JAH and Fazakerley GV (1997) Solution structure as a function of pH of two central mismatches, C•T and C•C, in the 29 to 39 K‐ras gene sequence, by nuclear magnetic resonance and molecular dynamics. Journal of Molecular Biology 268: 331–347.

Chou SH, Zhu L, Gao Z, Cheng JW and Reid BR (1996) Hairpin loops consisting of single adenine residues closed by sheared A.A and G.G pairs formed by the DNA triplets AAA and GAG: solution structure of the d(GTACAAAGTAC) hairpin. Journal of Molecular Biology 264: 981–1001.

Dutta R, Gao YG, Priebe W and Wang AH (1998) Binding of the modified daunorubicin WP401 adjacent to a T–G base pair induces the reverse Watson–Crick conformation: crystal structures of the WP401–TGGCCG and WP401–CGG[br5C]CG complexes. Nucleic Acids Research 26: 3001–3005.

Famulok M and Mayer G (1999) Aptamers as tools in molecular biology and immunology. Current Topics in Microbiology and Immunology 243: 123–136.

Kang C, Berger I, Lockshin C et al. (1995) Stable loop in the crystal structure of the intercalated four‐stranded cytosine‐rich metazoan telomere. Proceedings of the National Academy of Sciences of the USA 92: 3874–3878.

Lin CH and Patel DJ (1996) Encapsulating an amino acid in a DNA fold. Nature Structural Biology 3: 1046–1050.

Ramakrishnan B and Sundaralingam M (1995) Crystal structure of the A‐DNA decamer d(CCIGGCCm5CGG) at 1.6 A showing the unexpected wobble I.m5C base pair. Biophysical Journal 69: 553–558.

Rippe K, Fritsch V, Westhof E and Jovin TM (1992) Alternating d(G–A) sequences form a parallel‐stranded DNA homoduplex. EMBO Journal 11: 3777–3786.

Wang Y and Patel DJ (1994) Solution structure of the d(T‐C‐G‐A) duplex at acidic pH. A parallel‐stranded helix containing C+.C, G.G and A.A pairs. Journal of Molecular Biology 242: 508–526.

Webster GD, Sanderson MR, Skelly JV et al. (1990) Crystal structure and sequence‐dependent conformation of the A.G mispaired oligonucleotide d(CGCAAGCTGGCG). Proceedings of the National Academy of Sciences of the USA 87: 6693–6697.

Further Reading

Donohue J (1956) Hydrogen‐bonded helical configurations of polynucleotides. Proceedings of the National Academy of Sciences of the USA 42: 60–65.

Donohue J and Trueblood KN (1960) Base pairing in DNA. Journal of Molecular Biology 2: 363–371.

Gold L (1995) Conformational properties of oligonucleotides. Nucleic Acids Symposium Series 33: 20–22.

Saenger W (1983) Principles of Nucleic Acid Structure. New York: Springer‐Verlag.

Van Meervelt L, Vlieghe D, Dautant A et al. (1995) High‐resolution structure of a DNA helix forming (C.G)*G base triplets. Nature 374: 742–744.

Watson JD and Crick FHC (1953) A structure of deoxy ribonucleic acid. Nature 171: 737.

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. http://www.els.net [doi: 10.1038/npg.els.0003127]