Nucleic Acids Research, 1992, Vol. 20, No. 18 4753-4759
© 1992
STRUCTURAL BIOLOGY |
The conformational variability of an adenosine inosine base-pair in a synthetic DNA dodecamer
1Department of Chemistry, University of Edinburgh King's Buildings, West Mains Road, Edinburgh EH9 3JJ 2Department of Chemistry, University of Manchester Oxford Road, Manchester M13 9PL, UK
*To whom correspondence should be addressed at: Department of Chemistry, University of Manchester, Oxford Road Manchester M13 9PL, UK
Received July 2, 1992. Revised August 21, 1992. Accepted August 21, 1992.
A crystal structure analysis of the synthetic deoxydodecamer d(CGCAAATTIGCG) which contains two adenosine·Inosine (A·I) mispairs has revealed that, in this sequence, the A·I base-pairs adopt a A(anti)·I(syn) configuration. The refinement converged at R=0.158 for 2004 reflections with FE
2
(F) in the range 7.0–2.5Å for a model consisting of the DNA duplex and 71 water molecules. A notable feature of the structure is the presence of an almost complete spine of hydration spanning the minor groove of the whole of the (AAATTI)2 core region of the duplex. pH-dependent ultraviolet melting studies have suggested that the base-pair observed in the crystal structure is, in fact, a protonated AH+(anti)-I(syn) species and that the A·I base-pairs in the sequence studied display the same conformational variability as A·G mispairs in the sequence d(CGCAAATTGGCG). The AH+(anti)·I(syn) base-pair predominates below pH 6.5 and an A(anti)·I(anti) mispair is the major species present between pH 6.5 and 8.0. The protonated base-pairs are held together by two hydrogen bonds one between N6(A) and O6(I) and the other between N1(A) and N7(I). This second hydrogen bond is a direct result of the protonation of the N1 of adenosine. The ultraviolet melting studies indicate that the A(anti)·I(anti) base-pair is more stable than the A(anti)·G(anti) base-pair but that the AH+(anti)·I(syn) base pair is less stable than its AH+(anti)·G(syn) analogue. Possible reasons for this observation are discussed.
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