1d81
From Proteopedia
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THE CONFORMATIONAL VARIABILITY OF AN ADENOSINE. INOSINE BASE-PAIR IN A SYNTHETIC DNA DODECAMER
Overview
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 F greater than or equal to 2 sigma(F) in the range 7.0-2.5A 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.
About this Structure
1D81 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
The conformational variability of an adenosine.inosine base-pair in a synthetic DNA dodecamer., Leonard GA, Booth ED, Hunter WN, Brown T, Nucleic Acids Res. 1992 Sep 25;20(18):4753-9. PMID:1408788
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