223d
From Proteopedia
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DIRECT OBSERVATION OF TWO BASE-PAIRING MODES OF A CYTOSINE-THYMINE ANALOGUE WITH GUANINE IN A DNA Z-FORM DUPLEX: SIGNIFICANCE FOR BASE ANALOGUE MUTAGENESIS
Overview
The pyrimidine nucleobase analogue 6H,8H-3,4-dihydropyrimido[4,5-c]-, [1,2]oxazin-7-one (P) is a mimic both of cytosine and thymine, since it, can form stable hydrogen-bonded base-pairs with either guanine or adenine., To investigate the geometric properties of pairing with guanine in a DNA, double helix, the structure of d(CGCGPG)2 has been determined by single, crystal X-ray analysis. The oligonucleotide crystallised as a left-handed, Z-DNA duplex in the orthorhombic space group P2(1)2(1)2(1) with cell, dimensions a = 18.23 A, b = 30.63 A, c = 43.78 A. Refinement using NUCLSQ, with 51 water molecules included in the final model converged at R = 0.179, (Rw = 0.159) for 2798 reflections (F > 2 sigma (F)) in the range 8 A to, 1.7 A. Remarkably, the two P.G pairs in the hexamer duplex are different:, Watson-Crick and wobble types separately illustrate both cytosine-like and, thymine-like behaviour. The result suggests that mutagenesis experiments, involving P and other analogues which display pronounced base-pairing, ambivalence can be used to examine the structural basis of substrate, discrimination by polymerases that is essential to accurate genetic, replication.
About this Structure
223D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Direct observation of two base-pairing modes of a cytosine-thymine analogue with guanine in a DNA Z-form duplex: significance for base analogue mutagenesis., Moore MH, Van Meervelt L, Salisbury SA, Lin PK, Brown DM, J Mol Biol. 1995 Sep 1;251(5):665-73. PMID:7666418
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