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

摘要

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 Angstrom, b = 30.63 Angstrom, c = 43.78 Angstrom. Refinement using NUCLSQ with 51 water molecules included in the final model converged at R = 0.179 (R(w) = 0.159) for 2798 reflections (F > 2 sigma(F)) in the range 8 Angstrom to 1.7 Angstrom. 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. (C) 1995 Academic Press Limited [References: 42]