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.
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.
Moore
M H
MH
Department of Chemistry, York University, Heslington, UK.
Van Meervelt
L
L
Salisbury
S A
SA
Lin
P K
PK
Brown
D M
DM
D001482:Base Composition; D003196:Computer Graphics; D018360:Crystallography, X-Ray; D003596:Cytosine / Q000031:analogs & derivatives; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D006147:Guanine / Q000737:chemistry*; D008958:Models, Molecular; D016296:Mutagenesis; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D010078:Oxazines / Q000737:chemistry*; D011743:Pyrimidines / Q000737:chemistry*; D013941:Thymine / Q000031:analogs & derivatives; D014867:Water / Q000378:metabolism
D009692:Nucleic Acid Heteroduplexes; D009838:Oligodeoxyribonucleotides; D010078:Oxazines; D011743:Pyrimidines; D014867:Water; C062254:6H,8H-3,4-dihydropyrimido(4,5-c)(1,2)oxazin-7-one; D006147:Guanine; D003596:Cytosine; D004247:DNA; D013941:Thymine