417D

A THYMINE-LIKE BASE ANALOGUE FORMS WOBBLE PAIRS WITH ADENINE

Summary for 417D

• Entry DOI: 10.2210/pdb417d/pdb
• Descriptor: DNA (5'-D(*CP*AP*CP*GP*(C46)P*G)-3') (2 entities in total)
• Functional Keywords: p.a base-pairs, pyrimidine analogue, z-dna, dna
• Total number of polymer chains: 2
• Total formula weight: 3672.49

Authors

Lin, P.K.T.,Schuerman, M.H.,Moore, G.S.,Van Meervelt, L.,Loakes, D.,Brown, D.M.,Moore, M.H. (deposition date: 1998-07-15, release date: 1998-09-30, Last modification date: 2024-04-03)

Primary citation

Schuerman, G.S.,Van Meervelt, L.,Loakes, D.,Brown, D.M.,Kong Thoo Lin, P.,Moore, M.H.,Salisbury, S.A.
A thymine-like base analogue forms wobble pairs with adenine in a Z-DNA duplex.
J.Mol.Biol., 282:1005-1011, 1998

PubMed Abstract: The DNA hexamer d(CACGPG), in which dP is the ambivalent pyrimidine nucleoside analogue 2'-deoxy-beta-d-ribofuranosyl-(6H,8H-3, 4-dihydropyrimido[4,5-c][1,2]oxazin-7-one), crystallises as a left-handed Z-DNA duplex. X-ray analysis at 1.5 A shows that both P. A base-pairs are of the wobble type. This result appears inconsistent with other evidence from hybridisation and NMR studies of P-containing oligonucleotides, which suggests that, while P can form stable base-pairs with either A or G, thymine-like properties are more pronounced. Thermal denaturation experiments over a range of solution pH values indicate that protonation of the P.A base-pairs is unlikely to be responsible for the anomalous behaviour. No specific crystal packing effects can be identfied as an explanation, and it is concluded that base stacking and other interactions between nucleotide residues in Z-DNA are responsible.

PubMed: 9753550
DOI: 10.1006/jmbi.1998.2080

Experimental method

X-RAY DIFFRACTION (1.5 Å)