456D

MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGMO6AATCCGCG): THE WATSON-CRICK TYPE N6-METHOXYADENOSINE/CYTIDINE BASE-PAIRS IN B-DNA

Summary for 456D

• Entry DOI: 10.2210/pdb456d/pdb
• Descriptor: DNA (5'-D(*CP*GP*CP*GP*(A47)P*AP*TP*CP*CP*GP*CP*G)-3'), MAGNESIUM ION (3 entities in total)
• Functional Keywords: modified nucleotide, mismatch, methoxyadenosine, dna damage, b-dna, double helix, dna
• Total number of polymer chains: 2
• Total formula weight: 7381.12

Authors

Chatake, T.,Ono, A.,Ueno, Y.,Matsuda, A.,Takenaka, A. (deposition date: 1999-03-06, release date: 2000-01-01, Last modification date: 2023-12-27)

Primary citation

Chatake, T.,Ono, A.,Ueno, Y.,Matsuda, A.,Takenaka, A.
Crystallographic studies on damaged DNAs. I. An N(6)-methoxyadenine residue forms a Watson-Crick pair with a cytosine residue in a B-DNA duplex.
J.Mol.Biol., 294:1215-1222, 1999

PubMed Abstract: Oxyamines such as hydroxylamine and methoxylamine disturb DNA replication and act as potent mutagens, causing nucleotide transition from one purine to another or one pyrimidine to another. In order to investigate mismatch base-pairing in DNA damaged with oxyamines, a dodecamer with the sequence d(CGCGmo(6)AATCCGCG), where mo(6) A is 2'-deoxy-N(6)-methoxyadenosine, was synthesized and its crystal structure determined. No significant conformational changes are found between the present dodecamer and the original undamaged B-form dodecamer. Electron density maps clearly show that the mo(6)A residue forms a base-pair with a 2'-deoxycytidine residue through hydrogen bonds similar to a Watson-Crick G.C base-pair. For these hydrogen bonds to be made, N(6)-methoxyadenine must chemically take the imino form. The methoxylation thus enables the adenine base to mimic a guanine base. As a result, misincorporation of 2'-deoxycytidine instead of thymidine, or 2'-deoxyadenosine instead of 2'-deoxyguanosine, can occur in DNA replication.

PubMed: 10600379
DOI: 10.1006/jmbi.1999.3303

Experimental method

X-RAY DIFFRACTION (1.6 Å)