457D

MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGMO6AATTCGCG): N6-METHOXYADENOSINE/ THYMIDINE BASE-PAIRS IN B-DNA

Summary for 457D

• Entry DOI: 10.2210/pdb457d/pdb
• Descriptor: DNA (5'-D(*CP*GP*CP*GP*(A47)P*AP*TP*TP*CP*GP*CP*G)-3'), MAGNESIUM ION (3 entities in total)
• Functional Keywords: modified nucleotide, methoxyadenosine, dna damage, b-dna, double helix, dna
• Total number of polymer chains: 2
• Total formula weight: 7411.14

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.,Hikima, T.,Ono, A.,Ueno, Y.,Matsuda, A.,Takenaka, A.
Crystallographic studies on damaged DNAs. II. N(6)-methoxyadenine can present two alternate faces for Watson-Crick base-pairing, leading to pyrimidine transition mutagenesis.
J.Mol.Biol., 294:1223-1230, 1999

PubMed Abstract: In a previous paper, 2'-deoxy-N(6)-methoxyadenosine (mo(6)A) was shown to form a mismatch base-pair with 2'-deoxycytidine with a Watson-Crick-type geometry. To fully understand the structural basis of genetic mutations with damaged DNA, it is necessary to examine whether the methoxylated adenine residue still has the ability to form the regular Watson-Crick pairing with a thymine residue. Therefore, a DNA dodecamer with the sequence d(CGCGmo(6)AATTCGCG) has been synthesized and its crystal structure determined. The methoxylation has no significant effect on the overall DNA conformation, which is that of a standard B-form duplex. The methoxylated adenine moieties adopt the amino tautomer with an anti conformation around the C(6)-N(6) bond to the N(1) atom, and they form a Watson-Crick base-pair with thymine residues on the opposite strand, similar to an unmodified adenine residue. It is concluded that methoxylated adenine can present two alternate faces for base-pairing, thanks to the amino<-->imino tautomerism allowed by methoxylation. Based on this property, two gene transition routes are proposed.

PubMed: 10600380
DOI: 10.1006/jmbi.1999.3304

Experimental method

X-RAY DIFFRACTION (2 Å)