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A model for the [C + ‐G⋅C] n triple helix derived from observation of the C + ‐G⋅C base triplet in a crystal structure
Author(s) -
Nunn Christine M,
Trent John O,
Neidle Stephen
Publication year - 1997
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/s0014-5793(97)01130-7
Subject(s) - triple helix , crystal structure , crystallography , netropsin , helix (gastropod) , chemistry , cytosine , base pair , oligonucleotide , protonation , stereochemistry , crystal (programming language) , dna , minor groove , ecology , ion , biochemistry , organic chemistry , snail , biology , computer science , programming language
A molecular modelling study on the [C + ‐G⋅C] n triple helix is reported. We have observed the C + ‐G⋅C base triplet in the crystal structure of an oligonucleotide‐drug complex, between the minor‐groove drug netropsin and the decanucleotide d(CGCAATTGCG) 2 . The complex was crystallised at pH 7.0, but the crystal structure, at a resolution of 2.4 Å, shows that a terminal cytosine has become protonated and participates in a parallel C + ‐G⋅C base triplet. The structure of this triplet and its associated sugar‐phosphate backbones have been energy‐refined and then used to generate a triple helix. This has characteristics of the B‐type family of DNA structures for two strands, with the third, the C + strand, having backbone conformations closer to the A family.