Novel Hoogsteen-like bases for configurational recognition of the T-A base pair by DNA triplex formation

Biopolymers
J H Rothman, W G Richards

Abstract

Effective sequence-specific recognition of duplex DNA is possible by triplex formation with natural oligonucleotides via Hoogsteen H-bonding. However, triplex formation is in practice limited to pyrimidine oligonucleotides binding duplex A-T or G-C base-pair DNA sequences specifically at homopurine sites in the major groove as T-A-T and C+.G-C triplets. Here we report the successful modeling of novel unnatural nucleosides that recognize the T-A DNA base pair by Hoogsteen interaction. Since the DNA triplex can be considered to assume an A-type or B-type conformation, these novel Hoogsteen nucleotides are tested within model A-type and B-type conformation triplex structures. A triplet consisting of the T-A base pair and one of the novel Hoogsteen nucleotides replaces the central T.A-T triplet in the triplex using the same deoxyribose-phosphodiester and base-deoxyribose dihedral angle configuration. The entire triplex is energy minimized and the presence of any structural or energetic perturbations due to the central triplet is assessed with respect to the unmodified energy-minimized (T.A-T)11 proposed starting structures. Incorporation of these novel triplets into both A-type and B-type natural tiplex structures provokes minimal ...Continue Reading

References

Oct 1, 1976·Nucleic Acids Research·S ArnottP J Smith
Jan 20, 1992·Journal of Molecular Biology·C A Laughton, S Neidle
Dec 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·G E PlumK J Breslauer
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Sep 1, 1995·Biopolymers·G RaghunathanV Sasisekharan
Dec 7, 1993·Biochemistry·S K ChiuC M Radding
Jan 19, 1993·Biochemistry·G RaghunathanV Sasisekharan

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