Evidence from CD spectra and melting temperatures for stable Hoogsteen-paired oligomer duplexes derived from DNA and hybrid triplexes | Zendy

Gihan M. Hashem | Zendy; JinDer Wen | Zendy; Quang Dương Đỗ | Zendy; Donald M. Gray | Zendy

Open Access

Evidence from CD spectra and melting temperatures for stable Hoogsteen-paired oligomer duplexes derived from DNA and hybrid triplexes

Author(s) -

Gihan M. Hashem,

JinDer Wen,

Quang Dương Đỗ,

Donald M. Gray

Publication year - 1999

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/27.16.3371

Subject(s) - dna , oligomer , nucleic acid denaturation , circular dichroism , nucleic acid , biology , pyrimidine , antiparallel (mathematics) , rna , molecular structure of nucleic acids: a structure for deoxyribose nucleic acid , stereochemistry , crystallography , base pair , biochemistry , chemistry , base sequence , physics , organic chemistry , quantum mechanics , magnetic field , gene

The pyr*pur.pyr type of nucleic acid triplex has a purine strand that is Hoogsteen-paired with a parallel pyrimidine strand (pyr*pur pair) and that is Watson-Crick-paired with an antiparallel pyrimidine strand (pur.pyr pair). In most cases, the Watson-Crick pair is more stable than the Hoogsteen pair, although stable formation of DNA Hoogsteen-paired duplexes has been reported. Using oligomer triplexes of repeating d(AG)12 and d(CT)12 or r(CU)12 sequences that were 24 nt long, we found that hybrid RNA*DNA as well as DNA*DNA Hoogsteen-paired strands of triplexes can be more stable than the Watson-Crick-paired strands at low pH. The structures and relative stabilities of these duplexes and triplexes were evaluated by circular dichroism (CD) spectroscopy and UV absorption melting studies of triplexes as a function of pH. The CD contributions of Hoogsteen-paired RNA*DNA and DNA*DNA duplexes were found to dominate the CD spectra of the corresponding pyr*pur.pyr triplexes.

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