Oligonucleotide interactions. II. Differences in base stacking in linear and cyclic deoxythymidine oligonucleotides

Charles R. Cantor, Robert H Fairclough, R. A. Newmark

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

The circular dichroism, ultraviolet absorption, and nuclear magnetic resonance of linear and cyclic thymidine diand trinucleotides have been studied. In aqueous solution the long-wavelength Cotton effects of the cyclic dinucleotide are opposite in sign to the corresponding bands of the linear compound. Thus cyclic thymidine dinucleotide must have a stacked conformation which is quite different from the base-stacking geometry of any other known oligonucleotide. Nuclear magnetic resonance spectra of the cyclic dimer suggests that the two bases are magnetically equivalent. It is possible to construct a plausible model of the conformation of the cyclic dimer which explains both the optical and magnetic resonance data. In methanol solution the linear oligothymidylates are unstacked and show optical properties very similar to those of thymidylic acid. Methanol causes substantial changes in the conformation of cyclic thymidine dinucleotide while, in contrast, there is virtually no effect on the cyclic trinucleotide. The vast differences in the base stacking of linear and cyclic oligonucleotides may have implications for the possible structures of loops and hairpins in transfer and ribosomal ribonucleic acids.

Original languageEnglish (US)
Pages (from-to)3610-3617
Number of pages8
JournalBiochemistry
Volume8
Issue number9
StatePublished - 1969
Externally publishedYes

Fingerprint

Oligonucleotides
Thymidine
Conformations
Magnetic Resonance Spectroscopy
Dimers
Methanol
Nuclear magnetic resonance
Thymidine Monophosphate
Magnetic resonance
Circular Dichroism
Transfer RNA
Cotton
Optical properties
RNA
Wavelength
Geometry

ASJC Scopus subject areas

  • Biochemistry

Cite this

Oligonucleotide interactions. II. Differences in base stacking in linear and cyclic deoxythymidine oligonucleotides. / Cantor, Charles R.; Fairclough, Robert H; Newmark, R. A.

In: Biochemistry, Vol. 8, No. 9, 1969, p. 3610-3617.

Research output: Contribution to journalArticle

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N2 - The circular dichroism, ultraviolet absorption, and nuclear magnetic resonance of linear and cyclic thymidine diand trinucleotides have been studied. In aqueous solution the long-wavelength Cotton effects of the cyclic dinucleotide are opposite in sign to the corresponding bands of the linear compound. Thus cyclic thymidine dinucleotide must have a stacked conformation which is quite different from the base-stacking geometry of any other known oligonucleotide. Nuclear magnetic resonance spectra of the cyclic dimer suggests that the two bases are magnetically equivalent. It is possible to construct a plausible model of the conformation of the cyclic dimer which explains both the optical and magnetic resonance data. In methanol solution the linear oligothymidylates are unstacked and show optical properties very similar to those of thymidylic acid. Methanol causes substantial changes in the conformation of cyclic thymidine dinucleotide while, in contrast, there is virtually no effect on the cyclic trinucleotide. The vast differences in the base stacking of linear and cyclic oligonucleotides may have implications for the possible structures of loops and hairpins in transfer and ribosomal ribonucleic acids.

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