Nucleic Acids Research, 1985, Vol. 13, No. 17 6375-6386
© 1985
Articles |
Nuclear magnetic resonance and circular dichroism studies of a duplex - single-stranded hairpin loop equilibrium for the oligodeoxyribonucleotide sequence d(CGCGATTCGCG)
1Biophysics BranchDivision of Biochemistry and Biophysics, Food and Drug Administration 8800 Rockville Pike, Bethesda, MD 20205, USA 2Molecular Pharmacology Branch, Division of Biochemistry and Biophysics, Food and Drug Administration 8800 Rockville Pike, Bethesda, MD 20205, USA
*To whom correspondence should be addressed
Received May 6, 1985. Revised August 15, 1985. Accepted August 15, 1985.
Nuclear magnetic resonance (NMR) and circular dichroism (CD) studies have been carried out with the oligodeoxyribonucleotide mismatch sequence, d(CGCGATTCGCG), 1. It has been found that 1 exists, in solution, as an equilibrium mixture of slowly interconverting, structured conformational isomers, 1a and 1b. On the basis of the concentration dependence of the 1a – 1b equilibrium, the 1H NMR spectrum of the imino protons of the nucleotide bases, and the individual CD spectra of 1a and 1b, it is suggested that the two species correspond to a B-type DNA duplex and a single-stranded, hairpin-loop structure; the portion of the single-stranded species not involved in the loop appears to have a B-type DNA structure (on the basis of the CD measurements). To facilitate 1H NMR resonance assignments, the two possible des-methyl thymidine derivatives of 1 were synthesized; the effect of this substitution on the physical chemical properties of 1 was explored. The 1H NMR spectra of 1, as a function of temperature, showed that, under conditions wherein both species were present to a significant extent, the duplex form melted at a lower temperature than the single-stranded, hairpin loop structure.