Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC.
Salt effects on duplex formation by dGCATGC have been studied with spectroscopic, thermodynamic, and kinetic methods. Circular dichroism spectra indicate different salt conditions have little effect on the structures of the duplex and single strand. NMR chemical shifts indicate the structure of the duplex in 1 M NaCl is similar to that of the B-form determined previously in 0.5 M KCl [Nilges, M., Clore, G. M., Gronenborn, A. M., Brunger, A. T., Karplus, M., & Nilsson, L. (1987) Biochemistry 26, 3718-3733]. Optical melting experiments indicate the effect of Na+ concentration on melting temperature is similar to that expected for a polynucleotide with the same GC content. Laser temperature-jump experiments indicate the effect of Na+ concentration on the rate of duplex formation is much less than is observed for polynucleotides. The observations are consistent with expectations based on a counterion condensation model. This is surprising for a duplex with only 10 phosphates.
Department of Chemistry, University of Rochester, New York 14627.
A P
AP
Williams
C E
CE
Longfellow
S M
SM
Freier
R
R
Kierzek
D H
DH
Turner
D002942:Circular Dichroism; D007700:Kinetics; D007834:Lasers; D008274:Magnesium; D015636:Magnesium Chloride; D009682:Magnetic Resonance Spectroscopy; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides; D012965:Sodium Chloride; D013696:Temperature; D013816:Thermodynamics
D009838:Oligodeoxyribonucleotides; D015636:Magnesium Chloride; D012965:Sodium Chloride; D008274:Magnesium