Studies of DNA dumbbells. VI. Analysis of optical melting curves of dumbbells with a sixteen-base pair duplex stem and end-loops of variable size and sequence

Biopolymers
T M PanerAlbert S Benight

Abstract

Optical melting curves of 22 DNA dumbbells with the 16-base pair duplex sequence 5'-G-C-A-T-C-A-T-C-G-A-T-G-A-T-G-C-3' linked on both ends by single-strand loops of A, or C, sequences (iota = 2, 3, 4, 6, 8, 10, 14). T sequences (iota = 2, 3, 4, 6, 8, 10), and G iota sequences (iota = 2, 4) were measured in phosphate buffered solvents containing 30, 70, and 120 mM Na+. For dumbbells with loops comprised of at least three nucleotides, stability is inversely proportional to end-loop size. Dumbbells with loops comprised of only two nucleotide bases generally have lower stabilities than dumbbells with three base nucleotide loops. Experimental melting curves were analyzed in terms of the numerically exact (multistate) statistical thermodynamic model of DNA dumbbell melting previously described (T. M. paner, M. Amaratunga & A. S. Benight (1992), Biopolymers 32, 881). Theoretically calculated melting curves were fitted to experimental curves by simultaneously adjusting model parameters representing statistical weights of intramolecular hairpin loop and single-strand circle states. The systematically determined empirical parameters provided evaluations of the energetics of hairpin loop formation as a function of loop size, sequence, and...Continue Reading

References

Nov 4, 1976·Journal of Molecular Biology·M T RecordP De Haseth
Mar 19, 1991·Biochemistry·G W Ashley, D M Kushlan
Feb 5, 1990·Biopolymers·R D Blake, S G Delcourt
Jan 10, 1989·Biochemistry·D A ErieK J Breslauer
Dec 9, 1985·Nucleic Acids Research·D E Wemmer, A S Benight

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Citations

Sep 26, 2009·The Journal of Physical Chemistry. B·Binh Nguyen, W David Wilson
Sep 22, 2011·PloS One·Jan ZollFrank J M van Kuppeveld

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