Hairpin formation in the self-complementary dodecamer d-GGTACGCGTACC and derivatives containing GA and IA mispairs.
The dodecamer d-GGTACGCGTACC and four derivatives with GA and IA mispairs in the 6,7 and 5,8 positions have been examined in dilute solution and 0.01-0.1 M sodium chloride. Concentration dependence of Tm, gel electrophoresis, and equilibrium centrifugation indicate that these self-complementary oligomers can form hairpins under the present conditions. Thermal transitions measured in the ultraviolet primarily represent melting of hairpin to coil [cf. Scheffler et al. (1968, 1970)]. The Tm values show little or no depression for 6,7 substitution but rather large depression for 5,8 replacement. We interpret the results to indicate that the 6,7 sequences have two-base loops and five base pair stems and that the 5,8 sequences have four-base loops and four base pair stems. A concurrent theoretical modeling study [Raghunathan et al. (1991) Biochemistry (following paper in this issue)] provides support for this interpretation.
Howard
F B
FB
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892.
Chen
C Q
CQ
Ross
P D
PD
Miles
H T
HT
D001482:Base Composition; D001483:Base Sequence; D004247:DNA / Q000737:chemistry; D003854:Deoxyribonucleotides / Q000737:chemistry*; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D013696:Temperature; D013816:Thermodynamics
D003854:Deoxyribonucleotides; D004247:DNA