Book of Abstracts: Albany 2007

category image Albany 2007
Conversation 15
June 19-23 2007

Hairpin Formation Affects the Electrophoretic Mobilities Observed for Single-stranded DNA Oligomers

The electrophoretic mobilities of twelve double-stranded DNA oligomers containing 26 base pairs, and their component single strands, have been measured in polyacrylamide gels and in free solution. The oligomers varied in composition from 38% to 81% A+T. The mobilities observed for the dsDNAs in polyacrylamide gels were essentially independent of base pair composition; however, the mobilities observed for the single-stranded oligomers varied by ±20%. The mobilities observed for the dsDNAs in free solution decreased slowly with increasing A+T content; the mobilities of the single-stranded oligomers varied by ±10%. The mobilities observed for the single-stranded DNAs did not correlate with their A+T contents or their purine/pyrimidine ratios. However, the mobilities did correlate with the free energy of the most stable hairpin predicted for each sequence by the Zuker structure-prediction algorithm. Thermal melting curves were, therefore, measured for eight of the single-stranded oligomers, using capillary electrophoresis. The melting temperatures correlate with their free solution mobilities, indicating that the variable mobilities observed for single-stranded DNA molecules reflect the relative populations of hairpin and random coil structures in the solution.

Nancy C. Stellwagen*
Arian Abdulla
Earle Stellwagen
Qian Dong

Department of Biochemistry
University of Iowa
Iowa City, IA 52242

*Email: nancy-stellwagen@uiowa.edu