B-S transition in short oligonucleotides.
Stretching experiments with long double-stranded DNA molecules in physiological ambient revealed a force-induced transition at a force of 65 pN. During this transition between B-DNA and highly overstretched S-DNA the DNA lengthens by a factor of 1.7 of its B-form contour length. Here, we report the occurrence of this so-called B-S transition in short duplexes consisting of 30 basepairs. We employed atomic-force-microscope-based single molecule force spectroscopy to explore the unbinding mechanism of two short duplexes containing 30 or 20 basepairs by pulling at the opposite 5' termini. For a 30-basepair-long DNA duplex the B-S transition is expected to cause a length increase of 6.3 nm and should therefore be detectable. Indeed 30% of the measured force-extension curves exhibit a region of constant force (plateau) at 65 pN, which corresponds to the B-S transition. The observed plateaus show a length between 3 and 7 nm. This plateau length distribution indicates that the dissociation of a 30-basepair duplex mainly occurs during the B-S transition. In contrast, the measured force-extension curves for a 20-basepair DNA duplex exhibited rupture forces below 65 pN and did not show any evidence of a B-S transition.
Morfill
Julia
J
Lehrstuhl für Angewandte Physik & Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany. julia@morfill.de
Kühner
Ferdinand
F
Blank
Kerstin
K
Lugmaier
Robert A
RA
Sedlmair
Julia
J
Gaub
Hermann E
HE
D020029:Base Pairing; D001483:Base Sequence; D001703:Biophysics / Q000379:methods*; D004247:DNA / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D018625:Microscopy, Atomic Force; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry; D009841:Oligonucleotides / Q000737:chemistry*
D009711:Nucleotides; D009841:Oligonucleotides; D004247:DNA