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B-S transition in short oligonucleotides.

Julia Morfill1, Ferdinand Kühner, Kerstin Blank

  • 1Lehrstuhl für Angewandte Physik & Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany. julia@morfill.de

Biophysical Journal
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Summary

Short DNA duplexes exhibit a force-induced B-DNA to S-DNA transition at 65 pN. This transition, observed in 30 basepair DNA, facilitates duplex dissociation, unlike shorter 20 basepair DNA.

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Area of Science:

  • Molecular Biology
  • Biophysics

Background:

  • Long double-stranded DNA exhibits a force-induced B-DNA to S-DNA transition at 65 pN, causing significant lengthening.
  • This transition involves a structural change in DNA under mechanical stress.

Purpose of the Study:

  • To investigate the B-S transition in short DNA duplexes (30 and 20 basepairs).
  • To explore the unbinding mechanism of short DNA duplexes using single-molecule force spectroscopy.

Main Methods:

  • Atomic-force-microscope-based single molecule force spectroscopy.
  • Mechanical stretching of DNA duplexes by pulling at 5' termini.
  • Analysis of force-extension curves to identify force-induced transitions and dissociation events.

Main Results:

  • A force-induced B-S transition was observed in 30% of 30-basepair DNA duplexes at a constant force of 65 pN.
  • Plateaus in force-extension curves for 30-basepair DNA ranged from 3-7 nm, indicating dissociation during the B-S transition.
  • 20-basepair DNA duplexes showed rupture forces below 65 pN, with no evidence of the B-S transition.

Conclusions:

  • The B-S transition is detectable in short 30-basepair DNA duplexes.
  • Duplex dissociation significantly occurs during the B-S transition for 30-basepair DNA.
  • Shorter DNA duplexes (20 basepairs) do not undergo the B-S transition under these experimental conditions.