Abstract

Electron-tunneling data suggest that a noncovalently-bonded complex of three molecules, two recognition molecules that present hydrogen-bond donor and acceptor sites via a carboxamide group, and a DNA base, remains bound for seconds. This is surprising, given that imino-proton exchange rates show that basepairs in a DNA double helix open on millisecond timescales. The long lifetime of the three-molecule complex was confirmed using force spectroscopy, but measurements on DNA basepairs are required to establish a comparison with the proton-exchange data. Here, we report on a dynamic force spectroscopy study of complexes between the bases adenine and thymine (A-T, two-hydrogen bonds) and 2-aminoadenine and thymine (2AA-T, three-hydrogen bonds). Bases were tethered to an AFM probe and mica substrate via long, covalently linked polymer tethers. Data for bond-survival probability versus force and the rupture-force distributions were well fitted by the Bell model. The resulting lifetime of the complexes at zero pulling force was ∼2 s for two-hydrogen bonds (A-T) and ∼4 s for three-hydrogen bonds (2AA-T). Thus, DNA basepairs in an AFM pulling experiment remain bonded for long times, even without the stabilizing influence of base-stacking in a double helix. This result suggests that the pathways for opening, and perhaps the open states themselves, are very different in the AFM and proton-exchange measurements.

Original languageEnglish (US)
Pages (from-to)2381-2390
Number of pages10
JournalBiophysical Journal
Volume102
Issue number10
DOIs
StatePublished - May 16 2012

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Hydrogen
Spectrum Analysis
Protons
Thymine
DNA
Adenine
Rupture
Polymers
Electrons

ASJC Scopus subject areas

  • Biophysics

Cite this

Long lifetime of hydrogen-bonded dna basepairs by force spectroscopy. / Fuhrmann, Alexander; Getfert, Sebastian; Fu, Qiang; Reimann, Peter; Lindsay, Stuart; Ros, Robert.

In: Biophysical Journal, Vol. 102, No. 10, 16.05.2012, p. 2381-2390.

Research output: Contribution to journalArticle

Fuhrmann, Alexander ; Getfert, Sebastian ; Fu, Qiang ; Reimann, Peter ; Lindsay, Stuart ; Ros, Robert. / Long lifetime of hydrogen-bonded dna basepairs by force spectroscopy. In: Biophysical Journal. 2012 ; Vol. 102, No. 10. pp. 2381-2390.
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