Long lifetime of hydrogen-bonded DNA basepairs by force spectroscopy.
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.
Department of Physics, Arizona State University, Tempe, Arizona, USA.
Alexander
A
Fuhrmann
Sebastian
S
Getfert
Qiang
Q
Fu
Peter
P
Reimann
Stuart
S
Lindsay
Robert
R
Ros
D015075:2-Aminopurine / Q000031:analogs & derivatives / Q000737:chemistry; D000225:Adenine / Q000737:chemistry; D020029:Base Pairing; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D007700:Kinetics; D013057:Spectrum Analysis / Q000379:methods*; D013816:Thermodynamics; D013941:Thymine / Q000737:chemistry; D013997:Time Factors
D015075:2-Aminopurine; C007300:2,6-diaminopurine; D004247:DNA; D000225:Adenine; D013941:Thymine