Session L28: Nucleic Acids: Structure & Function
2:30 PM–5:30 PM, Tuesday, March 16, 2010
Room: C124
Sponsoring Unit:
DBP
Chair: Ralf Bundschuh, Ohio State University
Abstract ID: BAPS.2010.MAR.L28.7
Abstract: L28.00007 : Ethanol Induced Shortening of DNA in Nanochannels
3:42 PM–3:54 PM
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Abstract 
Authors:
Greg Gemmen
(University of Oregon)
Walter Reisner
(McGill University)
Jonas Tegenfeldt
(Lund University)
Heiner Linke
(Lund University)
The confinement of DNA in nanochannels has greatly facilitated the study of DNA polymer physics and holds promise as a powerful tool for genomic sequencing. Ethanol precipitation of DNA is a common tool in molecular biology, typically in $>$70{\%} [EtOH]. Even at lower ethanol concentrations, however, DNA transforms from B-form to A-form, a shorter yet slightly less twisted conformation. Accordingly, we isolated individual YOYO-1 labeled $\lambda $-DNA molecules in 100nm$\times $100nm channels in 0, 20, 40 and 60{\%} [EtOH]. We observed a dramatic shortening in the mean measured lengths with increasing [EtOH] and a broadening of the distribution of measured lengths at the intermediate concentrations. These observed lengths are less than those expected from fully A-form $\lambda $-DNA, suggesting that poor solvency effects are involved. Also, substantial spatial variations in intensity in a small number of molecules at the higher [EtOH] suggest the presence of higher order DNA conformations, in accord with the observation that the effective persistence length of DNA has been greatly reduced.
To cite this abstract, use the following reference: http://meetings.aps.org/link/BAPS.2010.MAR.L28.7