Paper Citing NAMD - Abstract
Qamar, Shahid; Williams, Phil M.; Lindsay, S. M.
Can an atomic force microscope sequence DNA using a nanopore?
BIOPHYSICAL JOURNAL, 94:1233-1240, FEB 15 2008
R. Bension has proposed that single molecules of DNA could be sequenced rapidly, in long sequential reads, by reading off the force required to pull a tightly fitting molecular ring over each base in turn using an atomic force microscope (AFM). We present molecular dynamics simulations that indicate that pulling DNA very rapidly (m/s) could generate large force peaks as each base is passed (similar to 1 nN) with significant differences (similar to 0.5 nN) between purine and pyrimidine. These speeds are six orders of magnitude faster than could be read out by a conventional AFM, and extending the calculations to accessible speeds using Kramers' theory shows that thermal fluctuations dominate the process with the result that purine and pyrimidine cannot be distinguished with the pulling speeds attained by current AFM technology.
