7,257 research outputs found
Homologous Pairing between Long DNA Double Helices
Molecular recognition between two double stranded (ds) DNA with homologous
sequences may not seem compatible with the B-DNA structure because the sequence
information is hidden when it is used for joining the two strands.
Nevertheless, it has to be invoked to account for various biological data.
Using quantum chemistry, molecular mechanics, and hints from recent genetics
experiments I show here that direct recognition between homologous dsDNA is
possible through formation of short quadruplexes due to direct complementary
hydrogen bonding of major groove surfaces in parallel alignment. The
constraints imposed by the predicted structures of the recognition units
determine the mechanism of complexation between long dsDNA. This mechanism and
concomitant predictions agree with available experimental data and shed light
upon the sequence effects and the possible involvement of topoisomerase II in
the recognition.Comment: 10 pages, 7 figures, Includes Supplemental Material. To appear in
Phys. Rev. Let
The torque transfer coefficient in DNA under torsional stress
In recent years, significant progress in understanding the properties of
supercoiled DNA has been obtained due to nanotechniques that made stretching
and twisting of single molecules possible. Quantitative interpretation of such
experiments requires accurate knowledge of torques inside manipulated DNA. This
paper argues that it is not possible to transfer the entire magnitudes of
external torques to the twisting stress of the double helix, and that a
reducing torque transfer coefficient (TTC<1) should always be assumed. This
assertion agrees with simple physical intuition and is supported by the results
of all-atom molecular dynamics (MD) simulations. According to MD, the TTCs
around 0.8 are observed in nearly optimal conditions. Reaching higher values
requires special efforts and it should be difficult in practice. The TTC can be
partially responsible for the persistent discrepancies between the twisting
rigidity of DNA measured by different methods.Comment: 5 pages, 4 figures. To appear in Phys. Rev.
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