TY - JOUR
T1 - Formation of loops in DNA under tension
AU - Sankararaman, Sumithra
AU - Marko, John F.
PY - 2005/2/1
Y1 - 2005/2/1
N2 - We study the formation of loops along a DNA molecule under applied tension, as might occur in single-DNA micromanipulation experiments with proteins which are able to simultaneously bind two DNA sites. We consider the case of "bare" DNA in the loop, which forms a "teardrop" shape, and the case where a single DNA-bending protein produces a "kink" in the middle of the loop; the presence of a right-angle kink in the loop reduces its bending energy by a factor of 3. Using the bending energy plus an estimate of the free energies associated with fluctuations and the elasticity of the extended nonlooped DNA, we obtain a probability distribution for loops as a function of loop size and force. Force strongly suppresses formation of all loops, but suppresses large loops more severely than small ones. This quenching effect of force is reduced in the presence of a kink in the loop. We also calculate the speed at which length is absorbed into loops between arbitrary positions along the DNA (i.e., for non-sequence-specific loop forming proteins). The speed of retraction of the molecule decays as a stretched exponential function of the force with characteristic force scales depending on the geometry of the loops.
AB - We study the formation of loops along a DNA molecule under applied tension, as might occur in single-DNA micromanipulation experiments with proteins which are able to simultaneously bind two DNA sites. We consider the case of "bare" DNA in the loop, which forms a "teardrop" shape, and the case where a single DNA-bending protein produces a "kink" in the middle of the loop; the presence of a right-angle kink in the loop reduces its bending energy by a factor of 3. Using the bending energy plus an estimate of the free energies associated with fluctuations and the elasticity of the extended nonlooped DNA, we obtain a probability distribution for loops as a function of loop size and force. Force strongly suppresses formation of all loops, but suppresses large loops more severely than small ones. This quenching effect of force is reduced in the presence of a kink in the loop. We also calculate the speed at which length is absorbed into loops between arbitrary positions along the DNA (i.e., for non-sequence-specific loop forming proteins). The speed of retraction of the molecule decays as a stretched exponential function of the force with characteristic force scales depending on the geometry of the loops.
UR - http://www.scopus.com/inward/record.url?scp=37649031368&partnerID=8YFLogxK
U2 - 10.1103/PhysRevE.71.021911
DO - 10.1103/PhysRevE.71.021911
M3 - Article
C2 - 15783356
AN - SCOPUS:37649031368
SN - 1539-3755
VL - 71
JO - Physical Review E - Statistical, Nonlinear, and Soft Matter Physics
JF - Physical Review E - Statistical, Nonlinear, and Soft Matter Physics
IS - 2
M1 - 021911
ER -