Deoxyribonucleic acid (DNA) is a long flexible polyelectrolyte that is housed in the aqueous environment within the cell of an organism. When a length of torsionally relaxed (untwisted) DNA is held in tension, such as is the case in many single molecule experiments, the thermal fluctuations arising from the constant bombardment of the DNA by the surrounding fluid molecules induce bending in it, while the applied tension tends to keep it extended. The combined effect of these influences is that DNA is never at its full extension but eventually attains an equilibrium value of end-to-end extension under these influences. An analytical model was developed to estimate the tension-dependent value of this extension. This model, however, does not provide any insight into the dynamics of the extensional response of DNA to applied tension nor the kinetics of DNA at equilibrium under said tension. This paper reports the results of Brownian dynamics simulations using a discrete wormlike-chain model of DNA that provide some insight into these dynamics and kinetics.

References

References
1.
Strick
,
T.
,
Allemand
,
J.
, and
Bensimon
,
D.
,
1996
, “
The Elasticity of a Single Supercoiled DNA Molecule
,”
Science
,
271
(
5257
), pp.
1835
1837
.
2.
Moroz
,
J. D.
, and
Nelson
,
P.
,
1997
, “
Torsional Directed Walks, Entropic Elasticity, and DNA Twist Stiffness
,”
Proc. Natl. Acad. Sci. U.S.A.
,
94
(
26
), pp.
14418
14422
.
3.
Moroz
,
J.
, and
Nelson
,
P.
,
1998
, “
Entropic Elasticity of Twist-Storing Polymers
,”
Macromolecules
,
31
(
18
), pp.
6333
6347
.
4.
Ivenso
,
I. D.
, and
Lillian
,
T. D.
,
2014
, “
Brownian Dynamics Simulation of the Dynamics of Stretched DNA
,”
ASME
Paper No. DETC2014-35487.
5.
Klenin
,
K.
,
Merlitz
,
H.
, and
Langowski
,
J.
,
1998
, “
A Brownian Dynamics Program for the Simulation of Linear and Circular DNA and Other Wormlike Chain Polyelectrolytes
,”
Biophys. J.
,
74
(
2 Pt 1
), pp.
780
788
.
6.
Chirico
,
G.
, and
Langowski
,
J.
,
1996
, “
Brownian Dynamics Simulations of Supercoiled DNA With Bent Sequences
,”
Biophys. J.
,
71
(
2
), pp.
955
971
.
7.
Chirico
,
G.
, and
Langowski
,
J.
,
1994
, “
Kinetics of DNA Supercoiling Studied by Brownian Dynamics Simulation
,”
Biopolymers
,
34
(
3
), pp.
415
433
.
8.
Allison
,
S.
,
1986
, “
Brownian Dynamics Simulation of Wormlike Chains. Fluorescence Depolarization and Depolarized Light Scattering
,”
Macromolecules
,
19
(
1
), pp.
118
124
.
9.
Vologodskii
,
A.
,
2007
, “
Monte Carlo Simulation of DNA Topological Properties
,”
Topology in Molecular Biology
,
Springer, Berling
,
Heidelberg
, pp.
23
41
.
10.
Charvin
,
G.
,
Vologodskii
,
A.
,
Bensimon
,
D.
, and
Croquette
,
V.
,
2005
, “
Braiding DNA: Experiments, Simulations, and Models
,”
Biophys. J.
,
88
(
6
), pp.
4124
4136
.
11.
Klenin
,
K. V.
,
Vologodskii
,
A. V.
,
Anshelevich
,
V. V.
,
Dykhne
,
A. M.
, and
Frank-Kamenetskii
,
M. D.
,
1991
, “
Computer Simulation of DNA Supercoiling
,”
J. Mol. Biol.
,
217
(
3
), pp.
413
419
.
12.
Vologodskii
,
A.
,
2006
, “
Brownian Dynamics Simulation of Knot Diffusion Along a Stretched DNA Molecule
,”
Biophys. J.
,
90
(
5
), pp.
1594
1597
.
13.
Vologodskii
,
A.
,
2009
, “
Determining Protein-Induced DNA Bending in Force-Extension Experiments: Theoretical Analysis
,”
Biophys. J.
,
96
(
9
), pp.
3591
3599
.
14.
Vologodskii
,
A.
,
2006
, “
Simulation of Equilibrium and Dynamic Properties of Large DNA Molecules
,”
Comput. Stud. RNA DNA
, pp.
579
604
.
15.
Jian
,
H.
,
Vologodskii
,
A. V.
, and
Schlick
,
T.
,
1997
, “
A Combined Wormlike-Chain and Bead Model for Dynamic Simulations of Long Linear DNA
,”
J. Comput. Phys.
,
136
(
1
), pp.
168
179
.
16.
Jian
,
H.
,
Schlick
,
T.
, and
Vologodskii
,
A.
,
1998
, “
Internal Motion of Supercoiled DNA: Brownian Dynamics Simulations of Site Juxtaposition
,”
J. Mol. Biol.
,
284
(
2
), pp.
287
296
.
17.
Huang
,
J.
,
Schlick
,
T.
, and
Vologodskii
,
A.
,
2001
, “
Dynamics of Site Juxtaposition in Supercoiled DNA
,”
Proc. Natl. Acad. Sci. U.S.A.
,
98
(
3
), pp.
968
973
.
18.
Vologodskii
,
A.
, and
Cozzarelli
,
N.
,
1995
, “
Modeling of Long-Range Electrostatic Interactions in DNA
,”
Biopolymers
,
35
(
3
), pp.
289
296
.
19.
Mielke
,
S. P.
,
Fink
,
W. H.
,
Krishnan
,
V. V.
,
Grønbech Jensen
,
N.
, and
Benham
,
C. J.
,
2004
, “
Transcription-Driven Twin Supercoiling of a DNA Loop: A Brownian Dynamics Study
,”
J. Chem. Phys.
,
121
(
16
), pp.
8104
8112
.
20.
Rotne
,
J.
, and
Prager
,
S.
,
1969
, “
Variational Treatment of Hydrodynamic Interaction in Polymers
,”
J. Chem. Phys.
,
50
(
11
), pp.
4831
4837
.
21.
Wajnryb
,
E.
,
Mizerski
,
K. A.
,
Zuk
,
P. J.
, and
Szymczak
,
P.
,
2013
, “
Generalization of the Rotne–Prager–Yamakawa Mobility and Shear Disturbance Tensors
,”
J. Fluid Mech.
,
731
, p.
R3
.
22.
Iniesta
,
A.
, and
dela Torre
,
J.
,
1990
, “
A Second-Order Algorithm for the Simulation of the Brownian Dynamics of Macromolecular Models
,”
J. Chem. Phys.
,
92
(
3
), pp.
2015
2018
.
23.
Ermak
,
D. L.
, and
McCammon
,
J. A.
,
1978
, “
Brownian Dynamics With Hydrodynamic Interactions
,”
J. Chem. Phys.
,
69
(
4
), pp.
1352
1360
.
24.
Crut
,
A.
,
Koster
,
D. A.
,
Seidel
,
R.
,
Wiggins
,
C. H.
, and
Dekker
,
N. H.
,
2007
, “
Fast dynamics of Supercoiled DNA Revealed by Single-Molecule Experiments
,”
Proc. Natl. Acad. Sci. U.S.A.
,
104
(
29
), pp.
11957
11962
.
You do not currently have access to this content.