臺灣博碩士論文加值系統

Experiments have shown that a semiflexible polyelectrolyte, such as a DNA,
can be condensed by multivalent counterions and the preferred form is toroid. By
using molecular dynamics simulations, a single DNA molecule is condensed into
a compact toroid-like structure. DNA is treated as a bead-spring chain, using
parameters of dsDNA. The influence of the counterion size and DNA monomer
size on the DNA structure is studied. We found that for a DNA monomer size
of ¾ and counterion size of 0.5¾, the complex (DNA plus condensed counterions)
forms a well-defined toroidal structure. The dependence of the structure of the
condensed DNA on the initial configuration is investigated. We observed that the
final conformation does not depend on the initial state. The condensed DNA toroid
is then stretched by pulling one end of the chain at various constant velocities to
investigate the effects of the pulling velocity on the force-extension curve (FEC).
We found that the pulling velocity influences the force profile and the internal
structure of the condensed DNA molecule. Moreover, the responses at both DNA
ends are different if the pulling velocity is larger than the reference Rouse velocity,
Vo. For velocities larger than Vo, the FEC’s dependence over the pulling velocity
is linear at the DNA end which is moving at constant velocity; nevertheless, these
FECs oscillate around a constant force (¼ 2.5KBT/¾) at the other end. We
found that a pulling velocity equals to 5×10−4¾/¿ does not perturb the complex.
Moreover, the influence of the pulling velocity on the bond length is linear. We
observed that the entropic behavior of the DNA molecule is strongly affected by
the condensed counterions. The FEC shows a series of “stick-release patterns”.
It gradually increases with increasing extension and then abruptly decreases; this
behavior appears repeatedly and becomes stronger and stronger as the condensed
DNA molecule is losing its turns. We showed that these ”stick-release patterns”
are a consequence of turn-by-turn unfolding of the condensed DNA toroid. The extensible worm-like chain (EWLC) model is found able to describe qualitatively
the behavior of the DNA molecule when its extention is close to the overall contour
length. We presented a clear evidence and described the mechanism of why the
condensed DNA molecule forms a “stick-release patterns”. Our results provide
new microscopic information about the internal structure of a single condensed
DNA toroid being stretched and are in qualitative agreement with experiments.

Experiments have shown that a semiflexible polyelectrolyte, such as a DNA,
can be condensed by multivalent counterions and the preferred form is toroid. By
using molecular dynamics simulations, a single DNA molecule is condensed into
a compact toroid-like structure. DNA is treated as a bead-spring chain, using
parameters of dsDNA. The influence of the counterion size and DNA monomer
size on the DNA structure is studied. We found that for a DNA monomer size
of ¾ and counterion size of 0.5¾, the complex (DNA plus condensed counterions)
forms a well-defined toroidal structure. The dependence of the structure of the
condensed DNA on the initial configuration is investigated. We observed that the
final conformation does not depend on the initial state. The condensed DNA toroid
is then stretched by pulling one end of the chain at various constant velocities to
investigate the effects of the pulling velocity on the force-extension curve (FEC).
We found that the pulling velocity influences the force profile and the internal
structure of the condensed DNA molecule. Moreover, the responses at both DNA
ends are different if the pulling velocity is larger than the reference Rouse velocity,
Vo. For velocities larger than Vo, the FEC’s dependence over the pulling velocity
is linear at the DNA end which is moving at constant velocity; nevertheless, these
FECs oscillate around a constant force (¼ 2.5KBT/¾) at the other end. We
found that a pulling velocity equals to 5×10−4¾/¿ does not perturb the complex.
Moreover, the influence of the pulling velocity on the bond length is linear. We
observed that the entropic behavior of the DNA molecule is strongly affected by
the condensed counterions. The FEC shows a series of “stick-release patterns”.
It gradually increases with increasing extension and then abruptly decreases; this
behavior appears repeatedly and becomes stronger and stronger as the condensed
DNA molecule is losing its turns. We showed that these ”stick-release patterns”
are a consequence of turn-by-turn unfolding of the condensed DNA toroid. The extensible worm-like chain (EWLC) model is found able to describe qualitatively
the behavior of the DNA molecule when its extention is close to the overall contour
length. We presented a clear evidence and described the mechanism of why the
condensed DNA molecule forms a “stick-release patterns”. Our results provide
new microscopic information about the internal structure of a single condensed
DNA toroid being stretched and are in qualitative agreement with experiments.

Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Agradecimientos . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Table of Contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
List of Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
List of Figures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
1 Introduction 15
1.1 Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
1.2 Reentrant condensation of DNA molecule . . . . . . . . . . . . . . . 20
1.3 Morphology of a condensed DNA molecule . . . . . . . . . . . . . . 22
1.4 Present research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
2 Simulation Method and Setup 27
2.1 DNA structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
2.2 Coarse-grained model . . . . . . . . . . . . . . . . . . . . . . . . . . 30
2.3 Molecular dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
2.4 Force fields . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
2.4.1 Non-bonded interactions . . . . . . . . . . . . . . . . . . . . 33
2.4.2 Bonded interactions . . . . . . . . . . . . . . . . . . . . . . . 35
2.5 Integration algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . 36
2.6 Simulation setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
3 Results and Discussions 39
3.1 Toroidal structure of a single condensed DNA molecule . . . . . . . 39
3.1.1 Gyration tensor . . . . . . . . . . . . . . . . . . . . . . . . . 41
3.1.2 Asphericity . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
3.2 Counterion size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
3.3 Size and shape of a condensed DNA molecule . . . . . . . . . . . . 45
3.3.1 Gyration tensor . . . . . . . . . . . . . . . . . . . . . . . . . 45
3.3.2 The winding number . . . . . . . . . . . . . . . . . . . . . . 48
3.4 Stretching process and pulling velocity . . . . . . . . . . . . . . . . 49
3.4.1 Stretching process . . . . . . . . . . . . . . . . . . . . . . . . 51
3.4.2 Pulling velocity . . . . . . . . . . . . . . . . . . . . . . . . . 52
3.5 Force-extension curve (FEC) . . . . . . . . . . . . . . . . . . . . . . 58
3.5.1 NL and NR . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
3.5.2 Stick-release behavior . . . . . . . . . . . . . . . . . . . . . . 61
3.5.3 Asphericity . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
3.5.4 Minor radius, ro, and major radius, R . . . . . . . . . . . . . 72
3.5.5 Effective fractional extension, x/Leff . . . . . . . . . . . . . 74
3.6 How do our results depend on different initial configuration? . . . . 76
3.7 Snapshots of our condensed DNA toroid during the stretching process 77
4 Conclusion 79
Appendix 83
A The Worm-Like Chain 84
A.1 Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
A.2 Experimental results and their models . . . . . . . . . . . . . . . . 86
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