Entropic Attraction: DNA Condensation and Expansion Induced by Nano-particles in Confinement
碩士 === 國立臺灣大學 === 物理研究所 === 102 === We investigate nanoparticle-induced DNA condensation in a confined suspension of dilute DNA molecules and ideal nano-particles (NP) using Langevin dynamics simulation. DNA condensation has been observed in a solution of dilute DNA molecules (persistence length Lp...
Main Authors: | , |
---|---|
Other Authors: | |
Format: | Others |
Language: | en_US |
Published: |
2013
|
Online Access: | http://ndltd.ncl.edu.tw/handle/v38n3w |
id |
ndltd-TW-102NTU05198046 |
---|---|
record_format |
oai_dc |
spelling |
ndltd-TW-102NTU051980462019-05-15T21:32:53Z http://ndltd.ncl.edu.tw/handle/v38n3w Entropic Attraction: DNA Condensation and Expansion Induced by Nano-particles in Confinement 熵致吸引力:在奈米侷限下由奈米粒子誘發之DNA凝縮與伸展 Guo-Jun Liao 廖國鈞 碩士 國立臺灣大學 物理研究所 102 We investigate nanoparticle-induced DNA condensation in a confined suspension of dilute DNA molecules and ideal nano-particles (NP) using Langevin dynamics simulation. DNA condensation has been observed in a solution of dilute DNA molecules (persistence length Lp ~ 50 nm) and high concentration of electrostatically neutral nano-particles (diameter Sigma_NP ~ 5 to 35 nm) in recent experimental measurements. It is believed that nano-particles entropically induce an attraction between DNA segments. For nano-particles much smaller than Lp, a DNA molecule can be considered as a chain of connected rods, and the nanoparticle-induced depletion attraction between DNA segments can be regarded as rod-rod attraction. Thus, the strength of the depletion attraction is proportional to the number of persistence length in a DNA chain, Np = L/Lp, the depletion volume NpLp^2(Sigma_ NP + Sigma_ M), and the NP volume fraction Phi , where L is the DNA contour length. We performed Langevin dynamics simulation with coarse-grained DNA molecules and accounted for the most important factors: (1) excluded volume forces between a DNA segment and NP, (2) elasticity of the semi-flexible DNA molecule, (3) bending rigidity of the DNA segment, and (4) steric repulsion between DNA segments. In nano-slit confinement with ionic strength corresponding to intra-cellular environment, owing to the repulsion from the walls, the local density of nano-particles near two walls is lower than the central region, which indicates the strength of intra-DNA attraction is weaker near walls. Thus, as the density of nano-particles Phi increases, the DNA chain will be pushed toward one wall. DNA conformation changes are much different from in an unconfined environment. The height of the nano-slit H relative to the nanoparticle size Sigma_ NP strongly influences the DNA conformation. For H/Lp ~ 1, DNA size decreases monotonically as Phi increases. In contrast, the dependence on Phi is non-monotonic for H/Lp ~ 6, due to the competition between DNA-DNA, DNA-NP, DNA-wall and NP-wall interactions. Chun-Yi David Lu Yeng-Long Chen 陸駿逸 陳彥龍 2013 學位論文 ; thesis 43 en_US |
collection |
NDLTD |
language |
en_US |
format |
Others
|
sources |
NDLTD |
description |
碩士 === 國立臺灣大學 === 物理研究所 === 102 === We investigate nanoparticle-induced DNA condensation in a confined suspension of dilute DNA molecules and ideal nano-particles (NP) using Langevin dynamics simulation. DNA condensation has been observed in a solution of dilute DNA molecules (persistence length Lp ~ 50 nm) and high concentration of electrostatically neutral nano-particles (diameter Sigma_NP ~ 5 to 35 nm) in recent experimental measurements. It is believed that nano-particles entropically induce an attraction between DNA segments. For nano-particles much smaller than Lp, a DNA molecule can be considered as a chain of connected rods, and the nanoparticle-induced depletion attraction between DNA segments can be regarded as rod-rod attraction. Thus, the strength of the depletion attraction is proportional to the number of persistence length in a DNA chain, Np = L/Lp, the depletion volume NpLp^2(Sigma_ NP + Sigma_ M), and the NP volume fraction Phi , where L is the DNA contour length.
We performed Langevin dynamics simulation with coarse-grained DNA molecules and accounted for the most important factors: (1) excluded volume forces between a DNA segment and NP, (2) elasticity of the semi-flexible DNA molecule, (3) bending rigidity of the DNA segment, and (4) steric repulsion between DNA segments. In nano-slit confinement with ionic strength corresponding to intra-cellular environment, owing to the repulsion from the walls, the local density of nano-particles near two walls is lower than the central region, which indicates the strength of intra-DNA attraction is weaker near walls. Thus, as the density of nano-particles Phi increases, the DNA chain will be pushed toward one wall. DNA conformation changes are much different
from in an unconfined environment. The height of the nano-slit H relative to the nanoparticle size Sigma_ NP strongly influences the DNA conformation. For H/Lp ~ 1, DNA size decreases monotonically as Phi increases. In contrast,
the dependence on Phi is non-monotonic for H/Lp ~ 6, due to the competition between DNA-DNA, DNA-NP, DNA-wall and NP-wall interactions.
|
author2 |
Chun-Yi David Lu |
author_facet |
Chun-Yi David Lu Guo-Jun Liao 廖國鈞 |
author |
Guo-Jun Liao 廖國鈞 |
spellingShingle |
Guo-Jun Liao 廖國鈞 Entropic Attraction: DNA Condensation and Expansion Induced by Nano-particles in Confinement |
author_sort |
Guo-Jun Liao |
title |
Entropic Attraction: DNA Condensation and Expansion Induced by Nano-particles in Confinement |
title_short |
Entropic Attraction: DNA Condensation and Expansion Induced by Nano-particles in Confinement |
title_full |
Entropic Attraction: DNA Condensation and Expansion Induced by Nano-particles in Confinement |
title_fullStr |
Entropic Attraction: DNA Condensation and Expansion Induced by Nano-particles in Confinement |
title_full_unstemmed |
Entropic Attraction: DNA Condensation and Expansion Induced by Nano-particles in Confinement |
title_sort |
entropic attraction: dna condensation and expansion induced by nano-particles in confinement |
publishDate |
2013 |
url |
http://ndltd.ncl.edu.tw/handle/v38n3w |
work_keys_str_mv |
AT guojunliao entropicattractiondnacondensationandexpansioninducedbynanoparticlesinconfinement AT liàoguójūn entropicattractiondnacondensationandexpansioninducedbynanoparticlesinconfinement AT guojunliao shāngzhìxīyǐnlìzàinàimǐjúxiànxiàyóunàimǐlìziyòufāzhīdnaníngsuōyǔshēnzhǎn AT liàoguójūn shāngzhìxīyǐnlìzàinàimǐjúxiànxiàyóunàimǐlìziyòufāzhīdnaníngsuōyǔshēnzhǎn |
_version_ |
1719116542803705856 |