Spatial Constraint Corrections to the Elasticity of dsDNA Measured with Magnetic Tweezers
28 pages, 6 figures An explanatory figure has been added. The physical interpretation of the results has been made somewhat more transparent In this paper, we have studied, within a discrete WLC model, the spatial constraints in magnetic tweezers used in single molecule experiments. Two elements are...
Main Author: | |
---|---|
Other Authors: | , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
HAL CCSD
2007
|
Subjects: | |
Online Access: | https://hal.archives-ouvertes.fr/hal-00287744 |
id |
ftccsdartic:oai:HAL:hal-00287744v1 |
---|---|
record_format |
openpolar |
spelling |
ftccsdartic:oai:HAL:hal-00287744v1 2023-05-15T18:22:59+02:00 Spatial Constraint Corrections to the Elasticity of dsDNA Measured with Magnetic Tweezers Bouchiat, C. Laboratoire de Physique Théorique de l'ENS (LPTENS) Université Pierre et Marie Curie - Paris 6 (UPMC)-Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS) École normale supérieure - Paris (ENS Paris) Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris) Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) 2007 https://hal.archives-ouvertes.fr/hal-00287744 en eng HAL CCSD IOP Publishing info:eu-repo/semantics/altIdentifier/arxiv/q-bio/0702043 hal-00287744 https://hal.archives-ouvertes.fr/hal-00287744 ARXIV: q-bio/0702043 ISSN: 1742-5468 Journal of Statistical Mechanics: Theory and Experiment https://hal.archives-ouvertes.fr/hal-00287744 Journal of Statistical Mechanics: Theory and Experiment, IOP Publishing, 2007, pp.P06001 [PHYS.COND.CM-SCM]Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft] [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph] info:eu-repo/semantics/article Journal articles 2007 ftccsdartic 2021-11-21T05:13:51Z 28 pages, 6 figures An explanatory figure has been added. The physical interpretation of the results has been made somewhat more transparent In this paper, we have studied, within a discrete WLC model, the spatial constraints in magnetic tweezers used in single molecule experiments. Two elements are involved: first, the fixed plastic slab on which is stuck the initial strand, second, the magnetic bead which pulls (or twists) the attached molecule free end. We have shown that the bead surface can be replaced by its tangent plane at the anchoring point, when it is close to the bead south pole relative to the force. We are led to a model with two parallel repulsive plates: the fixed anchoring plate and a fluctuating plate, simulating the bead, in thermal equilibrium with the system. The bead effect is a slight upper shift of the elongation, about four times smaller than the similar effect induced by the fixed plate. This rather unexpected result, has been qualitatively confirmed within the soluble Gaussian model. A study of the molecule elongation versus the countour length exhibits a significant non-extensive behaviour. The curve for short molecules (with less than 2 kbp) is well fitted by a straight line, with a slope given by the WLC model, but it does not go through the origin. The non-extensive offset gives a 15% upward shift to the elongation of a 2 kbp molecule stretched by a 0.3 pN force. Article in Journal/Newspaper South pole Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) South Pole |
institution |
Open Polar |
collection |
Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) |
op_collection_id |
ftccsdartic |
language |
English |
topic |
[PHYS.COND.CM-SCM]Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft] [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph] |
spellingShingle |
[PHYS.COND.CM-SCM]Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft] [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph] Bouchiat, C. Spatial Constraint Corrections to the Elasticity of dsDNA Measured with Magnetic Tweezers |
topic_facet |
[PHYS.COND.CM-SCM]Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft] [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph] |
description |
28 pages, 6 figures An explanatory figure has been added. The physical interpretation of the results has been made somewhat more transparent In this paper, we have studied, within a discrete WLC model, the spatial constraints in magnetic tweezers used in single molecule experiments. Two elements are involved: first, the fixed plastic slab on which is stuck the initial strand, second, the magnetic bead which pulls (or twists) the attached molecule free end. We have shown that the bead surface can be replaced by its tangent plane at the anchoring point, when it is close to the bead south pole relative to the force. We are led to a model with two parallel repulsive plates: the fixed anchoring plate and a fluctuating plate, simulating the bead, in thermal equilibrium with the system. The bead effect is a slight upper shift of the elongation, about four times smaller than the similar effect induced by the fixed plate. This rather unexpected result, has been qualitatively confirmed within the soluble Gaussian model. A study of the molecule elongation versus the countour length exhibits a significant non-extensive behaviour. The curve for short molecules (with less than 2 kbp) is well fitted by a straight line, with a slope given by the WLC model, but it does not go through the origin. The non-extensive offset gives a 15% upward shift to the elongation of a 2 kbp molecule stretched by a 0.3 pN force. |
author2 |
Laboratoire de Physique Théorique de l'ENS (LPTENS) Université Pierre et Marie Curie - Paris 6 (UPMC)-Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS) École normale supérieure - Paris (ENS Paris) Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris) Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) |
format |
Article in Journal/Newspaper |
author |
Bouchiat, C. |
author_facet |
Bouchiat, C. |
author_sort |
Bouchiat, C. |
title |
Spatial Constraint Corrections to the Elasticity of dsDNA Measured with Magnetic Tweezers |
title_short |
Spatial Constraint Corrections to the Elasticity of dsDNA Measured with Magnetic Tweezers |
title_full |
Spatial Constraint Corrections to the Elasticity of dsDNA Measured with Magnetic Tweezers |
title_fullStr |
Spatial Constraint Corrections to the Elasticity of dsDNA Measured with Magnetic Tweezers |
title_full_unstemmed |
Spatial Constraint Corrections to the Elasticity of dsDNA Measured with Magnetic Tweezers |
title_sort |
spatial constraint corrections to the elasticity of dsdna measured with magnetic tweezers |
publisher |
HAL CCSD |
publishDate |
2007 |
url |
https://hal.archives-ouvertes.fr/hal-00287744 |
geographic |
South Pole |
geographic_facet |
South Pole |
genre |
South pole |
genre_facet |
South pole |
op_source |
ISSN: 1742-5468 Journal of Statistical Mechanics: Theory and Experiment https://hal.archives-ouvertes.fr/hal-00287744 Journal of Statistical Mechanics: Theory and Experiment, IOP Publishing, 2007, pp.P06001 |
op_relation |
info:eu-repo/semantics/altIdentifier/arxiv/q-bio/0702043 hal-00287744 https://hal.archives-ouvertes.fr/hal-00287744 ARXIV: q-bio/0702043 |
_version_ |
1766202396021620736 |