文献检索文档翻译深度研究
Suppr Zotero 插件Zotero 插件
邀请有礼套餐&价格历史记录

新学期,新优惠

限时优惠:9月1日-9月22日

30天高级会员仅需29元

1天体验卡首发特惠仅需5.99元

了解详情
不再提醒
插件&应用
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
高级版
套餐订阅购买积分包
AI 工具
文献检索文档翻译深度研究
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2025

具有弯曲或不同柔性片段的DNA分子的聚合物链统计与构象分析

Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility.

作者信息

Rivetti C, Walker C, Bustamante C

机构信息

Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.

出版信息

J Mol Biol. 1998 Jul 3;280(1):41-59. doi: 10.1006/jmbi.1998.1830.


DOI:10.1006/jmbi.1998.1830
PMID:9653030
Abstract

The worm-like chain model has often been employed to describe the average conformation of long, intrinsically straight polymer molecules, including DNA. The present study extends the applicability of the worm-like chain model to polymers containing bends or sections of different flexibility. Several cases have been explicitly considered: (i) polymers with a single bend; (ii) polymers with multiple coplanar bends; (iii) polymers with two non-coplanar bends; and (iv) polymers comprised of sections with different persistence lengths. Expressions describing the average conformation of such polymers in terms of the mean-square end-to-end distance have been derived for each case. For cases (i) and (iv), expressions for the projection of the end-to-end vector onto the initial orientation of the chain are presented. The expressions derived here have been used to investigate DNA molecules with sequence-induced bending (A-tracts). Mean-square end-to-end distance values determined from a large number of A-tract containing DNA molecules visualized by scanning force microscopy resulted in an average bend angle of 13.5 degrees per A-tract. A similar study was performed to characterize the flexibility of double-strandedDNA molecules containing a single-stranded region. Analysis of their mean-square end-to-end distance yielded a persistence length of 1.3 nm for single-stranded DNA.

摘要

蠕虫状链模型常被用于描述长的、本质上呈直线状的聚合物分子(包括DNA)的平均构象。本研究将蠕虫状链模型的适用性扩展到含有弯曲或不同柔性片段的聚合物。明确考虑了几种情况:(i)具有单个弯曲的聚合物;(ii)具有多个共面弯曲的聚合物;(iii)具有两个非共面弯曲的聚合物;以及(iv)由具有不同持久长度的片段组成的聚合物。针对每种情况,都推导出了用均方末端距来描述此类聚合物平均构象的表达式。对于情况(i)和(iv),给出了末端到末端向量在链的初始取向上的投影表达式。这里推导的表达式已用于研究具有序列诱导弯曲(A序列)的DNA分子。通过扫描力显微镜观察大量含有A序列的DNA分子所确定的均方末端距值,得出每个A序列的平均弯曲角度为13.5度。进行了一项类似的研究来表征含有单链区域的双链DNA分子的柔性。对其均方末端距的分析得出单链DNA的持久长度为1.3纳米。

相似文献

[1]
Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility.

J Mol Biol. 1998-7-3

[2]
Effect of genomic long-range correlations on DNA persistence length: from theory to single molecule experiments.

J Phys Chem B. 2010-4-22

[3]
Nanoscale mechanical and dynamical properties of DNA single molecules.

Biophys Chem. 2005-3-1

[4]
High flexibility of DNA on short length scales probed by atomic force microscopy.

Nat Nanotechnol. 2006-11

[5]
Persistence length and scaling properties of single-stranded DNA adsorbed on modified graphite.

J Chem Phys. 2009-9-7

[6]
Direct measurement of conformational changes on DNA molecule intercalating with a fluorescence dye in an electrophoretic buffer solution by means of atomic force microscopy.

Electrophoresis. 2001-10

[7]
Static curvature and flexibility measurements of DNA with microscopy. A simple renormalization method, its assessment by experiment and simulation.

J Mol Biol. 1999-1-22

[8]
Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis.

J Mol Biol. 1996-12-20

[9]
A-Tract bending: insights into experimental structures by computational models.

J Mol Biol. 2000-8-18

[10]
The persistence length of double stranded DNA determined using dark field tethered particle motion.

J Chem Phys. 2009-6-7

引用本文的文献

[1]
Melting Profile of DNA in Crowded Solution: Model-Based Study.

Int J Mol Sci. 2025-5-31

[2]
Visualization of Single Polymer Chains with Atomic Force Microscopy: A Review.

Polymers (Basel). 2025-5-19

[3]
Decoding collagen's thermally induced unfolding and refolding pathways.

Proc Natl Acad Sci U S A. 2025-5-20

[4]
Bubble DNA tweezer: A triple-conformation sensor responsive to concentration-ratios.

iScience. 2024-2-1

[5]
Polymer Modeling Reveals Interplay between Physical Properties of Chromosomal DNA and the Size and Distribution of Condensin-Based Chromatin Loops.

Genes (Basel). 2023-12-9

[6]
Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs.

Biophys J. 2023-8-22

[7]
Effect of temperature and nucleotide on the binding of BiP chaperone to a protein substrate.

Protein Sci. 2023-7

[8]
Direct monitoring of the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization from gaps and overhangs.

bioRxiv. 2023-4-10

[9]
Temperature dependent mechanical unfolding and refolding of a protein studied by thermo-regulated optical tweezers.

Biophys J. 2023-2-7

[10]
Design, Mechanical Properties, and Dynamics of Synthetic DNA Filaments.

Bioconjug Chem. 2023-1-18

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

推荐工具

医学文档翻译智能文献检索