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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Single-molecule derivation of salt dependent base-pair free energies in DNASingle-molecule derivation of salt dependent base-pair free energies in DNA
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Single-molecule derivation of salt dependent base-pair free energies in DNASingle-molecule derivation of salt dependent base-pair free energies in DNA

机译：DNA中盐依赖性碱基对自由能的单分子衍生DNA中盐依赖性碱基对自由能的单分子衍生

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摘要

Accurate knowledge of the thermodynamic properties of nucleic acids is crucial to predicting their structure and stability. To date most measurements of base-pair free energies in DNA are obtained in thermal denaturation experiments, which depend on several assumptions. Here we report measurements of the DNA base-pair free energies based on a simplified system, the mechanical unzipping of single DNA molecules. By combining experimental data with a physical model and an optimization algorithm for analysis, we measure the 10 unique nearest-neighbor base-pair free energies with 0.1 kcal mol~(-1) precision over two orders of magnitude of monovalent salt concentration. We find an improved set of standard energy values compared with Unified Oligonucleotide energies and a unique set of 10 base-pair-specific salt-correction values. The latter are found to be strongest for AA/TTand weakest for CC/GG. Our unique energy values and salt corrections improve predictions of DNA unzipping forces and are fully compatible with melting temperatures for oligos. The method should make it possible to obtain free energies, enthalpies, and entropies in conditions not accessible by bulk methodologies.
机译：准确了解核酸的热力学性质对于预测其结构和稳定性至关重要。迄今为止，DNA中大多数碱基对自由能的测量都是通过热变性实验获得的，这取决于几个假设。在这里，我们报告基于简化系统（单个DNA分子的机械解链）的DNA碱基对自由能的测量结果。通过将实验数据与物理模型和优化算法相结合进行分析，我们在两个数量级的一价盐浓度下以0.1 kcal mol〜（-1）的精度测量了10个唯一的最近邻碱基对自由能。我们发现与统一寡核苷酸能量相比，一组改进的标准能量值和一组独特的10个碱基对特定的盐校正值。后者对AA / TT最强，对CC / GG最弱。我们独特的能量值和盐校正可改善对DNA解链力的预测，并与寡核苷酸的解链温度完全兼容。该方法应使得在大体积方法无法达到的条件下获得自由能，焓和熵成为可能。

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  • 作者

    Josep M. Huguet; Cristiano V. Bizarro; Nuria Forns; Steven B. Smith; Carlos Bustamante; Felix Ritort;

  • 作者单位

    Departament de Fisica Fonarriental, Universitat de Barcelona, Diagonal 647, 08028 Barcelona, Spain;

    rnDepartament de Fisica Fonarriental, Universitat de Barcelona, Diagonal 647, 08028 Barcelona, Spain rnCIBER-BBN de Bioingenieria, Biomateriales y Nanomedicina, Instituto de Sanidad Carlos III, Madrid, Spain;

    rnDepartament de Fisica Fonarriental, Universitat de Barcelona, Diagonal 647, 08028 Barcelona, Spain rnCIBER-BBN de Bioingenieria, Biomateriales y Nanomedicina, Instituto de Sanidad Carlos III, Madrid, Spain;

    rnDepartment of Physics University of California, Berkeley, CA 94720;

    rnDepartment of Physics University of California, Berkeley, CA 94720rnDepartment of Molecular and Cell Biology and Howard Hughes Medical Institute,University of California, Berkeley, CA 94720;

    rnDepartament de Fisica Fonarriental, Universitat de Barcelona, Diagonal 647, 08028 Barcelona, Spain rnCIBER-BBN de Bioingenieria, Biomateriales y Nanomedicina, Instituto de Sanidad Carlos III, Madrid, Spain;

  • 收录信息 美国《科学引文索引》(SCI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

    DNA thermodynamics; DNA unzipping; nearest-neighbor model; optical tweezers;

    机译：DNA热力学;DNA解压缩;最近邻居模型;光学镊子;

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