一种通过变性凝胶电泳方法选择用于检测突变的DNA片段的程序。

A program for selecting DNA fragments to detect mutations by denaturing gel electrophoresis methods.

作者信息

Brossette S, Wartell R M

机构信息

School of Biology, Georgia Institute of Technology, Atlanta 30332.

出版信息

Nucleic Acids Res. 1994 Oct 11;22(20):4321-5. doi: 10.1093/nar/22.20.4321.

DOI:10.1093/nar/22.20.4321

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC331956/

Abstract

A computer program was developed to automate the selection of DNA fragments for detecting mutations within a long DNA sequence by denaturing gel electrophoresis methods. The program, MELTSCAN, scans through a user specified DNA sequence calculating the melting behavior of overlapping DNA fragments covering the sequence. Melting characteristics of the fragments are analyzed to determine the best fragment for detecting mutations at each base pair position in the sequence. The calculation also determines the optimal fragment for detecting mutations within a user specified mutational hot spot region. The program is built around the statistical mechanical model of the DNA melting transition. The optimal fragment for a given position is selected using the criteria that its melting curve has at least two steps, the base pair position is in the fragment's lowest melting domain, and the melting domain has the smallest number of base pairs among fragments that meet the first two criteria. The program predicted fragments for detecting mutations in the cDNA and genomic DNA of the human p53 gene.

摘要

开发了一种计算机程序，用于通过变性凝胶电泳方法自动选择用于检测长DNA序列中突变的DNA片段。该程序名为MELTSCAN，它会扫描用户指定的DNA序列，计算覆盖该序列的重叠DNA片段的解链行为。分析片段的解链特征，以确定用于检测序列中每个碱基对位置突变的最佳片段。该计算还确定了用于检测用户指定突变热点区域内突变的最佳片段。该程序是围绕DNA解链转变的统计力学模型构建的。对于给定位置的最佳片段，是根据其解链曲线至少有两个步骤、碱基对位置在片段的最低解链域中且解链域在满足前两个标准的片段中具有最少碱基对数量的标准来选择的。该程序预测了用于检测人类p53基因cDNA和基因组DNA中突变的片段。

相似文献

1

A program for selecting DNA fragments to detect mutations by denaturing gel electrophoresis methods.一种通过变性凝胶电泳方法选择用于检测突变的DNA片段的程序。

Nucleic Acids Res. 1994 Oct 11;22(20):4321-5. doi: 10.1093/nar/22.20.4321.

2

Selecting DNA fragments for mutation detection by temperature gradient gel electrophoresis: application to the p53 gene cDNA.通过温度梯度凝胶电泳选择用于突变检测的DNA片段：应用于p53基因cDNA

Electrophoresis. 1993 Jul;14(7):561-5. doi: 10.1002/elps.1150140188.

3

Improvement of fragment and primer selection for mutation detection by denaturing gradient gel electrophoresis.通过变性梯度凝胶电泳改进用于突变检测的片段和引物选择

Nucleic Acids Res. 1998 Dec 1;26(23):5432-40. doi: 10.1093/nar/26.23.5432.

4

DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory.通过单碱基对替换而不同的DNA片段在变性梯度凝胶中被分离：与解链理论的对应关系。

Proc Natl Acad Sci U S A. 1983 Mar;80(6):1579-83. doi: 10.1073/pnas.80.6.1579.

5

The use of denaturing gradient gel electrophoresis to screen for DNA sequence polymorphisms in the human factor VIII gene.使用变性梯度凝胶电泳筛选人凝血因子VIII基因中的DNA序列多态性。

Electrophoresis. 1989 May-Jun;10(5-6):390-6. doi: 10.1002/elps.1150100517.

6

Mutation screening of the TP53 gene by temporal temperature gradient gel electrophoresis.通过时间温度梯度凝胶电泳对TP53基因进行突变筛查。

Methods Mol Biol. 2005;291:207-16. doi: 10.1385/1-59259-840-4:207.

7

Modification of the melting properties of duplex DNA by attachment of a GC-rich DNA sequence as determined by denaturing gradient gel electrophoresis.通过变性梯度凝胶电泳测定，富含GC的DNA序列附着对双链DNA熔解特性的修饰。

Nucleic Acids Res. 1985 May 10;13(9):3111-29. doi: 10.1093/nar/13.9.3111.

8

Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis.与GC夹连接的DNA片段中的几乎所有单碱基替换都可以通过变性梯度凝胶电泳检测到。

Nucleic Acids Res. 1985 May 10;13(9):3131-45. doi: 10.1093/nar/13.9.3131.

9

Analysis of sequence alterations in a defined DNA region: comparison of temperature-modulated heteroduplex analysis and denaturing gradient gel electrophoresis.

Mutat Res. 1999 Nov 29;430(1):13-21. doi: 10.1016/s0027-5107(99)00150-5.

10

Detection of base mutations in genomic DNA using denaturing gradient gel electrophoresis (DGGE) followed by transfer and hybridization with gene-specific probes.采用变性梯度凝胶电泳（DGGE）检测基因组DNA中的碱基突变，随后进行转移并与基因特异性探针杂交。

Mutat Res. 1988 Nov;202(1):77-83. doi: 10.1016/0027-5107(88)90166-2.

本文引用的文献

1

Selecting DNA fragments for mutation detection by temperature gradient gel electrophoresis: application to the p53 gene cDNA.通过温度梯度凝胶电泳选择用于突变检测的DNA片段：应用于p53基因cDNA

Electrophoresis. 1993 Jul;14(7):561-5. doi: 10.1002/elps.1150140188.

2

Psoralen-modified oligonucleotide primers improve detection of mutations by denaturing gradient gel electrophoresis and provide an alternative to GC-clamping.补骨脂素修饰的寡核苷酸引物通过变性梯度凝胶电泳改善了突变检测，并为GC夹提供了一种替代方法。

Hum Mol Genet. 1993 Apr;2(4):393-7. doi: 10.1093/hmg/2.4.393.

3

Sequence-determined DNA separations.序列决定的DNA分离

Annu Rev Biophys Bioeng. 1984;13:399-423. doi: 10.1146/annurev.bb.13.060184.002151.

4

Human p53 cellular tumor antigen: cDNA sequence and expression in COS cells.人p53细胞肿瘤抗原：cDNA序列及在COS细胞中的表达。

EMBO J. 1985 May;4(5):1251-5. doi: 10.1002/j.1460-2075.1985.tb03768.x.

5

A general method for saturation mutagenesis of cloned DNA fragments.一种用于克隆DNA片段饱和诱变的通用方法。

Science. 1985 Jul 19;229(4710):242-7. doi: 10.1126/science.2990046.

6

Computational simulation of DNA melting and its application to denaturing gradient gel electrophoresis.DNA解链的计算模拟及其在变性梯度凝胶电泳中的应用。

Methods Enzymol. 1987;155:482-501. doi: 10.1016/0076-6879(87)55032-7.

7

Attachment of a 40-base-pair G + C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes.通过聚合酶链反应将一段40个碱基对的富含G + C的序列（GC夹）连接到基因组DNA片段上，可提高对单碱基变化的检测。

Proc Natl Acad Sci U S A. 1989 Jan;86(1):232-6. doi: 10.1073/pnas.86.1.232.

8

Inverted repeat sequences can influence the melting transitions of linear DNAs.反向重复序列可影响线性DNA的解链转变。

Biopolymers. 1989 Oct;28(10):1745-58. doi: 10.1002/bip.360281008.

9

Mutations in the p53 gene occur in diverse human tumour types.p53基因的突变发生在多种人类肿瘤类型中。

Nature. 1989 Dec 7;342(6250):705-8. doi: 10.1038/342705a0.

10

Temperature-gradient gel electrophoresis. Thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extracts.温度梯度凝胶电泳。纯化形式及细胞提取物中核酸与蛋白质的热力学分析。

Biophys Chem. 1987 May 9;26(2-3):235-46. doi: 10.1016/0301-4622(87)80026-1.

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。

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

文档翻译

学术文献翻译模型，支持多种主流文档格式。