Identifying sequence similarities between DNA molecules

被引:5
作者
Hoyt, PR
Doktycz, MJ
Modrich, P
Warmack, RJ
Allison, DP
机构
[1] Oak Ridge Natl Lab, Div Life Sci, Oak Ridge, TN 37831 USA
[2] Duke Univ, Howard Hughes Med Inst, Dept Biochem, Durham, NC 27710 USA
关键词
atomic force microscope; heteroduplex; genomic research; sequence verification;
D O I
10.1016/S0304-3991(99)00153-9
中图分类号
TH742 [显微镜];
学科分类号
摘要
An atomic force microscope (AFM) imaging technique is described to compare sequences between two different DNA molecules and precisely locate nonhomologies in DNA strands. Sequence comparisons are made by forming heteroduplexes between the two molecules and, by AFM imaging the intact molecules formed, identifying both homologous and nonhomologous regions. By forming heteroduplexes between linearized wildtype pSV-beta-galactosidase plasmid (6821 bp) and a series of deletion mutants we have identified nonhomologies (deletions) as small as 22 bp and as large as 418 bp. Furthermore, by incorporating our technique for AFM-mediated restriction mapping of DNA these mutations can be positioned relative to EcoRI restriction sites. These results suggest AFM can be useful in identifying molecular level similarities and differences in DNA. (C) 2000 Elsevier Science B.V. All rights reserved.
引用
收藏
页码:237 / 244
页数:8
相关论文
共 25 条
[1]   TIP-RADIUS-INDUCED ARTIFACTS IN AFM IMAGES OF PROTAMINE-COMPLEXED DNA FIBERS [J].
ALLEN, MJ ;
HUD, NV ;
BALOOCH, M ;
TENCH, RJ ;
SIEKHAUS, WJ ;
BALHORN, R .
ULTRAMICROSCOPY, 1992, 42 :1095-1100
[2]   Direct atomic force microscope imaging of EcoRI endonuclease site specifically bound to plasmid DNA molecules [J].
Allison, DP ;
Kerper, PS ;
Doktycz, MJ ;
Spain, JA ;
Modrich, P ;
Larimer, FW ;
Thundat, T ;
Warmack, RJ .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1996, 93 (17) :8826-8829
[3]   Mapping individual cosmid DNAs by direct AFM imaging [J].
Allison, DP ;
Kerper, PS ;
Doktycz, MJ ;
Thundat, T ;
Modrich, P ;
Larimer, FW ;
Johnson, DK ;
Hoyt, PR ;
Mucenski, ML ;
Warmack, RJ .
GENOMICS, 1997, 41 (03) :379-384
[4]  
ALLISON DP, 1997, AUTOMATION TECHNOLOG
[5]   ATOMIC FORCE MICROSCOPE [J].
BINNIG, G ;
QUATE, CF ;
GERBER, C .
PHYSICAL REVIEW LETTERS, 1986, 56 (09) :930-933
[6]   CIRCULAR DNA-MOLECULES IMAGED IN AIR BY SCANNING FORCE MICROSCOPY [J].
BUSTAMANTE, C ;
VESENKA, J ;
TANG, CL ;
REES, W ;
GUTHOLD, M ;
KELLER, R .
BIOCHEMISTRY, 1992, 31 (01) :22-26
[7]  
FERGUSON J, 1978, ADV TECHNIQUES BIOL
[8]   ATOMIC FORCE MICROSCOPY OF DNA IN AQUEOUS-SOLUTIONS [J].
HANSMA, HG ;
BEZANILLA, M ;
ZENHAUSERN, F ;
ADRIAN, M ;
SINSHEIMER, RL .
NUCLEIC ACIDS RESEARCH, 1993, 21 (03) :505-512
[9]   REPRODUCIBLE IMAGING AND DISSECTION OF PLASMID DNA UNDER LIQUID WITH THE ATOMIC FORCE MICROSCOPE [J].
HANSMA, HG ;
VESENKA, J ;
SIEGERIST, C ;
KELDERMAN, G ;
MORRETT, H ;
SINSHEIMER, RL ;
ELINGS, V ;
BUSTAMANTE, C ;
HANSMA, PK .
SCIENCE, 1992, 256 (5060) :1180-1184
[10]   THE SYNAPSIS EVENT IN THE HOMOLOGOUS PAIRING OF DNAS - RECA RECOGNIZES AND PAIRS LESS THAN ONE HELICAL REPEAT OF DNA [J].
HSIEH, P ;
CAMERINIOTERO, CS ;
CAMERINIOTERO, RD .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1992, 89 (14) :6492-6496