Identifying sequence similarities between DNA molecules

An atomic force microscope (AFM) imaging technique is described to compare sequences between two different DNA molecules and precisely locate nonhomol ogies in DNA strands. Sequence comparisons are made by forming heteroduplex es between the two molecules and, by AFM imaging the intact molecules forme d, identifying both homologous and nonhomologous regions. By forming hetero duplexes between linearized wildtype pSV-beta-galactosidase plasmid (6821 b p) and a series of deletion mutants we have identified nonhomologies (delet ions) as small as 22 bp and as large as 418 bp. Furthermore, by incorporati ng our technique for AFM-mediated restriction mapping of DNA these mutation s can be positioned relative to EcoRI restriction sites. These results sugg est AFM can be useful in identifying molecular level similarities and diffe rences in DNA. (C) 2000 Elsevier Science B.V. All rights reserved.