Standard Article

Optical Mapping in Genomic Analysis

Nucleic Acids Structure and Mapping

  1. Christopher Aston1,
  2. David C. Schwartz2

Published Online: 15 SEP 2006

DOI: 10.1002/9780470027318.a1421

Encyclopedia of Analytical Chemistry

Encyclopedia of Analytical Chemistry

How to Cite

Aston, C. and Schwartz, D. C. 2006. Optical Mapping in Genomic Analysis. Encyclopedia of Analytical Chemistry. .

Author Information

  1. 1

    Wyeth-Ayerst Research, Princeton, NJ, USA

  2. 2

    University of Wisconsin, Madison, W1, USA

Publication History

  1. Published Online: 15 SEP 2006


Optical mapping is a system for the construction of ordered restriction maps from single deoxyribonucleic acid (DNA) molecules. DNA molecules bound to derivatized glass surfaces are cleaved with restriction enzymes and imaged by fluorescence microscopy. Cut sites are visualized as gaps between cleaved DNA fragments, which retain their original order. Optical mapping offers advantages over electrophoretic methods of restriction enzyme analysis, which require separate techniques for separating cleaved DNA fragments and determining fragment order. Furthermore, small amounts of DNA are required for optical mapping analysis. By determining the existence of these sequence-specific cut sites and the distances between them, a precise landmark map of the DNA sequence can be constructed. Prokaryote and eukaryote DNA can be mapped. Maps can be constructed from both cloned DNA and genomic DNA. Restriction maps can be constructed for whole genomes by overlapping maps derived from individual molecules. Such maps provide a useful scaffold for accurate alignment of sequence contigs generated by a shotgun sequencing approach and a means of comparing populations and strains.