© 1995 Oxford University Press
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Quantitative DNA fiber mapping
Center for Molecular Cytogenetics 1Human Genonie Center Life Sciences Division, MS 74-157 University of California, Lawrence Berkeley Laboratory 1 Cyclotron Road, Berkeley, California 94720, USA 2Laboratoire de Biophysique de I'ADN, Institut Pasteur 75015 Paris, France
*To whom correspondence should be addressed
Received May 30, 1995; Revised July 21, 1995; Accepted July 21, 1995
The assembly of sequence ready, high-resolution physical maps and construction of minimally overlapping contigs for the human as well as model genomes requires accurate determination of the extent of overlap between adjacent clones as well as their relative orientation. This is presently done by procedures such as clone fingerprinting, Southern blot analysis or clone end sequencing. We present a complementary analytical technique to map directly cloned DNA sequences on to individual stretched DNA molecules. This approach uses the hydrodynamic force of a receding meniscus to prepare straight high molecular weight DNA molecules that provide a linear template of 
2.3 kb/µm on to which the cloned probes can be mapped by in situ hybridization. This technique has numerous advantages such as a very high density of mapping templates, reproducible stretching of the mapping template providing a linear genomic scale, determination of clone orientation and direct visualization of DNA repeats. The utility and accuracy of quantitative DNA fiber mapping are illustrated through three examples: (i) mapping of lambda DNA restriction fragments along linearized 49 kb long lambda phage DNA molecules with 1 kb precision; (ii) localization of the overlap between a cosmid and a colinear P1 clone; and (iii) mapping of P1 clones along a 490 kb yeast artificial chromosome (YAC) with 5 kb precision and estimation of the 25 kb gap between them.
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