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Nucleic Acids Research, 2000, Vol. 28, No. 8 E30-00
© 2000 Oxford University Press

Rational design of landmark probes for quantitative DNA fiber mapping (QDFM)

Huangpin B. Hsieh, Mei Wang, Robert A. Lersch, Ung-Jin Kim1 and Heinz-Ulrich G. Weier*

Life Sciences Division, MS 74-157, University of California, E. O. Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA and 1Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA

Rapid construction of high-resolution physical maps requires accurate information about overlap between DNA clones and the size of gaps between clones or clone contigs. We recently developed a procedure termed ‘quantitative DNA fiber mapping’ (QDFM) to help construct physical maps by measuring the overlap between clones or the physical distance between non-overlapping contigs. QDFM is based on hybridization of non-isotopically labeled probes onto DNA molecules that were bound to a solid support and stretched homogeneously to ~2.3 kb/µm. In this paper, we describe the design of probes that bind specifically to the cloning vector of DNA recombinants to facilitate physical mapping. Probes described here delineate the most frequently used cloning vectors such as BACs, P1s, PACs and YACs. As demonstrated in representative hybridizations, vector-specific probes provide valuable information about molecule integrity, insert size and orientation as well as localization of hybridization domains relative to specifically-marked vector sequences.

* To whom correspondence should be addressed. Tel: +1 510 486 5347; Fax: +1 510 486 5343; Email: ugweier@lbl.gov


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