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

Hsieh, Huangpin B. and Wang, Mei and Lersch, Robert A. and Kim, Ung-Jin and Weler, Heinz-Ulrich G. (2000) Rational design of landmark probes for quantitative DNA fiber mapping (QDFM). Nucleic Acids Research, 28 (8). Art. No. e30. ISSN 0305-1048. PMCID PMC102834. doi:10.1093/nar/28.8.e30.

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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.

Item Type:Article
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Additional Information:© 2000 Oxford University Press. Received December 28, 1999; Revised February 15, 2000; Accepted February 27, 2000. This work was supported by a grant from the Director, Office of Energy Research, Office of Health and Environmental Research, US Department of Energy, under contract DE-AC-03-76SF00098, a training grant from the U.C. Systemwide Biotechnology Research and Education Program (S96-25) and a postdoctoral fellowship from the Cancer Research Foundation of America to H.B.H.
Funding AgencyGrant Number
Department of Energy (DOE)DE-AC-03-76SF00098
U.C. Systemwide Biotechnology Research and Education ProgramS96-25
Cancer Research Foundation of AmericaUNSPECIFIED
Issue or Number:8
PubMed Central ID:PMC102834
Record Number:CaltechAUTHORS:20111208-091813151
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Official Citation:Rational design of landmark probes for quantitative DNA fiber mapping (QDFM) Huangpin B. Hsieh, Mei Wang, Robert A. Lersch, Ung-Jin Kim, and Heinz-Ulrich G. Weier Nucl. Acids Res.(2000) 28(8):e30-00 doi:10.1093/nar/28.8.e30
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:28366
Deposited By: Ruth Sustaita
Deposited On:08 Dec 2011 17:52
Last Modified:09 Nov 2021 16:56

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