Quantitative DNA Fiber Mapping

  • Lu Chun-Mei
  • Mei Wang
  • Karin M. Greulich-Bode
  • F. Weier Jingly
  • G. Weier Heinz-UlliEmail author
Part of the Springer Protocols Handbooks book series (SPH)

Several hybridization-based methods that are used to delineate single-copy or repeated DNA sequences over larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound to a solid substrate at one end (at least). The DNA molecules are then stretched by the action of a receding meniscus at the water–air interface, which results in the DNA molecules being stretched homogeneously to about 2.3 kb/µm. When nonisotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, and their respective binding sites are visualized under the fluorescence microscope, their relative distances can be measured and converted into kilobasepairs (kb). The QDFM technique has found a variety of useful applications, ranging from the detection and delineation of deletions or overlaps between linked clones, to the construction of high-resolution physical maps and studies of stalled DNA replication and transcription.


Yeast Artificial Chromosome Yeast Artificial Chromosome Clone Maleic Acid Buffer Alkaline Lysis Protocol Alkaline Lysis Solution 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



Bacterial artificial chromosome


Centre des Études du Polymorphisms Humain, Paris, F


Low melting point


Polymerase chain reaction


Pulsed field gel electrophoresis


Quantitative DNA fiber mapping


Untranslated region


Yeast artificial chromosome



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-AC02-05CH11231.


  1. Admire A, Shanks L, Danzl N, Wang M, Weier U, Stevens W, Hunt E, Weinert T (2006) Cycles of chromosome instability are associated with a fragile site and are increased by defects in DNA replication and checkpoint controls in yeast. Genes Dev 20:159–173CrossRefPubMedGoogle Scholar
  2. Breier AM, Weier HU, Cozzarelli NR (2005) Independence of replisomes in Escherichia coli chromosomal replication. Proc Natl Acad Sci USA 102:3942–3947CrossRefPubMedGoogle Scholar
  3. Cassel MJ, Munné S, Fung J, Weier H-UG (1997) Carrier-specific breakpoint-spanning DNA probes for pre-implantation genetic diagnosis [PGD] in interphase cells. Hum Reprod 12: 2019–2027CrossRefPubMedGoogle Scholar
  4. Cheng J-F, Weier H-UG (1997) Approaches to high resolution physical mapping of the human genome. In: Fox CF, Connor TH (eds) Biotechnology international. Universal Medical Press, San Francisco, CA, pp. 149–157Google Scholar
  5. Cohen D, Chumakov I, Weissenbach J (1993) A first-generation physical map of the human genome. Nature 366:698–701CrossRefPubMedGoogle Scholar
  6. Duell T, Wang M, Wu J, Kim U-J, Weier H-UG (1997) High resolution physical map of the immu-noglobulin lambda variant gene cluster assembled by quantitative DNA fiber mapping. Genomics 45:479–486CrossRefPubMedGoogle Scholar
  7. Duell T, Nielsen LB, Jones A, Wang M, Young SG, Weier H-UG (1998) Construction of two near-kilobase resolution restriction maps of the 5′ regulatory region of the human apolipoprotein B gene by Quantitative DNA Fiber Mapping (QDFM). Cytogenet Cell Genet 79:64–70CrossRefGoogle Scholar
  8. Hsieh HB, Wang M, Lersch RA, Kim U-J, Weier H-UG (2000) Rational design of landmark probes for quantitative DNA fiber mapping (QDFM). Nucl Acids Res 28:e30CrossRefPubMedGoogle Scholar
  9. Hu J, Wang M, Weier H-UG, Frantz P, Kolbe W, Olgletree DF, Salmeron M (1996) Imaging of single extended DNA molecules on flat (aminopropyl)triethoxysilane-mica by atomic force microscopy. Langmuir 12:1697–1700CrossRefGoogle Scholar
  10. Maniatis T, Fritsch EF, Sambrook J (1986) Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NYGoogle Scholar
  11. Wang M, Duell T, Gray JW, Weier H-UG (1996) High sensitivity, high resolution physical mapping by fluorescence in situ hybridization [FISH] on to individual straightened DNA molecules. Bioimaging 4:1–11CrossRefGoogle Scholar
  12. Weier HU (2001) DNA fiber mapping techniques for the assembly of high-resolution physical maps. J Histochem Cytochem 49:939–948PubMedGoogle Scholar
  13. Weier HUG, Chu L (2006) Quantitative DNA fiber mapping in genome research and construction of physical maps. Meth Mol Biol 338:31–57Google Scholar
  14. Weier H-UG, Wang M, Mullikin JC, Zhu Y, Cheng J-F, Greulich KM, Bensimon A, Gray JW (1995) Quantitative DNA fiber mapping. Hum Mol Genet 4:1903–1910CrossRefPubMedGoogle Scholar
  15. Weier H-UG, Munné S, Fung J (1999) Patient-specific probes for preimplantation genetic diagnosis (PGD) of structural and numerical aberrations in interphase cells. J Assist Reprod Genet 16: 182–189CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Lu Chun-Mei
    • 1
  • Mei Wang
    • 2
  • Karin M. Greulich-Bode
    • 3
  • F. Weier Jingly
    • 4
    • 5
  • G. Weier Heinz-Ulli
    • 6
    Email author
  1. 1.E.O. Lawrence Berkeley National Laboratory (LBNL), Life Sciences DivisionUniversity of CaliforniaBerkeleyUSA
  2. 2.US DOE Joint Genome Institute/E.O. LBNLWalnut CreekUSA
  3. 3.Deutsches Krebsforschungszentrum (DKFZ), DKFZ/ZMBH AllianzAbteilung Genetik der HautkarzinogeneseHeidelbergGermany
  4. 4.Life Sciences DivisionUniversity of California, E.O. LBNLBerkeleyUSA
  5. 5.Reprogenetics, LLCSouth San FranciscoUSA
  6. 6.Life Sciences Division, MS 74-157University of California, E.O. LBNLBerkeleyUSA

Personalised recommendations