Skip to main content
Log in

Invited Review. Imaging of Single DNA Molecule: Applications to High-Resolution Genomic Studies

  • Published:
Chromosome Research Aims and scope Submit manuscript

Abstract

Single molecule analysis of DNA has revealed new insights into its structural and physical properties. The application of new methods for manipulating and visualizing DNA has resulted in important advances in high-resolution physical mapping of the genome and quantitative cytogenetic studies of genomic abnormalities (Lichter 1997). Studies of single molecules of DNA have employed a variety of approaches including electron microscopy, atomic force microscopy, scanning-tunneling microscopy and fluorescence microscopy. A number of new technologies have recently been developed to exploit fluorescence microscopy's full potential for genomic analysis and the fine mapping of subtle genetic alterations. In the case of the latter application, particular emphasis has been placed on developing new methods for stretching DNA for high-resolution fluorescence in-situ hybridization studies. We have recently described a process called molecular combing according to which single DNA molecules bound by their extremities to a solid surface are uniformly stretched and aligned by a receding air/water interface (Bensimon et al. 1994). In the following, we will review recent developments concerning molecular combing and discuss its current and potential applications for the high-resolution mapping of the human genome, the detection and quantification of subtle genomic imbalances and the positional cloning of disease-related genes.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  • Allemand J-F, Bensimon D, Jullien L, Bensimon A, Croquette V (1997) pH-dependent specific binding and combing of DNA. Biophys J 73: 2064–2070.

    Google Scholar 

  • Austin B (1997) Straightening out DNA. Phys Today 31–38.

  • Bensimon A, Simon A, Chiffaudel A, Croquette V, Heslot F, Bensimon D (1994) Alignment and sensitive detection of DNA by a moving interface. Science 265: 2096–2098.

    Google Scholar 

  • Bensimon D, Simon A, Croquette V, Bensimon A (1995) Stretching DNA with a receding meniscus: Models and Experiments. Phys Rev Lett 74: 4754–4757.

    Google Scholar 

  • Cluzel P, Lebrun A, Heller C et al. (1996) DNA an extensible molecule. Science 271: 792–794.

    Google Scholar 

  • Dean M, Park M, Le Beau MM et al. (1985) The human met oncogene is related to the tyrosine kinase oncogenes. Nature 318: 385–388.

    Google Scholar 

  • European Chromosome 16 Tuberous Sclerosis Consortium (1993) Identification and characterization of the Tuberous Sclerosis Gene on Chromosome 16. Cell 75: 1305.

    Google Scholar 

  • Fidlerova H, Senger G, Kost M, Sanseau P, Sheer D (1994) Two simple procedures for releasing chromatin from routinely fixed cells for fluorescence in situ hybridization. Cytogenet Cell Genet 65: 203–205.

    Google Scholar 

  • Florijn RJ, van de Rijke FM, Vrolijk H et al. (1996) Exon mapping by fiber-FISH or LR-PCR. Genomics 38: 277–282.

    Google Scholar 

  • Fougerousse F, Broux O, Richard I et al. (1994) Mapping of a chromosome 15 region involved in limb girdle muscular dystrophy. Hum Mol Genet 3: 285–93.

    Google Scholar 

  • Glukhova L, Goguel A-F, Chudoba I et al. (1998) Overrepresentation of 7q31 and 17q in renal cell carcinomas. Genes Chromosomes Cancer 22: 171–178.

    Google Scholar 

  • Heiskanen M, Hellsten E, Kallioniemi OP et al. (1995) Visual mapping by fiber-FISH. Genomics 30: 31–36.

    Google Scholar 

  • Heiskanen M, Kallioniemi O, Palotie A (1996) Fiber-FISH: experiences and a refined protocol. Genet Anal 12: 179–184.

    Google Scholar 

  • Heng HH, Squire J, Tsui LC (1992) High-resolution mapping of mammalian genes by in situ hybridization to free chromatin. Proc Nat Acad Sci 89: 9509–9513.

    Google Scholar 

  • Herrick J, Michalet X, Conti C, Schurra C, Bensimon D (1999) Quantifying single gene copy number by measuring fluorescent probe lengths on combed genomic DNA. Proc Natl Acad Sci USA (in press).

  • Houseal TW, Dackowski WR, Landes GM, Klinger KW (1994) High resolution mapping of overlapping cosmids by fluorescence in situ hybridization. Cytometry 15: 193–198.

    Google Scholar 

  • Houseal TW, Klinger KW (1994) What's in a spot. Hum Mol Genet 3: 1215–1216.

    Google Scholar 

  • Hu J, Wang M, Weier H-U et al. (1996) Imaging of single extended DNA molecules on flat aminopropyl-triethoxysilane-mica by atomic force microscopy. Langmuir 12: 1697–1700.

    Google Scholar 

  • Kallioniemi A, Kallioniemi OP, Sudar D et al. (1992) Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258: 818–821.

    Google Scholar 

  • Lamartine J, Nichols KE, Yin L et al. (1996) Physical map and cosmid contig encompassing a new interstitial deletion of the X-linked lymphoproliferative syndrome region. Eur J Hum Genet 4: 342–351.

    Google Scholar 

  • Langer-Safer PR, Levine M, Ward D (1982) Immunological method for mapping genes on Drosophila polytene chromosomes. Proc Nat Acad Sci 79: 4381–4385.

    Google Scholar 

  • Lanyi A, Li B, Li S et al. (1997) A yeast artificial chromosome (YAC) contig encompassing the critical region of the X-linked lymphoproliferative disease (XLP) locus. Genomics 39: 55–65.

    Google Scholar 

  • Lebrun A, Lavery R (1996) Modelling extreme stretching of DNA. Nucleic Acids Res 24: 2260–2267.

    Google Scholar 

  • Lichter P (1997) Multicolor FISHing: what's the catch? Trends Genet 13: 475–479.

    Google Scholar 

  • Manuelidis L, Langer-Safer PR, Ward D (1982) High-resolution mapping of satellite DNA using biotin-labelled DNA probes. J Cell Biol 95: 619–625.

    Google Scholar 

  • Michalet X, Ekong R, Fougerousse F et al. (1997) Dynamic molecular combing: stretching the whole human genome for high-resolution studies. Science 277: 1518–1523.

    Google Scholar 

  • Monier K, Michalet X, Lamartine J et al. (1998) High-resolution mapping of the X-linked lymphoproliferative syndrome region by FISH on combed DNA. Cytogenet Cell Genet 81: 259–264.

    Google Scholar 

  • Nahmias J, Hornigold N, Fitzgibbon J et al. (1995) Cosmid contigs spanning 9q34 including the candidate region for TSC1. Eur J Hum Genet 3: 65–77.

    Google Scholar 

  • Nobile C, Galvagni F, Marchi J, Roberts R, Vitiello L (1995) Genomic organization of the human dystrophin gene across the major deletion hot spot and the 3′ region. Genomics 28: 97–100.

    Google Scholar 

  • Okano, M Purtilo DT (1995) Simple assay for evaluation of Epstein-Barr virus specific cytotoxic T lymphocytes. J. Immunol Meth 184: 149–152.

    Google Scholar 

  • Parra I, Windle B (1993) High resolution visual mapping of stretched DNA by fluorescent hybridization. Nature Genet 5: 17–21.

    Google Scholar 

  • Perkins TT, Smith, DE Larson RG, Chu S (1995) Stretching of a single tethered polymer in a uniform flow. Science 286: 83–87.

    Google Scholar 

  • Peters DJ, Spruit L, Saris JJ et al. (1993) Chromosome 4 localization of a second gene for autosomal dominant polycystic kidney disease. Nature Gen 5: 359–362.

    Google Scholar 

  • Petrij-Bosch A, Peelen T, van Vliet M et al. (1997) BRCA1 genomic deletions are major founder mutations in Dutch breast cancer patients. Nature Gen 17: 341–345.

    Google Scholar 

  • Pinkel D, Straume T, Gray JW (1986) Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization. Proc Nat Acad Sci 83: 2934–2938.

    Google Scholar 

  • Povey S, Burley MW, Attwood J et al. (1994) Two loci for tuberous sclerosis: one on 9q34 and one on 16p13. Ann Hum Genet 58: 107–127.

    Google Scholar 

  • Quake SR, Babcock H, Chu S (1997) The dynamics of partially extended single molecules of DNA. Nature 388: 151–154.

    Google Scholar 

  • Richard I, Roudant C, Fougerousse F, Chiannilkulchai N, Beckmann JS (1995a) An STS map of the limb girdle muscular dystrophy type 2A region. Mammalian Genome 6: 754–756.

    Google Scholar 

  • Richard I, Broux O, Allamand V et al. (1995b) Mutations in the proteolytic enzyme calpain 3 cause limb-girdel muscular dystrophy type 2A. Cell 81: 27–40.

    Google Scholar 

  • Schrock E, du Manoir S, Veldman Tet al. (1996) Multicolor spectral karyotyping of human chromosomes. Science 273: 494–497.

    Google Scholar 

  • Schwartz DS, Samad A (1997) Optical mapping approaches to molecular genomics. Curr Opin Biotech 8: 70–74.

    Google Scholar 

  • Schwartz DC, Li X, Hernandez LI, Ramnarain SP, Huff EJ, Wang YK (1993) Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science 262: 110–114.

    Google Scholar 

  • Smith SB, Finzi L, Bustamante C (1992) Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science 258: 1122–1126.

    Google Scholar 

  • Speicher MR, Ballard S, Ward DC (1996) Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nature Genetics 12: 368–375.

    Google Scholar 

  • Stein VM, Bond JP, Capp MW, Anderson CF, Record MT Jr (1995) Importance of coulombic end effects on cation accumulation near oligoelectrolyte B-DNA: a demonstration using 23Na NMR. Biophys J 68: 1063–1072.

    Google Scholar 

  • Tavtigian SV, Simard J, Rommens J et al. (1996) The complete BRCA2 gene and mutations in chromosome 13q-linked kindreds. Nature Genet 12: 333–337.

    Google Scholar 

  • Trask BJ, Allen S, Massa H et al. (1993) Studies of metaphase and interphase chromosomes using fluorescence in situ hybridization. Cold Spring Harbor Symp Quant Biol 58: 767–775.

    Google Scholar 

  • Trask BJ (1991) DNA sequence localization in metaphase and interphase cells by fluorescence in situ hybridization. Meth Cell Biol 35: 3–35.

    Google Scholar 

  • van Slegtenhorst M, Janssen B, Nellist M et al. (1995) Cosmid contigs from the tuberous sclerosis candidate region on chromosome 9q34. Eur J Hum Genet 3: 78–86.

    Google Scholar 

  • van Slegtenhorst M, de Hoogt R, Hermans C et al. (1997). Identification of the tuberous scelerosis gene TSC1 on chromosome 9q34. Science 277: 805–808.

    Google Scholar 

  • Wang MD, Yin H, Landick R, Gelles J, Block SM (1997) Stretching DNA with optical tweezers. Biophys J 72: 1335–1346.

    Google Scholar 

  • Weier H-U, Wang M, Mullikin JC et al. (1995) Quantitative DNA fiber mapping. Hum Mol Genet 4: 1903–1910.

    Google Scholar 

  • Wiegant J, Kalle W, Mullenders L et al. (1992) High-resolution in situ hybridization using DNA halo preparations Hum Mol Genet 1: 587–591.

    Google Scholar 

  • Yokota H, Johnson F, Lu H et al. (1997) A new method for straightening DNA molecules for optical restriction mapping. Nucleic Acids Res 25: 1064–1070.

    Google Scholar 

  • Zimmermann RM, Cox EC (1994) DNA stretching on functionalized gold surfaces. Nucleic Acids Res 22: 492–497.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Aaron Bensimon.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Herrick, J., Bensimon, A. Invited Review. Imaging of Single DNA Molecule: Applications to High-Resolution Genomic Studies. Chromosome Res 7, 409–423 (1999). https://doi.org/10.1023/A:1009276210892

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1009276210892

Navigation