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A new method for straightening DNA molecules for optical restriction mapping. 1997

H Yokota, and F Johnson, and H Lu, and R M Robinson, and A M Belu, and M D Garrison, and B D Ratner, and B J Trask, and D L Miller
Department of Molecular Biotechnology, University of Washington, Seattle, WA 98195, USA.

We have developed an improved method of straightening DNA molecules for use in optical restriction mapping. The DNA was straightened on 3-aminopropyltriethoxysilane-coated glass slides using surface tension generated by a moving meniscus. In our method the meniscus motion was controlled mechanically, which provides advantages of speed and uniformity of the straightened molecules. Variation in the affinity of the silanized surfaces for DNA was compensated by precoating the slide with single-stranded non-target blocking DNA. A small amount of MgCl2 added to the DNA suspension increased the DNA-surface affinity and was necessary for efficient restriction enzyme digestion of the straightened surface-bound DNA. By adjusting the amounts of blocking DNA and MgCl2, we prepared slides that contained many straight parallel DNA molecules. Straightened lambda phage DNA (48 kb) bound to a slide surface was digested by EcoRI restriction endonuclease, and the resulting restriction fragments were imaged by fluorescence microscopy using a CCD camera. The observed fragment lengths showed excellent agreement with their predicted lengths.

UI MeSH Term Description Entries
D008856 Microscopy, Fluorescence Microscopy of specimens stained with fluorescent dye (usually fluorescein isothiocyanate) or of naturally fluorescent materials, which emit light when exposed to ultraviolet or blue light. Immunofluorescence microscopy utilizes antibodies that are labeled with fluorescent dye. Fluorescence Microscopy,Immunofluorescence Microscopy,Microscopy, Immunofluorescence,Fluorescence Microscopies,Immunofluorescence Microscopies,Microscopies, Fluorescence,Microscopies, Immunofluorescence
D009690 Nucleic Acid Conformation The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape. DNA Conformation,RNA Conformation,Conformation, DNA,Conformation, Nucleic Acid,Conformation, RNA,Conformations, DNA,Conformations, Nucleic Acid,Conformations, RNA,DNA Conformations,Nucleic Acid Conformations,RNA Conformations
D010582 Bacteriophage lambda A temperate inducible phage and type species of the genus lambda-like viruses, in the family SIPHOVIRIDAE. Its natural host is E. coli K12. Its VIRION contains linear double-stranded DNA with single-stranded 12-base 5' sticky ends. The DNA circularizes on infection. Coliphage lambda,Enterobacteria phage lambda,Phage lambda,lambda Phage
D004262 DNA Restriction Enzymes Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1. Restriction Endonucleases,DNA Restriction Enzyme,Restriction Endonuclease,Endonuclease, Restriction,Endonucleases, Restriction,Enzymes, DNA Restriction,Restriction Enzyme, DNA,Restriction Enzymes, DNA
D004277 DNA, Single-Stranded A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle. Single-Stranded DNA,DNA, Single Stranded,Single Stranded DNA
D004279 DNA, Viral Deoxyribonucleic acid that makes up the genetic material of viruses. Viral DNA
D013500 Surface Tension The force acting on the surface of a liquid, tending to minimize the area of the surface. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed) Interfacial Force,Interfacial Tension,Surface Tensions,Tension, Surface,Tensions, Surface
D015183 Restriction Mapping Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA. Endonuclease Mapping, Restriction,Enzyme Mapping, Restriction,Site Mapping, Restriction,Analysis, Restriction Enzyme,Enzyme Analysis, Restriction,Restriction Enzyme Analysis,Analyses, Restriction Enzyme,Endonuclease Mappings, Restriction,Enzyme Analyses, Restriction,Enzyme Mappings, Restriction,Mapping, Restriction,Mapping, Restriction Endonuclease,Mapping, Restriction Enzyme,Mapping, Restriction Site,Mappings, Restriction,Mappings, Restriction Endonuclease,Mappings, Restriction Enzyme,Mappings, Restriction Site,Restriction Endonuclease Mapping,Restriction Endonuclease Mappings,Restriction Enzyme Analyses,Restriction Enzyme Mapping,Restriction Enzyme Mappings,Restriction Mappings,Restriction Site Mapping,Restriction Site Mappings,Site Mappings, Restriction
D015636 Magnesium Chloride Magnesium chloride. An inorganic compound consisting of one magnesium and two chloride ions. The compound is used in medicine as a source of magnesium ions, which are essential for many cellular activities. It has also been used as a cathartic and in alloys. MgCl2,Chloride, Magnesium

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