Hybridization of Labeled RNA to DNA in Agarose Gels

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1975 Oct 1

PMID 1103090

Citations 55

Authors

T M Shinnick

E Lund

O SMITHIES

F R Blattner

Affiliations

Soon will be listed here.

Abstract

Specific DNA restriction endonuclease fragments can be identified after electrophoresis in agarose gels by hybridization in the gel (in situ) to radioactive homologous RNA. RNA-DNA hybrids are detected by autoradiography of the gel. Comparison of band patterns of the autoradiogram and the ethidium bromide stained gel allows the identification of the DNA fragment which is complementary to the RNA probe. The technique is rapid, easy and inexpensive. It is sensitive enough to detect individual genes in a mixture of fragments produced by restriction enzyme digestion of complex cellular DNA. We have used this technique to determine which of the Hin III and Eco R1 fragments of phi80d3ilv+su+7 and E. coli DNAs contain the 5S, 16S and 23S ribosomal RNA (rRNA) genes of E. coli.

Citing Articles

The applications of synthetic oligonucleotides to molecular biology.

Ellis R Pharm Res. 2013; 3(4):195-207.

PMID: 24271582 DOI: 10.1023/A:1016382512330.

Cytochrome oxidase subunit II gene in mitochondria of Oenothera has no intron.

Hiesel R, Brennicke A EMBO J. 1983; 2(12):2173-8.

PMID: 16453484 PMC: 555430. DOI: 10.1002/j.1460-2075.1983.tb01719.x.

Plasmids in Yersinia pestis.

Ferber D, Brubaker R Infect Immun. 1981; 31(2):839-41.

PMID: 7216478 PMC: 351389. DOI: 10.1128/iai.31.2.839-841.1981.

Polarity of amber mutations in ribosomal protein genes of Escherichia coli.

Cabezon T, Delcuve G, Faelen M, Desmet L, Bollen A J Bacteriol. 1980; 141(1):41-51.

PMID: 6986365 PMC: 293527. DOI: 10.1128/jb.141.1.41-51.1980.

Use of randomly cloned DNA fragments for identification of Bacteroides thetaiotaomicron.

Salyers A, Lynn S, GARDNER J J Bacteriol. 1983; 154(1):287-93.

PMID: 6833179 PMC: 217458. DOI: 10.1128/jb.154.1.287-293.1983.

References

Fry M, ARTMAN M . Deoxyribonucleic acid-ribonucleic acid hybridization. Annealing and quantitative recovery of intact ribosomal ribonucleic acid molecules from hybrids. Biochem J. 1969; 115(2):287-94. PMC: 1185101. DOI: 10.1042/bj1150287. View

Kelly Jr T, Smith H . A restriction enzyme from Hemophilus influenzae. II. J Mol Biol. 1970; 51(2):393-409. DOI: 10.1016/0022-2836(70)90150-6. View

Tanaka T, Weisblum B . Construction of a colicin E1-R factor composite plasmid in vitro: means for amplification of deoxyribonucleic acid. J Bacteriol. 1975; 121(1):354-62. PMC: 285650. DOI: 10.1128/jb.121.1.354-362.1975. View

Ikemura T, Dahlberg J . Small ribonucleic acids of Escherichia coli. I. Characterization by polyacrylamide gel electrophoresis and fingerprint analysis. J Biol Chem. 1973; 248(14):5024-32. View

Kossman C, Stamato T, PETTIJOHN D . Tandem synthesis of the 16S and 23S ribosomal RNA sequences of Escherichia coli. Nat New Biol. 1971; 234(47):102-4. DOI: 10.1038/newbio234102a0. View

Blattner F, Dahlberg J . RNA synthesis startpoints in bacteriophage lambda: are the promoter and operator transcribed?. Nat New Biol. 1972; 237(77):227-32. DOI: 10.1038/newbio237227a0. View

Griffin B, Fried M, Cowie A . Polyoma DNA: a physical map. Proc Natl Acad Sci U S A. 1974; 71(5):2077-81. PMC: 388389. DOI: 10.1073/pnas.71.5.2077. View

Helling R, Goodman H, Boyer H . Analysis of endonuclease R-EcoRI fragments of DNA from lambdoid bacteriophages and other viruses by agarose-gel electrophoresis. J Virol. 1974; 14(5):1235-44. PMC: 355640. DOI: 10.1128/JVI.14.5.1235-1244.1974. View

Hedgpeth J, Goodman H, Boyer H . DNA nucleotide sequence restricted by the RI endonuclease. Proc Natl Acad Sci U S A. 1972; 69(11):3448-52. PMC: 389791. DOI: 10.1073/pnas.69.11.3448. View

10.

Danna K, Nathans D . Specific cleavage of simian virus 40 DNA by restriction endonuclease of Hemophilus influenzae. Proc Natl Acad Sci U S A. 1971; 68(12):2913-7. PMC: 389558. DOI: 10.1073/pnas.68.12.2913. View

11.

Otsubo E, Soll L, Deonier R, Lee H, Davidson N . Electron microscope heteroduplex studies of sequence relations among plasmids of Escherichia coli. VIII. The structure of bacteriophage phi 80d-3ilv+su+7, including the mapping of the ribosomal RNA genes. J Mol Biol. 1974; 89(4):631-46. DOI: 10.1016/0022-2836(74)90040-0. View

12.

Ehresmann C, Stiegler P, Fellner P, Ebel J . The determination of the primary structure of the 16S ribosomal RNA of Escherichia coli. 2. Nucleotide sequences of products from partial enzymatic hydrolysis. Biochimie. 1972; 54(7):901-67. DOI: 10.1016/s0300-9084(72)80007-5. View