cleavage of ss DNA and hybrids by restriction enzymes

Dr. Richard Roberts at Cold Spring Harbor Laboratory roberts at CSHL.ORG
Wed Aug 7 09:55:46 EST 1991


Here is the list of references from my database


<CODE>R
<RECORD_NUMBER>95
<AUTHORS>Molloy, P.L., Symon, R.H.
<TITLE>Cleavage of DNA.RNA hybrids by Type II restriction enzymes.
<JOURNAL>Nucl. Acids Res.
<VOLUME>8
<PAGE>2939-2946
<YEAR>1980
<ABSTRACT>The action of a number of restriction enzymes on DNA.RNA hybrids has been examined using hybrids synthesised with RNAs of cucumber mosaic virus as templates.  The enzymes EcoRI, HindII, SalI, MspI, HhaI, AluI, TaqI and HaeIII cleaved the DNA strand of the hybrids (and possibly also the RNA strand) into specific fragments.  For four of these enzymes, HhaI, AluI, TaqI and HaeIII, comparison of the restriction fragments produced with the known sequences of the viral RNAs confirmed that they were recognising and cleaving the DNA strand of the hybrids at their correct recognition sequences.  It is likely that the ability to utilise DNA.RNA hybrids as substrates is a general property of Type II restriction enzymes.
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<CODE>R
<RECORD_NUMBER>1449
<AUTHORS>Nazarenko, I.A., Gorbunov, Y.A., Malysgin, E.G.
<TITLE>Cleavage of synthetic RNA-DNA hybrids with restriction endonucleases BamHI and Sau3AI.
<JOURNAL>Bioorg. Khim.
<VOLUME>13
<PAGE>928-933
<YEAR>1987
<ABSTRACT>Synthetic oligodeoxyribonucleotides, containing one or two ribonucleotides in the recognition sequence, and RNA-DNA hybrids were tested for their activity in cleavage with BamHI and Sau3AI endonucleases.  The replacement of dG with G in the first position of BamHI-site (GGATCC) of one of the chains does not affect the rate of the BamHI hydrolysis.  The similar heteroduplex, containing G residue in the second position, displays a decreased rate of the BamHI hydrolysis of the modified strand and to a lesser extent, of the unmodified complementary strand.  Oligodeoxyribonucleotides in complex with oligoribonucleotides can be cleaved with the excess of BamHI and Sau3AI oligoribonucleotides remaining intact.
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<CODE>R
<RECORD_NUMBER>956
<AUTHORS>Horiuchi, K., Zinder, N.D.
<TITLE>Site-specific cleavage of single-stranded DNA by a Hemophilus restriction endonuclease.
<JOURNAL>Proc. Natl. Acad. Sci. USA
<VOLUME>72
<PAGE>2555-2558
<YEAR>1975
<ABSTRACT>Single-stranded viral DNA of bacteriophage f1 is cleaved into specific fragments by endo R.HaeIII, a restriction endonuclease isolated from Hemophilus aegyptius.  The sites of the single strand cleavage correspond to those of the double strand cleavage.  A single-stranded DNA fragment containing only one HaeIII site is also cleaved by this enzyme.  This observation suggests that the reaction of single-stranded DNA cleavage does not require the formation of a symmetrical double-stranded structure that would result from the intramolecular base-pairing between two different HaeIII sites.  Other restriction endonucleases may also cleave single-stranded DNA.
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<CODE>R
<RECORD_NUMBER>50
<AUTHORS>Nishigaki, K., Kaneko, Y., Wakuda, H., Husimi, Y., Tanaka, T.
<TITLE>Type II restriction endonucleases cleave single-stranded DNAs in general.
<JOURNAL>Nucl. Acids Res.
<VOLUME>13
<PAGE>5747-5759
<YEAR>1985
<ABSTRACT>Restriction endonucleases (13 out of 18 species used for the test) were certified to cleave single-stranded(ss)DNA.  Such enzymes as AvaII, HaeII, DdeI, AluI, Sau3AI, AccII, TthHB81 and HapII were newly reported to cleave ssDNA.  A model to account for the cleavage of ssDNA by restriction enzyes was proposed with supportive data.  The essential part of the model was that restriction enzymes preferentially cleave transiently formed secondary structures (called canonical structures) in ssDNA composed of two recognition sequences with two fold rotational symmetry.  This means that a restriction enzyme can cleave ssDNAs in general so far as the DNAs have the sequences of restriction sites for the enzyme, and that the rate of cleavage depends on the stabilities of canonical structures.
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<CODE>R
<RECORD_NUMBER>378
<AUTHORS>Blakesley, R.W., Dodgson, J.B., Nes, I.F., Wells, R.D.
<TITLE>Duplex regions in "single-stranded" PhiX174 DNA are cleaved by a restriction endonuclease from Haemophilus aegyptius.
<JOURNAL>J. Biol. Chem.
<VOLUME>252
<PAGE>7300-7306
<YEAR>1977
<ABSTRACT>DNA from bacteriophage PhiX174 is cleaved by several DNA restriction endonucleases.  We wish to determine whether or not the recognition sites are within duplex regions in this single-stranded DNA.  We report here the influence of two perturbants of duplex DNA structure, temperature and actinomycin, on the cleavage of PhiX174 (single-stranded, circular) DNA and its double-stranded, replicative form (RF DNA) by the restriction endonuclease, HaeIII.  The conditions for optimal rates of cleavage for the (+)-strand and RF DNA's by HaeIII were virtually identical (25 mM Tris/HCl, pH 7.5; 5 mM MgCl2; 30 mM NaCl).  At 37C, RF DNA was cleaved 16 times faster than (+)-strand DNA.  When the initial rates of reaction for both DNA's were measured as a function of temperature of incubation, the maximum rates occurred at 72C and 47C for the RF and (+)-strand DNA's, respectively.  At 10-15C above the respective maxima, the rates fell to zero.  Near the temperature optima, a prefe!
rential disappearance of certain 
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<CODE>R
<RECORD_NUMBER>539
<AUTHORS>Reckmann, B., Krauss, G.
<TITLE>The cleavage of single-stranded DNA by the isoschizomeric restriction endonuclease HhaI and CfoI.
<JOURNAL>Biochim. Biophys. Acta
<VOLUME>908
<PAGE>90-96
<YEAR>1987
<ABSTRACT>The cleavage of single-stranded (ss) M13mp8(+) DNA by the isoschizomeric restriction endonucleases HhaI and CfoI has been investigated.  The two enzymes differ considerably in their ability tot cleave ssDNA.  HhaI cleaves ssDNA about two orders of magnitude faster than does CfoI, although both enzymes show the same activity when assayed on double-stranded DNA.  From the cleavage of oligonucleotides and o f M13mp8(+) DNA fragments it is concluded that cleavage of ssDNA occurs via transiently formed double-stranded hairpin structures.  A rough correlation exists between the stability of the secondary structures and the cleavage efficiency.
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<CODE>R
<RECORD_NUMBER>956
<AUTHORS>Horiuchi, K., Zinder, N.D.
<TITLE>Site-specific cleavage of single-stranded DNA by a Hemophilus restriction endonuclease.
<JOURNAL>Proc. Natl. Acad. Sci. USA
<VOLUME>72
<PAGE>2555-2558
<YEAR>1975
<ABSTRACT>Single-stranded viral DNA of bacteriophage f1 is cleaved into specific fragments by endo R.HaeIII, a restriction endonuclease isolated from Hemophilus aegyptius.  The sites of the single strand cleavage correspond to those of the double strand cleavage.  A single-stranded DNA fragment containing only one HaeIII site is also cleaved by this enzyme.  This observation suggests that the reaction of single-stranded DNA cleavage does not require the formation of a symmetrical double-stranded structure that would result from the intramolecular base-pairing between two different HaeIII sites.  Other restriction endonucleases may also cleave single-stranded DNA.
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<CODE>R
<RECORD_NUMBER>1374
<AUTHORS>Bischofberger, N., Ng, P.G., Webb,T.R., Matteucci, M.D.
<TITLE>Cleavage of single stranded oligonucleotides by EcoRI restriction endonuclease.
<JOURNAL>Nucl. Acids Res.
<VOLUME>15
<PAGE>709-716
<YEAR>1987
<ABSTRACT>The 31mer 5'-TCA ACG CTA GAA TTC GGA TCC ATC GCT TGG T, the complementary 33mer 5'-CCA AGC GAT GGA TCC GAA TTC TAG CGT TGA GAT, the 40 mer 5'-GGC CAG GAT GGT GAA GAA TTC GAT CCG GTA CGT AGC TAA G, and the complementary 42mer 5'-TAC TTA GCT ACG TAC CGG ATC GAA TTC TTC ACC ATC CTG GCC were synthesized and their reactivity towards EcoRI was studied.  It was found that the 31mer and the 40mer were cleaved at a comparable rate to the 31mer-33mer hybrid and the 40mer-42mer hybrid, respectively.  The rate of cleavage of the 33mer and the 42mer was an order of magnitude lower.  To rule out possible intermolecular duplex formation, the 33mer was immobilized on cellulose by ligation and labelled with a 32P-dCTP using Klenow fragment of E. coli DNA polymerase.  EcoRI cleaved this immobilized oligomer into specific fragments.
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<CODE>R
<RECORD_NUMBER>1877
<AUTHORS>Yoo, O.J., Agarwal, K.L.
<TITLE>Cleavage of single strand oligonucleotides and bacteriophage PhiX174 DNA by MspI endonuclease.
<JOURNAL>J. Biol. Chem.
<VOLUME>255
<PAGE>10559-10562
<YEAR>1980
<ABSTRACT>Type II restriction endonucleases cleave duplex DNA at nucleotide sequences displaying 2-fold symmetry.  Our data show that MspI cleaves single strand oligonucleotides, d(GAACCGGAGA) and d(TCTCGGTT) at 4, 25, and 37C reaction temperatures.  The rate of cleavage of d(GAACCGGAGA) is several-fold faster than that of d(TCTCCGGTT).  Single strand PhiX174 DNA is also cleaved by MspI endonuclease giving well defined fragments.  5'-nucleotide analysis of the fragments generated from single strand and replicating form DNA suggest that cleavage occurs at the recognition sequence d(CCGG).  The data show that MspI endonuclease cleaves single strand oligonucleotides and prefers a recognition sequence surrounded by purine nucleotides.  A general model for endonuclease cleavage of single strand and duplex DNA is presented.
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<CODE>R
<RECORD_NUMBER>1884
<AUTHORS>Hofer, B., Ruhe, G., Koch, A., Koster, H.
<TITLE>Primary and secondary structure specificity of the cleavage of single-stranded DNA by endonuclease HinfI.
<JOURNAL>Nucl. Acids Res.
<VOLUME>10
<PAGE>2763-2773
<YEAR>1982
<ABSTRACT>The interaction of endonuclease HinfI with single-stranded fd DNA was examined.  The sizes of the cleavage products indicate that the enzyme cuts this substrate at the same sequences as double-stranded DNA (GANTC).  To determine whether or not the recognition sites in a single-stranded DNA have to be present in double-stranded form in order to be cleaved, DNA fragments containing complementary or non-complementary HinfI sequences were prepared and tested as substrates.  The results suggest that completely base-paired recognition sites are necessary for cleavage.  Sequences surrounding the HinfI pentanucleotides significantly modulate the reaction rates.
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<CODE>R
<RECORD_NUMBER>1909
<AUTHORS>Wells, R.D., Neuendorf, S.K
<TITLE>Cleavage of single-stranded viral DNAs by certain restriction endonucleases.
<JOURNAL>none
<BOOK>Gene Amplification and Analysis
<EDITOR>Chirikjian, J.G.
<PUBLISHER>Elsevier North Holland
<CITY>
<VOLUME>1
<PAGE>101-111
<YEAR>1981
<ABSTRACT>I. Introduction II. Characterization of the HaeIII reaction on O/X174, M13 and f1 DNAs III. Features of DNA structure recognized by the endonucleases IV. Characteristics of other restriction endonucleases V. Types of DNA substrates cleaved VI. Some properties of isoschizomers VII. Application of the technique for cleaving other DNAs VIII. Reaction of DNA methylases on single-stranded DNA IX. Prospects for the future
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