Purine 8-substitution modulates the recognition by restriction endodeoxyribonuclease EcoRI of octadeoxyribonucleotides (dGGAATTCC)

Komatsu, Hiroshi; Kim, Sang-Gug; Sakabe, Ichiro; Ichikawa, Takashi; Nakai, Michiaki; Takaku, Hiroshi

doi:10.1016/s0960-894x(01)81198-7

Cited by 8 publications

(2 citation statements)

References 35 publications

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“…Thirteen type II restriction endonucleases-AfeI, [10] EcoRI, [11] KpnI, [12] PspGI, [13] PstI, [14] PvuII, [15] RsaI, [16] SacI, [17] ScaI, [18] SphI, [18] AflII, [19] ApaLI, [20] and BglII [21] -were selected and tested for their ability to cleave the sequences containing modified C or T in the recognition sequence. The selection contained some of the most important examples of REs used in molecular biology for cloning, included REs giving blunt ends, 3'-and 5'-overhang products, recognizing 4, 5, or 6 bp sequences containing one or two C or T bases in different positions of the sequence (including the cleavage site).…”

Section: Resultsmentioning

confidence: 99%

Cleavage of Functionalized DNA Containing 5‐Modified Pyrimidines by Type II Restriction Endonucleases

2011

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A series of six pyrimidine-modified dNTPs--5-ethynyl-, 5-phenyl-, and 5-(3-nitrophenyl)deoxycitidine and -deoxyuridine triphosphates--were prepared and incorporated by primer extension with Vent (exo-)polymerase to specific DNA sequences within or next to the recognition sequences of selected restriction endonucleases. The cleavage of these pyrimidine-modified DNA sequences by 13 restriction enzymes was then studied. Whereas the presence of any modified C within the target sequence completely prevented any restriction cleavage, most enzymes tolerated the presence of 5-ethynylU and two of them even the presence of 5-phenyl- and 5-(3-nitrophenyl)U. Modifications outside the recognition sequence were tolerated except in the case of phenyl derivatives with the PvuII enzyme. 5-EthynylC was used for protection of the recognition sequence from cleavage in the presence of the second unmodified copy of the same sequence that was cleaved.

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Section: Resultsmentioning

confidence: 99%

Cleavage of Functionalized DNA Containing 5‐Modified Pyrimidines by Type II Restriction Endonucleases

2011

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“…There is only very little knowledge about cleavage of other types of base-modified DNA. Komatsu et al ( 36 ) published a study on resistance of 8-hydroxy-adenosine, 8-methoxy-adenosine and 8-methoxy-guanosine containing octadeoxyribonucleotides to cleavage by EcoRI. DNA containing 7-deazaadenine (37–43) or 7-deazaguanine ( 38 ) in recognition sequence was repeatedly reported to be resistant to some endonucleases apparently due to the lack of N7 atom capable of formation of H-bonds in major groove.…”

Section: Introductionmentioning

confidence: 99%

Cleavage of adenine-modified functionalized DNA by type II restriction endonucleases

Macíčková-Cahová

Hocek

2009

Nucleic Acids Research

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A set of 6 base-modified 2′-deoxyadenosine derivatives was incorporated to diverse DNA sequences by primer extension using Vent (exo-) polymerase and the influence of the modification on cleavage by diverse restriction endonucleases was studied. While 8-substituted (Br or methyl) adenine derivatives were well tolerated by the restriction enzymes and the corresponding sequences were cleaved, the presence of 7-substituted 7-deazaadenine in the recognition sequence resulted in blocking of cleavage by some enzymes depending on the nature and size of the 7-substituent. All sequences with modifications outside of the recognition sequence were perfectly cleaved by all the restriction enzymes. The results are useful both for protection of some sequences from cleavage and for manipulation of functionalized DNA by restriction cleavage.

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Polymerase Synthesis of DNAs Bearing Vinyl Groups in the Major Groove and their Cleavage by Restriction Endonucleases

2014

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DNA molecules containing 5-vinyluracil, 5-vinylcytosine, or 7-deaza-7-vinyladenine were prepared by polymerase incorporation of the corresponding vinyl-modified 2'-deoxyribonucleoside triphosphates, and the influence of the vinyl group in the major groove of DNA on the cleavage by diverse type II restriction endonucleases (REs) was studied. The presence of 5-vinyluracil was tolerated by most of the REs, whereas only some REs were able to cleave sequences containing 7-deaza-7-vinyladenine. The enzyme ScaI was found to cleave DNA containing 5-vinylcytosine efficiently but not DNA containing the related 5-ethynylcytosine. All other REs failed to cleave sequences containing any cytosine modifications.

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Purine 8-substitution modulates the recognition by restriction endodeoxyribonuclease EcoRI of octadeoxyribonucleotides (dGGAATTCC)

Cited by 8 publications

References 35 publications

Cleavage of Functionalized DNA Containing 5‐Modified Pyrimidines by Type II Restriction Endonucleases

Cleavage of Functionalized DNA Containing 5‐Modified Pyrimidines by Type II Restriction Endonucleases

Cleavage of adenine-modified functionalized DNA by type II restriction endonucleases

Polymerase Synthesis of DNAs Bearing Vinyl Groups in the Major Groove and their Cleavage by Restriction Endonucleases

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