Relaxed specificity of endonuclease <i>Bam</i>H1 as determined by identification of recognition sites in SV 40 and pBR 322 DNAs

Kolesnikov, V. A.; Zinoviev, Victor V.; Yashina, L. N.; Karginov, Vladimir A.; Baclanov, M.M.; Malygin, E. G.

doi:10.1016/0014-5793(81)80437-1

Cited by 14 publications

(5 citation statements)

References 20 publications

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“…Although the major product in reactions with SmaI was a double-strand break at the 12th nucleotide from the 5' end, cleavage at the 11th nucleotide from the 5' end was also observed. The 11-mer results from`star' activity of SmaI that produces non-specific DNA breaks when excess amounts of enzyme are used (Kolesnikov et al, 1981). Utilizing less than one unit of SmaI reduces the star activity, however it also significantly lowers the efficiency of the reaction (less than 50 per cent of the total DNA is digested to produce double-strand breaks).…”

Section: Dna Substrates For Exonuclease Assaysmentioning

confidence: 99%

Substrate specificity of the p53-associated 3′-5′ exonuclease

et al. 2000

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p53 exhibits 3'-5' exonuclease activity and the signi®-cance of this biochemical function is currently not de®ned. In order to gain information about the potential role(s) of this exonuclease activity, recombinant and wild-type human p53 was examined for excision of nucleotides from de®ned synthetic DNA substrates. p53 removes nucleotides threefold faster from single-strand DNA than from DNA duplexes, exhibits a 1.5-fold preference for 3'-terminals of DNA that contain a single nucleotide mispair (mismatch) as compared to correctly paired DNA and eciently excises nucleotides from 3'-ends of blunt and cohesive (staggered) DNA doublestrand breaks. The p53 exonuclease is predominantly non-processive on DNA which is 17 nucleotides long (or shorter) and processive on the longer 30-mers. The processivity of nucleotide excision is decreased in the presence of 50 mM potassium phosphate and eliminated when full-length p53 is replaced with the core domain, comprised of amino acids 82 ± 292. Photoanity labeling indicates that (1) p53 monomers, rather than dimers, bind to single-strand forms of these oligomers; (2) complexes between p53 and 30-mers are more stable than those formed with 17-mers. The stability of these complexes determines processivity during nucleotide removal and modulates the 3'-5' exonuclease activity of p53. The relevance of substrate speci®city of the p53 exonuclease to DNA repair is discussed. Oncogene (2000) 19, 3321 ± 3329.

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Section: Dna Substrates For Exonuclease Assaysmentioning

confidence: 99%

Substrate specificity of the p53-associated 3′-5′ exonuclease

et al. 2000

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“…Many REases with star activity have been reported: AvaI (14), BamHI (15–20), BanI (21), Bme126I (22), BmrI (23), BspLU111III (24), BstI (25), BsuRI (26), BtsI (27), CeqI (28), CviJI (29,30), EcoRI (12,31–39), EcoRV (40–42), HaeIII (14), HhaI (20), HindIII (13,33,43), HinfI (44,45), KpnI (46), MamI (47), MboII (48), NcuI (49), NotI (50), PpiI (51), PstI (14,20,52), PvuII (17,43,53,54), RsrI (55,56), SacI (43), SalI (20), Sau3AI (57), SgrAI (58), SphI (59), SstI (20), TaqI (60–62), Tth111I (63) and XbaI (14,20). Experimentally, it has been found that the following general conditions may increase star activity: high glycerol concentration (>5% v/v) (18–20,34), high enzyme to DNA ratio (usually >100 U of enzyme per microgram of DNA) (12,17,20,34), low ionic strength (<25 mM salt) (12,17,20,34,35), high pH (>8.0) (41), the presence of organic solvents (such as DMSO, ethanol) (20,34,43) and substitution of Mg 2+ with other divalent cations (Mn 2+ , Co 2+ ) (15,33–35,64). It has been suggested that water-mediated interactions between the REase and DNA are the key differences between specific complexes and star complexes (17,38,65), but the actual situation may be even more complicated and remains to be clarified.…”

Section: Introductionmentioning

confidence: 99%

The Fidelity Index provides a systematic quantitation of star activity of DNA restriction endonucleases

Hua

Therrien

Blanchard

et al. 2008

Nucleic Acids Research

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Restriction endonucleases are the basic tools of molecular biology. Many restriction endonucleases show relaxed sequence recognition, called star activity, as an inherent property under various digestion conditions including the optimal ones. To quantify this property we propose the concept of the Fidelity Index (FI), which is defined as the ratio of the maximum enzyme amount showing no star activity to the minimum amount needed for complete digestion at the cognate recognition site for any particular restriction endonuclease. Fidelity indices for a large number of restriction endonucleases are reported here. The effects of reaction vessel, reaction volume, incubation mode, substrate differences, reaction time, reaction temperature and additional glycerol, DMSO, ethanol and Mn2+ on the FI are also investigated. The FI provides a practical guideline for the use of restriction endonucleases and defines a fundamental property by which restriction endonucleases can be characterized.

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“…Along with EcoRI, they are the only members of the type II restriction endonuclease family to be characterized by high-resolution structural analysis (4,(19)(20)(21)(22)(23). For these three enzymes, cleavage at alternate sites has been observed previously, either by addition of organic solvents to the reaction buffer or by changes in ionic strength, pH, or divalent cation concentration or identity (24)(25)(26)(27)(28). Cleavage at alternate sites by these and other restriction enzymes has been termed "star activity" by analogy with EcoRI star (EcoRI*) activity (29).…”

mentioning

confidence: 99%

Heterogeneity in molecular recognition by restriction endonucleases: osmotic and hydrostatic pressure effects on BamHI, Pvu II, and EcoRV specificity.

Robinson

Sligar

1995

Proc. Natl. Acad. Sci. U.S.A.

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The cleavage specificity of the Pvu II and BamHI restriction endonucleases is found to be dramatically reduced at elevated osmotic pressure. Relaxation in specificity of these otherwise highly accurate and specific enzymes, previously termed "star activity," is uniquely correlated with osmotic pressure between 0 and 100 atmospheres. No other colligative solvent property exhibits a uniform correlation with star activity for all of the compounds tested. Application of hydrostatic pressure counteracts the effects of osmotic pressure and restores the natural selectivity of the enzymes for their canonical recognition sequences. These results indicate that water solvation plays an important role in the sitespecific recognition of DNA by many restriction enzymes. Osmotic pressure did not induce an analogous effect on the specificity of the EcoRV endonuclease, implying that selective hydration effects do not participate in DNA recognition in this system. Hydrostatic pressure was found to have little effect on the star activity induced by changes in ionic strength, pH, or divalent cation, suggesting that distinct mechanisms may exist for these observed alterations in specificity. Recent evidence has indicated that BamHI and EcoRI share similar structural motifs, while Pvu II and EcoRV belong to a different structural family. Evidently, the use of hydration water to assist in site-specific recognition is a motif neither limited to nor defined by structural families.

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Relaxed specificity of endonuclease BamH1 as determined by identification of recognition sites in SV 40 and pBR 322 DNAs

Cited by 14 publications

References 20 publications

Substrate specificity of the p53-associated 3′-5′ exonuclease

Substrate specificity of the p53-associated 3′-5′ exonuclease

The Fidelity Index provides a systematic quantitation of star activity of DNA restriction endonucleases

Heterogeneity in molecular recognition by restriction endonucleases: osmotic and hydrostatic pressure effects on BamHI, Pvu II, and EcoRV specificity.

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