{"title":"Mechanism of specific site location and DNA cleavage by EcoR I endonuclease.","authors":"B J Terry, W E Jack, P Modrich","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":77851,"journal":{"name":"Gene amplification and analysis","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1987-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"14460849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The Pvu II restriction-modification system: cloning, characterization and use in revealing an E. coli barrier to certain methylases or methylated DNAs.","authors":"R M Blumenthal","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":77851,"journal":{"name":"Gene amplification and analysis","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1987-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"14460852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Restriction endonucleases and methylases.","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":77851,"journal":{"name":"Gene amplification and analysis","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1987-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13988368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Type II restriction endonucleases have attracted attention for two main reasons: firstly, their many applications in the dissection of DNA and in the construction of novel DNA molecules; secondly, as systems for studying the interactions of proteins with specific DNA sequences. With respect to the latter, the EcoR I restriction endonuclease has been examined in greater depth than any other type II enzyme [1-3]. However, the EcoR I enzyme has a major disadvantage as a system for studying DNA-protein interactions: the protein has a remarkably low solubility. The solutions in which EcoR I shows maximal activity, and also affinity for its recognition site, are saturated at less than 0.5 microM of this protein [4]. Consequently, many techniques that have been developed to study protein-ligand interactions but which require high concentrations of the protein in solution, such as NMR spectroscopy, cannot be used on EcoR I. But this drawback does not apply to all type II restriction enzymes. A different enzyme, the EcoR V restriction endonuclease [5-7], has special advantages as a system for studying DNA-protein interactions. In particular, this is the only type II restriction enzyme (apart from EcoR I [3]) for which crystals of the protein have been reported [7].
{"title":"The EcoR V restriction endonuclease.","authors":"P A Luke, S A McCallum, S E Halford","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Type II restriction endonucleases have attracted attention for two main reasons: firstly, their many applications in the dissection of DNA and in the construction of novel DNA molecules; secondly, as systems for studying the interactions of proteins with specific DNA sequences. With respect to the latter, the EcoR I restriction endonuclease has been examined in greater depth than any other type II enzyme [1-3]. However, the EcoR I enzyme has a major disadvantage as a system for studying DNA-protein interactions: the protein has a remarkably low solubility. The solutions in which EcoR I shows maximal activity, and also affinity for its recognition site, are saturated at less than 0.5 microM of this protein [4]. Consequently, many techniques that have been developed to study protein-ligand interactions but which require high concentrations of the protein in solution, such as NMR spectroscopy, cannot be used on EcoR I. But this drawback does not apply to all type II restriction enzymes. A different enzyme, the EcoR V restriction endonuclease [5-7], has special advantages as a system for studying DNA-protein interactions. In particular, this is the only type II restriction enzyme (apart from EcoR I [3]) for which crystals of the protein have been reported [7].</p>","PeriodicalId":77851,"journal":{"name":"Gene amplification and analysis","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1987-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"14460850","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
J M Rosenberg, J A McClarin, C A Frederick, J Grable, H W Boyer, P J Greene
{"title":"Structure and function of the EcoR I restriction endonuclease.","authors":"J M Rosenberg, J A McClarin, C A Frederick, J Grable, H W Boyer, P J Greene","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":77851,"journal":{"name":"Gene amplification and analysis","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1987-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"14630173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The enzymes of the BamH I restriction-modification system.","authors":"G Nardone, J G Chirikjian","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":77851,"journal":{"name":"Gene amplification and analysis","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1987-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"14630174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The organization and control of expression of the Pst I restriction-modification system.","authors":"R Y Walder, J A Walder","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":77851,"journal":{"name":"Gene amplification and analysis","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1987-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"14460851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Restriction and modification enzymes and their recognition sequences.","authors":"R J Roberts","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":77851,"journal":{"name":"Gene amplification and analysis","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1987-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13988369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In conclusion, one of the aspects of the DNA polymorphism observed is the formation of Z-DNA under a variety of conditions. Left-handed DNA stretches not only represent alternate structures, but also exert long-range effects due to their influence on superhelical properties on an entire supercoiled DNA as first shown six years ago [49, 50]. The examples given in this review emphasize the site-specificity of enzymes due to structural features rather than sequence itself. In this fashion, the reversible transition from B to Z DNA could modulate site-specific events on many levels of biological regulation. Considering all of the enzymes studied to date (S1, mung bean, BAL31, P1 nucleases, Hha I, BssH II, MHha I, BamH I, EcoR I, RNA polymerase, recl, recA, DNA glycosylase, O6-methylguanine-DNA methyltransferase), only the recl (and possibly the recA) protein seems to recognize and utilize left-handed DNA. A large number of questions related to the biology of Z-DNA are unanswered including: what is the DNA structure (B or Z or other) which is in physical contact with proteins; is Z-DNA recognized by proteins or are junctions the important features; do proteins revert the Z structure to B or to some other right-handed conformation; what other cofactors (perhaps chiral in nature) may be involved; what are the alternate forms of left-handed DNA; does left-handed DNA exist in vivo; what is the biological role(s) of left-handed DNA? The future of this field of investigation will be exciting indeed.
{"title":"Enzymatic probes for left-handed Z-DNA.","authors":"F Wohlrab, R D Wells","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>In conclusion, one of the aspects of the DNA polymorphism observed is the formation of Z-DNA under a variety of conditions. Left-handed DNA stretches not only represent alternate structures, but also exert long-range effects due to their influence on superhelical properties on an entire supercoiled DNA as first shown six years ago [49, 50]. The examples given in this review emphasize the site-specificity of enzymes due to structural features rather than sequence itself. In this fashion, the reversible transition from B to Z DNA could modulate site-specific events on many levels of biological regulation. Considering all of the enzymes studied to date (S1, mung bean, BAL31, P1 nucleases, Hha I, BssH II, MHha I, BamH I, EcoR I, RNA polymerase, recl, recA, DNA glycosylase, O6-methylguanine-DNA methyltransferase), only the recl (and possibly the recA) protein seems to recognize and utilize left-handed DNA. A large number of questions related to the biology of Z-DNA are unanswered including: what is the DNA structure (B or Z or other) which is in physical contact with proteins; is Z-DNA recognized by proteins or are junctions the important features; do proteins revert the Z structure to B or to some other right-handed conformation; what other cofactors (perhaps chiral in nature) may be involved; what are the alternate forms of left-handed DNA; does left-handed DNA exist in vivo; what is the biological role(s) of left-handed DNA? The future of this field of investigation will be exciting indeed.</p>","PeriodicalId":77851,"journal":{"name":"Gene amplification and analysis","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1987-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13988370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Restriction endonuclease: cleavage, ligation, and sensitivity.","authors":"R W Blakesley","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":77851,"journal":{"name":"Gene amplification and analysis","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1987-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13988372","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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