Photoinduced DNA Cleavage Reactions by Designed Analogues of Co(III)−Bleomycin:  The Metalated Core Is the Primary Determinant of Sequence Specificity

1996 ◽  
Vol 35 (9) ◽  
pp. 2637-2643 ◽  
Author(s):  
Edgardo T. Farinas ◽  
Jennifer D. Tan ◽  
Pradip K. Mascharak
Keyword(s):  
Dna Cleavage ◽  
Sequence Specificity ◽  
Primary Determinant ◽  
Cleavage Reactions

Conformational properties of topoisomerase II inhibitors and sequence specificity of DNA cleavage

1994 ◽  
Vol 7 (3) ◽  
pp. 227-231 ◽  
Author(s):  
M. Palumbo ◽  
M. Mabilia ◽  
A. Pozzan ◽  
G. Capranico ◽  
S. Tinelli ◽  
...  
Keyword(s):  
Dna Cleavage ◽  
Topoisomerase Ii ◽  
Sequence Specificity ◽  
Topoisomerase Ii Inhibitors ◽  
Conformational Properties

A New Method for Determining the Stereochemistry of DNA Cleavage Reactions:  Application to theSfiI andHpaII Restriction Endonucleases and to the MuA Transposase†

Biochemistry ◽  
1999 ◽  
Vol 38 (14) ◽  
pp. 4640-4648 ◽  
Author(s):  
Kiyoshi Mizuuchi ◽  
Timothy J. Nobbs ◽  
Stephen E. Halford ◽  
Kenji Adzuma ◽  
Jun Qin
Keyword(s):  
Dna Cleavage ◽  
Restriction Endonucleases ◽  
New Method ◽  
Cleavage Reactions

scholarly journals The Need for Speed: Run-On Oligomer Filament Formation Provides Maximum Speed with Maximum Sequestration of Activity

2018 ◽  
Vol 93 (5) ◽  
Author(s):  
Claudia J. Barahona ◽  
L. Emilia Basantes ◽  
Kassidy J. Tompkins ◽  
Desirae M. Heitman ◽  
Barbara I. Chukwu ◽  
...  
Keyword(s):  
Dna Cleavage ◽  
Biological Function ◽  
Enzyme Mechanism ◽  
Maximum Speed ◽  
Host Bacterium ◽  
Sequence Specificity ◽  
Filament Formation ◽  
Dna Sequence Specificity ◽  
Cleavage Activity ◽  
Dna Cleavage Activity

ABSTRACTHere, we investigate an unusual antiviral mechanism developed in the bacteriumStreptomyces griseus. SgrAI is a type II restriction endonuclease that forms run-on oligomer filaments when activated and possesses both accelerated DNA cleavage activity and expanded DNA sequence specificity. Mutations disrupting the run-on oligomer filament eliminate the robust antiphage activity of wild-type SgrAI, and the observation that even relatively modest disruptions completely abolish this anti-viral activity shows that the greater speed imparted by the run-on oligomer filament mechanism is critical to its biological function. Simulations of DNA cleavage by SgrAI uncover the origins of the kinetic advantage of this newly described mechanism of enzyme regulation over more conventional mechanisms, as well as the origin of the sequestering effect responsible for the protection of the host genome against damaging DNA cleavage activity of activated SgrAI.IMPORTANCEThis work is motivated by an interest in understanding the characteristics and advantages of a relatively newly discovered enzyme mechanism involving filament formation. SgrAI is an enzyme responsible for protecting against viral infections in its host bacterium and was one of the first such enzymes shown to utilize such a mechanism. In this work, filament formation by SgrAI is disrupted, and the effects on the speed of the purified enzyme as well as its function in cells are measured. It was found that even small disruptions, which weaken but do not destroy filament formation, eliminate the ability of SgrAI to protect cells from viral infection, its normal biological function. Simulations of enzyme activity were also performed and show how filament formation can greatly speed up an enzyme’s activation compared to that of other known mechanisms, as well as to better localize its action to molecules of interest, such as invading phage DNA.

Novel molecular beacon assays for DNA cleavage reactions

2001 ◽  
Author(s):  
Jianwei J. Li ◽  
Charles Z. Cao ◽  
Ronald Geyer ◽  
Weihong Tan
Keyword(s):  
Dna Cleavage ◽  
Molecular Beacon ◽  
Cleavage Reactions

Sequence specificity of DNA cleavage by bis(1,10-phenanthroline)copper(I)

Biochemistry ◽  
1988 ◽  
Vol 27 (6) ◽  
pp. 1822-1827 ◽  
Author(s):  
James M. Veal ◽  
Randolph L. Rill
Keyword(s):  
Dna Cleavage ◽  
Sequence Specificity

scholarly journals Nucleotide Sequence Specificity in DNA Cleavage Caused by Dihydropyrazines, a New Type of DNA Strand-Cleaving Agent.

2000 ◽  
Vol 23 (11) ◽  
pp. 1281-1286 ◽  
Author(s):  
Nobuhiro KASHIGE ◽  
Tadatoshi YAMAGUCHI ◽  
Fumio MIAKE ◽  
Kenji WATANABE
Keyword(s):  
Nucleotide Sequence ◽  
Dna Cleavage ◽  
Sequence Specificity ◽  
New Type ◽  
Dna Strand

Chromatin structure, not DNA sequence specificity, is the primary determinant of topoisomerase II sites of action in vivo

1991 ◽  
Vol 11 (10) ◽  
pp. 4973-4984
Author(s):  
A Udvardy ◽  
P Schedl
Keyword(s):  
Chromatin Structure ◽  
Topoisomerase Ii ◽  
Double Strand Breaks ◽  
General Mechanism ◽  
Sequence Specificity ◽  
Strand Breaks ◽  
Wide Range ◽  
Primary Determinant ◽  
Sites Of Action

In the studies reported here we have used topoisomerase II as a model system for analyzing the factors that determine the sites of action for DNA-binding proteins in vivo. To localize topoisomerase II sites in vivo we used an inhibitor of the purified enzyme, the antitumor drug VM-26. This drug stabilizes an intermediate in the catalytic cycle, the cleavable complex, and substantially stimulates DNA cleavage by topoisomerase II. We show that lysis of VM-26 treated tissue culture cells with sodium dodecyl sulfate induces highly specific double-strand breaks in genomic DNA, and we present evidence indicating that these double-strand breaks are generated by topoisomerase II. Using indirect end labeling to map the cleavage products, we have examined the in vivo sites of action of topoisomerase II in the 87A7 heat shock locus, the histone repeat, and a tRNA gene cluster at 90BC. Our analysis reveals that chromatin structure, not sequence specificity, is the primary determinant in topoisomerase II site selection in vivo. We suggest that chromatin organization may provide a general mechanism for generating specificity in a wide range of DNA-protein interactions in vivo.

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