scholarly journals Residues of E. coli topoisomerase I conserved for interaction with a specific cytosine base to facilitate DNA cleavage

2012 ◽  
Vol 40 (18) ◽  
pp. 9233-9243 ◽  
Author(s):  
Gagandeep Narula ◽  
Yuk-Ching Tse-Dinh
Keyword(s):  
Dna Cleavage ◽  
Topoisomerase I ◽  
E Coli

scholarly journals DNA sequence selectivity of human topoisomerase I-mediated DNA cleavage induced by camptothecin

2009 ◽  
Vol 18 (6) ◽  
pp. 1326-1331
Author(s):  
Chandanamali Punchihewa ◽  
Megan Carver ◽  
Danzhou Yang
Keyword(s):  
Dna Sequence ◽  
Dna Cleavage ◽  
Topoisomerase I ◽  
Sequence Selectivity

Glycosylated flavones as selective inhibitors of topoisomerase IV.

1997 ◽  
Vol 41 (5) ◽  
pp. 992-998 ◽  
Author(s):  
F X Bernard ◽  
S Sablé ◽  
B Cameron ◽  
J Provost ◽  
J F Desnottes ◽  
...  
Keyword(s):  
Dna Cleavage ◽  
Topoisomerase Ii ◽  
Coli Strain ◽  
Selective Inhibitors ◽  
Topoisomerase Iv ◽  
Gene Encoding ◽  
Cottonseed Flour ◽  
Dna Topoisomerase ◽  
E Coli ◽  
Pbr322 Dna

Three flavonoids which promoted Escherichia coli topoisomerase IV-dependent DNA cleavage were isolated from cottonseed flour and identified as quercetin 3-O-beta-D-glucose-[1,6]-O-alpha-L-rhamnose (rutin), quercetin 3-O-beta-D-galactose-[1,6]-O-alpha-L-rhamnose, and quercetin 3-O-beta-D-glucose (isoquercitrin). The most active one (rutin) also inhibited topoisomerase IV-dependent decatenation activity (50% inhibitory concentration, 64 microg/ml) and induced the SOS response of a permeable E. coli strain. Derivatives of quercetin glycosylated at position C-3 were shown to induce two site-specific DNA cleavages of pBR322 DNA, which were mapped by DNA sequence analysis to the gene encoding resistance to tetracycline. Cleavage at these sites was hardly detectable in cleavage reactions with quercetin or fluoroquinolones. None of the three flavonoids isolated from cottonseeds had any stimulatory activity on E. coli DNA gyrase-dependent or calf thymus topoisomerase II-dependent DNA cleavage, and they were therefore specific to topoisomerase IV. These results show that selective inhibitors of topoisomerase IV can be derived from the flavone structure. This is the first report on a DNA topoisomerase inhibitor specific for topoisomerase IV.

ISOLATION OF AN E. COLI DNA TOPOISOMERASE I MUTANT

1980 ◽  
pp. 833-837 ◽  
Author(s):  
Rolf Sternglanz ◽  
Stephen DiNardo ◽  
James C. Wang ◽  
Y. Nishimura ◽  
Y. Hirota
Keyword(s):  
Topoisomerase I ◽  
Dna Topoisomerase I ◽  
Dna Topoisomerase ◽  
E Coli

scholarly journals Antisense transcripts enhanced by camptothecin at divergent CpG-island promoters associated with bursts of topoisomerase I-DNA cleavage complex and R-loop formation

2013 ◽  
Vol 41 (22) ◽  
pp. 10110-10123 ◽  
Author(s):  
Jessica Marinello ◽  
Giovanni Chillemi ◽  
Susana Bueno ◽  
Stefano G. Manzo ◽  
Giovanni Capranico
Keyword(s):  
Dna Cleavage ◽  
Topoisomerase I ◽  
Cpg Island ◽  
Loop Formation ◽  
Antisense Transcripts ◽  
Cleavage Complex

scholarly journals The Acidaminococcus sp. Cas12a nuclease recognizes GTTV and GCTV as non-canonical PAMs

2019 ◽  
Vol 366 (8) ◽  
Author(s):  
Thomas Jacobsen ◽  
Chunyu Liao ◽  
Chase L Beisel
Keyword(s):  
Dna Cleavage ◽  
Mammalian Cells ◽  
Consensus Sequence ◽  
Wild Type ◽  
E Coli ◽  
Cleavage Efficiency ◽  
Protospacer Adjacent Motif ◽  
Short Palindromic Repeat ◽  
A Cell ◽  
Validation Experiments

ABSTRACT The clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) nuclease Acidaminococcus sp. Cas12a (AsCas12a, also known as AsCpf1) has become a popular alternative to Cas9 for genome editing and other applications. AsCas12a has been associated with a TTTV protospacer-adjacent motif (PAM) as part of target recognition. Using a cell-free transcription-translation (TXTL)-based PAM screen, we discovered that AsCas12a can also recognize GTTV and, to a lesser degree, GCTV motifs. Validation experiments involving DNA cleavage in TXTL, plasmid clearance in Escherichia coli, and indel formation in mammalian cells showed that AsCas12a was able to recognize these motifs, with the GTTV motif resulting in higher cleavage efficiency compared to the GCTV motif. We also observed that the -5 position influenced the activity of DNA cleavage in TXTL and in E. coli, with a C at this position resulting in the lowest activity. Together, these results show that wild-type AsCas12a can recognize non-canonical GTTV and GCTV motifs and exemplify why the range of PAMs recognized by Cas nucleases are poorly captured with a consensus sequence.

Molecular Beacon Enables Combination of Highly Processive and Highly Sensitive Rolling Circle Amplification Readouts for Detection of DNA-Modifying Enzymes

Nano LIFE ◽  
2015 ◽  
Vol 05 (02) ◽  
pp. 1541002 ◽  
Author(s):  
Emil L. Kristoffersen ◽  
Maria Gonzalez ◽  
Magnus Stougaard ◽  
Cinzia Tesauro
Keyword(s):  
Real Time ◽  
Dna Cleavage ◽  
Topoisomerase I ◽  
Drug Response ◽  
Molecular Beacon ◽  
Rolling Circle Amplification ◽  
Dna Topoisomerase ◽  
Rolling Circle ◽  
Topoisomerase Ib ◽  
Highly Sensitive

Here we present an optimized readout format for detection of the circularized products from a DNA-based sensor for measurement of DNA-modifying enzymes including DNA Topoisomerase I. The basic design of the DNA-sensor relies on the use of a substrate that can be circularized by the activity of DNA-modifying enzymes like type IB Topoisomerases and subsequently amplified by a rolling circle amplification (RCA) mechanism. The RCA process can be followed in real-time by the addition of a molecular beacon with a fluorophore/quencher pair. Upon hybridization to the amplified product, the fluorophore/quencher pair is separated, giving rise to a fluorescent signal, measurable in pseudo real-time using a qPCR machine or in a fluorimeter. The RCA products in complex with the molecular beacon can subsequently be moved to microscopic slides and analyzed in a fluorescence microscope. We describe the proof of the principle of this molecular beacon-based method combining the qPCR readout format with the standard Rolling circle Enhanced Enzymatic Assay previously reported. Although the qPCR setup is less sensitive, it allows easy, fast, and high-throughput measurement of enzyme activities. Human Topoisomerase IB (TopIB) is a well-known target for the clinically used anticancer drugs of the camptothecin family. The cytotoxic effect of camptothecins correlates directly with the intracellular TopIB activity affecting reversibly the Topoisomerase/DNA cleavage complexes. Therefore, we envisioned that the presented method may find use for the prediction of cellular drug response and for drug screening to discover novel molecules that specifically inhibit TopIB or other DNA-modifying enzymes.

scholarly journals DNA Topoisomerase I Inhibitory Activity of Quinochalcone C-glycosides from the Florets of Carthamus tinctorius

2017 ◽  
Vol 12 (11) ◽  
pp. 1934578X1701201
Author(s):  
Shi-Jun Yue ◽  
Wen-Xiao Wang ◽  
Cheng Qu ◽  
Lan-Ting Xin ◽  
Yu-Ping Tang ◽  
...  
Keyword(s):  
Inhibitory Activity ◽  
Dna Cleavage ◽  
Topoisomerase I ◽  
Docking Study ◽  
Carthamus Tinctorius ◽  
In Vitro Cytotoxicity ◽  
Molecular Docking Study ◽  
Dna Topoisomerase ◽  
Cleavage Complex

The DNA topoisomerase (Topo) I inhibitory activity of six quinochalcone C-glycosides (QCGs) isolated from the florets of Carthamus tinctorius were evaluated in vitro. Among them, anhydrosafflor yellow B (AHSYB, 4) and carthorquinoside B (6) could inhibit DNA Topo I at concentrations as low as 100 μM. Molecular docking study revealed that both of them have the capacity to stabilize Topo I-DNA cleavage complex in silico interacting with the essential binding sites, such as Arg364, Thr718 and TGP11. Besides, both compounds 4 and 6 exhibited no antitumor activity by in vitro cytotoxicity assays.

scholarly journals Metal ion and inter-domain interactions as functional networks in E. coli topoisomerase I

Gene ◽  
2013 ◽  
Vol 524 (2) ◽  
pp. 253-260 ◽  
Author(s):  
Claudia Sissi ◽  
Bokun Cheng ◽  
Valentina Lombardo ◽  
Yuk-Ching Tse-Dinh ◽  
Manlio Palumbo
Keyword(s):  
Metal Ion ◽  
Topoisomerase I ◽  
Functional Networks ◽  
E Coli ◽  
Domain Interactions
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