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Sample search results for: abasic site intermediate

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1 Oligonucleotides with Bistranded Abasic Sites Interfere with Substrate Binding and Catalysis by Human Apurinic/Apyrimidinic Endonuclease
 

Summary:  Oligonucleotides with Bistranded Abasic Sites Interfere with Substrate Binding and Catalysis... DNA repair. The enzyme, which repairs abasic sites, makes a single nick 5 to the phosphodeoxyribose... acting on an oligonucleotide with a single abasic site. We ...

  

Source: Strauss, Phyllis R. - Department of Biology, Northeastern University

 

Collection: Biology and Medicine

 
2 Molecular Cell, Vol. 13, 751762, March 12, 2004, Copyright 2004 by Cell Press Snapshots of Replication through
 

Summary:  B homolog) from two related Sulfolobus strains are able to extend primer strands past abasic sites... with the abasic site looped out and finger and little finger domains provides an entry channelthe incoming... when the abasic site remains extrahelical. incoming ...

  

Source: Ling, Hong - Department of Biochemistry, University of Alberta

 

Collection: Biology and Medicine

 
3 Submitted to J. Biol. Chem. Draft of July 13, 2001
 

Summary:  /apyrimidinic endonuclease; ASR, abasic site repair, bp, base pair; ds, double-stranded; ESR, electron spin resonance; HDP... structure, ss, single- stranded #12;3 Introduction Abasic site repair (ASR) refers to one of several repair... pathways that generate and repair an abasic ...

  

Source: Strauss, Phyllis R. - Department of Biology, Northeastern University

 

Collection: Biology and Medicine

 
4 Substrate Binding by Human Apurinic/Apyrimidinic Endonuclease Indicates a Briggs-Haldane Mechanism*
 

Summary:  Apurinic/apyrimidinic endonuclease (AP endo) makes a single nick 5 to a DNA abasic site. We have character... the abasic site during treatment with uracil-DNA glycosylase with a reducing agent. Otherwise, a 20-mer... M and 10 s 1 , respectively. Heat treatment of the abasic ...

  

Source: Strauss, Phyllis R. - Department of Biology, Northeastern University

 

Collection: Biology and Medicine

 
5 Abasic Site Repair in Higher Eukaryotes Phyllis R. Strauss and Noreen E. O'Regan
 

Summary:  3 Abasic Site Repair in Higher Eukaryotes Phyllis R. Strauss and Noreen E. O'Regan 1. INTRODUCTION... of abasic sites generated per mammalian cell per day run as high as 106/cell/d (88). Abasic sites... the large number of abasic ...

  

Source: Strauss, Phyllis R. - Department of Biology, Northeastern University

 

Collection: Biology and Medicine

 
6 Notes & Tips A nonisotopic assay for unambiguous assignment of DNA
 

Summary:  but leave be- hind an abasic or apurinic/apyrimidinic (AP)1 site in DNA [4]. Thus, for the analysis... strand scission adjacent to the abasic site. The lack of current DNA glycosylase assays to concur- rently... denaturing PAGE, taking into account the inherent lability of abasic ...

  

Source: Boston University, Center for Advanced Biotechnology

 

Collection: Biotechnology

 
7 DNA Repair 3 (2004) 14471455 Novel role of tyrosine in catalysis by human AP endonuclease 1
 

Summary:  ) recognizes abasic sites in ds DNA and makes a single nick in the backbone 5 to the abasic site... . We show that Tyr128 and Tyr269 , which interact upstream and downstream of the abasic site... , respectively, are involved in recognition and binding of ...

  

Source: Strauss, Phyllis R. - Department of Biology, Northeastern University

 

Collection: Biology and Medicine

 
8 Pure Appl. Chem., Vol. 83, No. 3, pp. 677686, 2011. doi:10.1351/PAC-CON-10-09-28
 

Summary:  on noncovalent interactions between a spin-labeled nucleobase and an abasic site in duplex DNA. Keywords: EPR... (a), intermediate (b), and slow (c) motion regime. #12;SITE-DIRECTED SPIN LABELING: CASE STUDIES... Postsynthetic spin labeling of nucleobases by click chemistry: Detection of ...

  

Source: Sigurdsson, Snorri Thor - Chemistry Division, Science Institute, University of Iceland.

 

Collection: Chemistry

 
9 Ubiquitinated proliferating cell nuclear antigen activates translesion DNA polymerases and REV1
 

Summary:  is a deoxycytidyl transferase that shows the highest catalytic activity opposite template guanines and abasic sites... (14, 15). Rev1 is primarily responsible for inserting dC residues opposite abasic sites during... oligonucleotide-based system was used in which the template strand contained a model ...

  

Source: Burgers, Peter M. - Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis

 

Collection: Biology and Medicine

 
10 Effect of lesions on the dynamics of DNA on the picosecond and nanosecond timescales using a
 

Summary:  DNA: an abasic site and a helix terminus. Because these comparisons are looking for small effects... of the oligonucleotides (Fig. 1). When paired with a tetrahydrofuran abasic site analog on the complementary strand... probe and its complementary abasic site. The ...

  

Source: Coleman, Robert S. - Department of Chemistry, Ohio State University

 

Collection: Chemistry

 
11 Noncovalent Spin Labeling DOI: 10.1002/anie.201002637
 

Summary:  ,7] The strategy for noncovalent labeling was to disconnect the glycosidic bond of C¸ to give an abasic site (F... ) and the free spin-labeled base ç (Figure 1). The spin label would bind in the abasic site through receptor... containing an abasic site with ç, a ...

  

Source: Sigurdsson, Snorri Thor - Chemistry Division, Science Institute, University of Iceland.

 

Collection: Chemistry

 
12 Human Apurinic/Apyrimidinic Endonuclease Is Processive, Daniel C. Carey and Phyllis R. Strauss*
 

Summary:  abasic sites in the base excision repair pathway. AP endo makes a single nick 5 to an abasic site... in double-stranded DNA. In this study, we investigated whether AP endo locates an abasic site through... a processive or a distributive mechanism. We used a linear ...

  

Source: Strauss, Phyllis R. - Department of Biology, Northeastern University

 

Collection: Biology and Medicine

 
13 Templated Synthesis of Peptide Nucleic Acids via Sequence-Selective Base-Filling Reactions
 

Summary:  to be a promising candidate for replication by base filling since the abasic reaction site is a versatile secondary... -PNA duplexes.8,9 We found that incorporation of an abasic site had a parallel, though more dramatic effect... of the duplex) (Table 1). Next we tested the ability of PNA bases to fill a ...

  

Source: Liu, David R. - Department of Chemistry and Chemical Biology, Harvard University

 

Collection: Chemistry ; Biology and Medicine

 
14 3-Methyladenine DNA glycosylases: structure,
 

Summary:  the accumulation of downstream BER intermediates (either abasic sites or single-strand breaks), which are respon... to produce an abasic site. The abasic site is then processed by one of two pathways, termed short... generates a DNA strand break ...

  

Source: Lau, Albert Y. - Department of Biophysics and Biophysical Chemistry, Johns Hopkins University

 

Collection: Biology and Medicine

 
15 Characterization of DNA Damage Induced by a Natural Product Antitumor Antibiotic Leinamycin in Human Cancer Cells
 

Summary:  to generate SSBs via a -elimination reaction that cleaves the O-P bond on the 3- side of the abasic site (22... of an abasic site (29, 30). To obtain clear evidence that leinamycin-induced DNA strand breaks may... spontaneously occur via -elimination reactions at aldehydic abasic ...

  

Source: Gates, Kent. S. - Departments of Chemistry & Biochemistry, University of Missouri-Columbia

 

Collection: Chemistry

 
16 INTRINSIC PROPERTIES OF THE TWO REPLICATIVE DNA POLYMERASES OF PYROCOCCUS ABYSSI IN REPLICATING ABASIC SITES: POSSIBLE ROLE IN DNA
 

Summary:  ABASIC SITES: POSSIBLE ROLE IN DNA DAMAGE TOLERANCE ? 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20... , France. Running Tittle : DNA synthesis by Pabpols of DNA containing abasic sites * Corresponding author... 39 40 41 Spontaneous and induced abasic sites in ...

  

Source: Ecole Polytechnique, Centre de mathématiques

 

Collection: Mathematics

 
17 Cell, Vol. 95, 249258, October 16, 1998, Copyright 1998 by Cell Press Crystal Structure of a Human Alkylbase-DNA
 

Summary:  ., 1997; David and Williams, 1998). The resultingBoston, Massachusetts 02115 abasic (AP) sites are further... nucleotide to flip into the en- sylase reaction, a pyrrolidine abasic nucleotide, which zyme active site... ) on either side of the pyrrolidine site (Fig- either side of the ...

  

Source: Lau, Albert Y. - Department of Biophysics and Biophysical Chemistry, Johns Hopkins University

 

Collection: Biology and Medicine

 
18 Charge Transport in DNA Oligonucleotides with Various Base-Pairing Patterns Irena Kratochvilova,*,
 

Summary:  A, G, C, and T) and dSpacer CE Phosphoramidite (for abasic sites) were purchased from Glen Research... duplex interior at the abasic sites can partially compen- sate for the loss of overlap between the base... . Structurally and thermally much less stable abasic duplexes have still lower ...

  

Source: Kužel, Petr - Institute of Physics, Academy of Sciences of the Czech Republic

 

Collection: Physics

 
19 DNA damage recognition and repair by 3-methyladenine DNA glycosylase I (TAG)
 

Summary:  to other glycosylase-DNA structures, the abasic ri- bose is not flipped into the TAG active site... a tetrahydrofuran (THF) abasic site analog. The THF moiety is isosteric with enzymatically generated apuri- nic... -chain and main- chain atoms from the HhH motif bind the phosphate groups 30 to the ...

  

Source: Eichman, Brandt F. - Department of Biological Sciences, Vanderbilt University

 

Collection: Biology and Medicine

 
20 Clustered DNA damages induced in isolated DNA and in human cells by low doses of ionizing radiation
 

Summary:  , abasic sites, or oxidized bases) on opposing strands--are suspects as critical lesions producing lethal... at an oxidized base or abasic site. If there are two closely spaced damages on opposing strands, such cleav- age... DNA damages containing abasic sites, ...

  

Source: Brookhaven National Laboratory, Environmental Chemistry Division, Department of Applied Science

 

Collection: Environmental Sciences and Ecology


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21 Molecular Cell, Vol. 20, 367375, November 11, 2005, Copyright 2005 by Elsevier Inc. DOI 10.1016/j.molcel.2005.09.018 MRE11/RAD50 Cleaves DNA
 

Summary:  by deamination of cytosine to uracil, followed by removal of uracil to create an abasic (AP) site. We find... in the hypermutation mecha- nism, and that purified, recombinant MRE/RAD50 (MR) can cleave DNA at abasic sites... can cleave at abasic sites, we adopted a ...

  

Source: Maizels, Nancy - Department of Biochemistry, University of Washington at Seattle

 

Collection: Biology and Medicine

 
22 Site-Directed Spin-Labeling of Nucleic Acids by Click Chemistry: Detection of Abasic Sites in Duplex DNA by EPR
 

Summary:  Site-Directed Spin-Labeling of Nucleic Acids by Click Chemistry: Detection of Abasic Sites... that can detect and identify local structural deformations in duplex DNA, in particular abasic sites... , for the first time, abasic sites in duplex DNA ...

  

Source: Sigurdsson, Snorri Thor - Chemistry Division, Science Institute, University of Iceland.

 

Collection: Chemistry

 
23 Effect of Protein Binding on Ultrafast DNA Dynamics: Characterization of a DNA:APE1 Complex
 

Summary:  oligonucleotide at the abasic site opposite the coumarin with only a fourfold reduction in rate. In addition... in binding constant relative to a native oligonucleotide containing a guanine opposite the abasic site. Thus... a fluorescent coumarin group replaces a native base (Fig. 1) (7). An ...

  

Source: Coleman, Robert S. - Department of Chemistry, Ohio State University

 

Collection: Chemistry

 
24 Single-Turnover Analysis of Mutant Human Apurinic/Apyrimidinic Endonuclease, Julie A. Lucas, Yuji Masuda,|, Richard A. O. Bennett,| Nathaniel S. Strauss,,@ and Phyllis R. Strauss*,
 

Summary:  and cleavage of abasic site-containing DNA. Apurinic/apyrimidinic endonuclease (AP endo) is a human enzyme... that is critical to the repair of abasic sites in DNA arising through either base excision repair or oxidative... damage. AP endo recognizes abasic sites in ...

  

Source: Strauss, Phyllis R. - Department of Biology, Northeastern University

 

Collection: Biology and Medicine

 
25 Domain Mapping of Human Apurinic/Apyrimidinic Endonuclease STRUCTURAL AND FUNCTIONAL EVIDENCE FOR A DISORDERED AMINO TERMINUS AND A TIGHT
 

Summary:  , became strikingly less accessible to protease digestion in the presence of abasic site-containing DNA... of the nuclease fold, there must be multiple means by which DNA containing an abasic site associates... in the repair of abasic sites in DNA. These ...

  

Source: Strauss, Phyllis R. - Department of Biology, Northeastern University

 

Collection: Biology and Medicine

 
26 An Overview of Chemical Processes That Damage Cellular DNA: Spontaneous Hydrolysis, Alkylation, and Reactions with Radicals
 

Summary:  Backbone 1749 2.4. Properties of Abasic Sites Arising from Depurination 1749 3. Overview: Common Reactions... ). The oxocarbenium ion undergoes subsequent hydrolysis to yield an abasic site 7 (often referred to as an apurinic... site or AP site). It is calculated that ...

  

Source: Gates, Kent. S. - Departments of Chemistry & Biochemistry, University of Missouri-Columbia

 

Collection: Chemistry

 
27 Investigating the Role of the Little Finger Domain of Y-family DNA Polymerases in Low Fidelity Synthesis and Translesion Replication*
 

Summary:  an abasic site and a thymine-thymine cyclobutane pyrimidine dimer, and predominantly makes base pair... -thymine cyclobutane pyrimidine dimers (CPDs) (15, 18, 19) and abasic sites (15, 20). In contrast, Dbh is a much more... , and bypasses an abasic site with very low ...

  

Source: Ling, Hong - Department of Biochemistry, University of Alberta

 

Collection: Biology and Medicine

 
28 Direct Real Time Observation of Base Flipping by the EcoRI DNA Methyltransferase*
 

Summary:  for the binding of the methyltransferase to DNA containing abasic sites or base analogs incorpo- rated... (purine), or a stable abasic site (spacer)); bot- tom strands, d(CCGCGAATTCCGCC), d(CCGCGAATTCCGCC), and d... active site. The ener- getics and kinetics of base flipping by the EcoRI ...

  

Source: Reich, Norbert O. - Department of Chemistry and Biochemistry, University of California at Santa Barbara

 

Collection: Chemistry ; Biology and Medicine

 
29 Mechanism of Abasic Lesion Bypass Catalyzed by a Y-family DNA Polymerase*S
 

Summary:  at the pause sites. Pre-steady State Kinetic Studies of Abasic Lesion Bypass MARCH 16, 2007·VOLUME 282·NUMBER... until the primer is fully extended. The A-rule intermediates, which possessed an intra- helical AP site... Mechanism of Abasic Lesion Bypass Catalyzed by a Y-family DNA ...

  

Source: Suo, Zucai - Department of Biochemistry, Ohio State University

 

Collection: Biology and Medicine

 
30 Z .Mutation Research 460 2000 201210 www.elsevier.comrlocaterdnarepair
 

Summary:  then expose the target nu- cleotide and cleave the glycosylic bond. The result- ing abasic site is processed... out 1-azaribose abasic nucleotide in the active site of AlkA shows that the 3-methyl- adenine base... , abasic site, base mismatch the probe, Leu125 in AlkA ...

  

Source: Lau, Albert Y. - Department of Biophysics and Biophysical Chemistry, Johns Hopkins University

 

Collection: Biology and Medicine

 
31 DNA Repair 1 (2002) 645659 The S. cerevisiae Mag1 3-methyladenine DNA glycosylase
 

Summary:  of any of several different BER intermediates, including uncleaved abasic sites, single strand breaks... ) pathway by removing damaged bases to create abasic apurinic/apyrimidinic (AP) sites that are subsequently... , BER intermediates (e.g. AP ...

  

Source: Engelward, Bevin - Division of Bioengineering, Massachusetts Institute of Technology (MIT)

 

Collection: Biology and Medicine

 
32 A Core Folding Model for Catalysis by the Hammerhead Ribozyme Accounts for Its Extraordinary Sensitivity to Abasic Mutations
 

Summary:  Sensitivity to Abasic Mutations Alessio Peracchi,,§ Alexander Karpeisky,| Lara Maloney,| Leonid Beigelman... ReceiVed April 17, 1998; ReVised Manuscript ReceiVed August 4, 1998 ABSTRACT: Introducing abasic... and larger ribozymes are described herein. The deleterious effects of the abasic mutations are not relieved

  

Source: Herschlag, Dan - Department of Biochemistry, Stanford University

 

Collection: Biology and Medicine

 
33 DNA polymerases in adaptive immunity Jean-Claude Weill and Claude-Agns Reynaud
 

Summary:  . Effectively, the action of UNG is restricted to uracil excision, giving rise to abasic sites, and... -passing abasic sites, one should expect that inactivation of a polymerase involved in SHM would result... a deoxycytidyltransferase activity that is directed opposite various damaged bases, as well as ...

  

Source: Ecole Polytechnique, Centre de mathématiques

 

Collection: Mathematics

 
34 Engineered Extrahelical Base Destabilization Enhances Sequence Discrimination of DNA Methyltransferase
 

Summary:  is replaced with an abasic site (Table 2). F84A is decreased dramatically in catalysis as well (Table 3, 1000... of Enzyme Intermediates #12;and the flexible loop and the recovery of DNA affinity using abasic DNA further... -GGGAATTCATGG^GCAGTGGGTGGATCCAG-3 3-CCCTTAAGTACCGCMe GTCACCCACCTAGGTC-5 ...

  

Source: Reich, Norbert O. - Department of Chemistry and Biochemistry, University of California at Santa Barbara

 

Collection: Chemistry ; Biology and Medicine

 
35 DEMETER DNA Glycosylase Establishes MEDEA Polycomb Gene Self-Imprinting
 

Summary:  -glycosylic bond, creating an abasic site, whereas the lyase activity nicks the DNA. An AP endonuclease generates... of the phospho- diester bonds (Figure 3A). Cleavage 50 to the abasic site of the b or d elimination produced... , perhaps due to the formation of mutagenic abasic ...

  

Source: Goldberg, Robert B. - Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles

 

Collection: Biology and Medicine

 
36 Forma: A Framework for Safe Automatic Array University of Alberta
 

Summary:  [k].satfield) &(Asati [k].satfield') 7 allocation site: Abase=new(N*E) A=new(N*E) for i [1, SatNum] Asati = Abase... [k].pointeri satfield') 7 allocation site: Abase=new(N*NewE) A=new(N*E) for i [1, SatNum] for j [0, N-1] Abase... in the ...

  

Source: Amaral, José Nelson - Department of Computing Science, University of Alberta

 

Collection: Computer Technologies and Information Sciences

 
37 A Ubiquitin-binding Motif in the Translesion DNA Polymerase Rev1 Mediates Its Essential Functional Interaction with
 

Summary:  and abasic sites (30, 31). This enzyme is primarily respon- sible for inserting dC residues opposite abasic... such on the template that Rev1 has to insert one dCMP opposite a template guanine prior to encountering the abasic site... (Fig. 1A). Remarkably, at 75 mM NaCl Rev1 is ...

  

Source: Burgers, Peter M. - Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis

 

Collection: Biology and Medicine

 
38 Dissociative electron attachment to abasic DNA Sylwia Ptasin ska* and Le on Sanche
 

Summary:  by the presence of an abasic site; in both XCAT and GCXT, the yield of detached bases was found to be up... not depend very much on the presence of an abasic site in GCAT. From a purely classical point of view... of an abasic site. In experiments with 40-base pair ...

  

Source: Simons, Jack - Department of Chemistry, University of Utah

 

Collection: Chemistry

 
39 NIST NCSTAR 1-5D (Draft) Federal Building and Fire Safety Investigation of the
 

Summary:  Study Team went to the site and began their assessment. This was to be a brief effort, as the study team... and the Advisory Committee. NIST maintained a publicly accessible Web site during this Investigation at http... ://wtc.nist.gov. The site contained extensive information on the background and progress of the Investigation. ...

  

Source: National Institute of Standards and Technology (NIST), Ceramics Division

 

Collection: Materials Science

 
40 Chemistry & Biology, Vol. 12, 357369, March, 2005, 2005 Elsevier Ltd All rights reserved. DOI 10.1016/j.chembiol.2004.12.011 Delineation of the Chemical Pathways Underlying
 

Summary:  double-strand breaks by direct reaction with DNA [32, 34, 35]. How- ever, base lesions, abasic sites... breaks, abasic sites, and base lesions induced and effective measure of recombination at a single lo... , abasic sites, and single- strand breaks. To gain a better ...

  

Source: Engelward, Bevin - Division of Bioengineering, Massachusetts Institute of Technology (MIT)

 

Collection: Biology and Medicine


Page:   1  2  3  4  5 
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41 Identification of the Hammerhead Ribozyme Metal Ion Binding Site Responsible for Rescue of the Deleterious Effect of a Cleavage Site Phosphorothioate
 

Summary:  and substrate variants at positions P9, G10.1, and P1.1 (the cleavage site). Abasic and phenyl... of the abasic ribozymes. Presumably, the Cd2+ ion is bound and sequestered at the P9/G10.1 site and occasionally... Identification of the Hammerhead Ribozyme Metal Ion Binding Site ...

  

Source: Herschlag, Dan - Department of Biochemistry, Stanford University

 

Collection: Biology and Medicine

 
42 Base Excision and DNA Binding Activities of Human Alkyladenine DNA Glycosylase Are Sensitive to the Base Paired with a Lesion*
 

Summary:  affinity of human alkylad- enine DNA glycosylase to a DNA product containing an abasic site was similar... , it had no effect when placed opposite G or A. Binding of hAAG 79 to DNA Duplexes Containing Abasic Sites... substrates containing a synthetic abasic site was ...

  

Source: Lau, Albert Y. - Department of Biophysics and Biophysical Chemistry, Johns Hopkins University

 

Collection: Biology and Medicine

 
43 A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli
 

Summary:  pair or an abasic site, we found a small number of proteins that could recognize each type of probe... 7 N = Control A:C mismatch G:T mismatch Abasic site:G Abasic site:A Abasic site:C Abasic ...

  

Source: Chen, Chien-Sheng - Institute of Systems Biology and Bioinformatics, National Central University

 

Collection: Biology and Medicine

 
44 ARTICLE IN PRESS An investigation of the variation in the transition bias among various
 

Summary:  . Oxygen free radicals have at least two mutagenic effects: (i) they generate abasic sites (Schaaper et al... -generation of abasic sites-is expected to affect the ts/tv ratio because DNA polymerases tend to incoporate A opposite... abasic sites; if the ...

  

Source: Eyre-Walker, Adam - Department of Biology and Environmental Science, University of Sussex

 

Collection: Biology and Medicine

 
45 ANRV260-GE39-03 ARI 21 June 2005 22:14 Immunoglobulin Gene
 

Summary:  , abasic endonucleases nick the phosphodi- ester backbone at the abasic site, DNA poly- merase synthesizes... the phosphodiester backbone at the abasic site, and DNA polymerase and ligases repair the gap. AID Deaminates Single... is the fate of the abasic ...

  

Source: Maizels, Nancy - Department of Biochemistry, University of Washington at Seattle

 

Collection: Biology and Medicine

 
46 Oxidative DNA Base Damage by the Antitumor Agent 3-Amino-1,2,4-benzotriazine 1,4-Dioxide (Tirapazamine)
 

Summary:  (endo IV), and abasic sites (exo III and endo IV) into strand breaks (Fig. 1).23,25,26 The base excision... duplex DNA (Fig. 1) and also catalyze subsequent strand clea- vage at the resulting abasic site (Scheme 2... that abasic sites and/or C10 -oxidized ...

  

Source: Gates, Kent. S. - Departments of Chemistry & Biochemistry, University of Missouri-Columbia

 

Collection: Chemistry

 
47 Proliferating Cell Nuclear Antigen Promotes Translesion Synthesis by DNA Polymerase *
 

Summary:  by Pol on undamaged DNA. PCNA also stimulated translesion synthesis of a model abasic site by Pol... experimental conditions, facile by- pass of the abasic site was also detected by DNA polym- erase or (Rad30... Synthesis of a Model Abasic Site--To determine which ...

  

Source: Burgers, Peter M. - Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis

 

Collection: Biology and Medicine

 
48 Homologous recombination prevents methylation-induced toxicity in Escherichia coli
 

Summary:  glycosylases remove methylated bases (filled circle) and the resulting abasic site is recognized and cleaved... formation. (C) Depurination of methylated bases results in the formation of abasic sites which... -endonucleases presumably owing to the pres- ence of abasic ...

  

Source: Engelward, Bevin - Division of Bioengineering, Massachusetts Institute of Technology (MIT)

 

Collection: Biology and Medicine

 
49 This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research
 

Summary:  t Apurinic/apyrimidinic endonuclease 1 (APE1) is a multifunctional enzyme with a well-established abasic DNA... -known transcription factors. APE1 has recently been shown to cleave at the UA, CA, and UG sites of c-myc RNA in vitro... intermediates for several mammalian genes have been described, but the responsible ...

  

Source: Rader, Stephen - Chemistry Program, University of Northern British Columbia

 

Collection: Biology and Medicine ; Chemistry

 
50 BioMed Central Page 1 of 6
 

Summary:  the DNA leaving an abasic site where the strand is nicked at both the 3' and 5' ends [6]. The abasic site... Y [9,10], which excises the mispaired adenine A leaving an abasic site. The abasic site opposite... ...

  

Source: Lunds Universitet, - Computational Biology and Biological Physics Group

 

Collection: Physics ; Biology and Medicine

 
51 The Role of Arg165 Towards Base Flipping, Base Stabilization and Catalysis in M.HhaI
 

Summary:  .46 520 Structural Snapshot of a Base Flipping Intermediate #12;recognized site. Thus, the R165A M... ), intermediate between the South and North conformers. In summary, Arg165 plays significant roles in base... exploit complex structural mechanisms to gain access to the target site of catalysis, including DNA

  

Source: Reich, Norbert O. - Department of Chemistry and Biochemistry, University of California at Santa Barbara

 

Collection: Chemistry ; Biology and Medicine

 
52 Multiple Cleavage Activities of Endonuclease V from Thermotoga maritima: Recognition and Strand Nicking Mechanism
 

Summary:  the uracil base and with AP endonucleases and other enzymes to repair the subsequent abasic site (4, 5... that E. coli endoV plays a significant role in deoxyinosine and abasic site repair (19). More recent... -stranded oligonucleotides containing the abasic site (AP ...

  

Source: Barany, Francis - Biochemistry and Structural Biology Program, Weill Cornell Graduate School of Medical Sciences

 

Collection: Biology and Medicine

 
53 Molecular Cell, Vol. 15, 607620, August 27, 2004, Copyright 2004 by Cell Press The Fanconi Anaemia Gene FANCC Promotes
 

Summary:  approach to identifyenously generated abasic sites. Moreover in these ver- the type of repair defect in FA... for the repair of endogenously generated abasic sites in theseen in human FA cells. FANCC knockout (KO) cells... Lines Have Reduced Templated and Untemplated Changes in Response to Endogenously ...

  

Source: Patel, KJ - Laboratory of Molecular Biology, MRC

 

Collection: Biology and Medicine

 
54 RNA folding and the origins of catalytic activity in the hairpin ribozyme Timothy J. Wilson a
 

Summary:  activity [26], while 10,000-fold loss of activity resulted from an abasic site at position 38 [27... of abasic sites in the core of the hammerhead ribozyme showed that some positions could be rescued while... The nucleolytic ribozymes catalyse site-specific phosphodiester cleavage and ...

  

Source: Ha, Taekjip - Department of Physics, University of Illinois at Urbana-Champaign

 

Collection: Physics ; Chemistry ; Biology and Medicine

 
55 University of Maryland Baltimore Graduate School Announcement of Doctoral Dissertation Defense
 

Summary:  of these damaged bases result in the formation of an abasic or AP site, allowing the next enzyme in the pathway... , Apurinic/Apyrimidinic Endonuclease 1 (APE1), to hydrolytically cleave the DNA backbone 5' to the AP site... binding sites for two redox (another APE1 function) inhibitors of APE1, one of which ...

  

Source: Weber, David J. - Department of Biochemistry and Molecular Biology, University of Maryland-Baltimore

 

Collection: Biology and Medicine

 
56 JOURNAL OF BACTERIOLOGY, July 2002, p. 35013507 Vol. 184, No. 13 0021-9193/02/$04.00 0 DOI: 10.1128/JB.184.13.35013507.2002
 

Summary:  and the deoxyribose, resulting in an abasic (AP) site. Subsequently, AP endonucleases incise the DNA backbone... intermediates (see above). While Fpg can create cleaved AP sites, Ung can create only uncleaved AP sites... abasic sites, rather than ...

  

Source: Engelward, Bevin - Division of Bioengineering, Massachusetts Institute of Technology (MIT)

 

Collection: Biology and Medicine

 
57 A novel function of DNA polymerase f regulated Matthew R Northam1,3
 

Summary:  the catalytic activity of Rev1 normally functions during TLS, particularly during abasic site bypass, Received... of UV-damage, we next investigated bypass of a model abasic site by these enzymes (Figure 5F and G... ). Bypass replication of the abasic site by Pold ...

  

Source: Burgers, Peter M. - Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis

 

Collection: Biology and Medicine

 
58 DNA Damage Induced by Low-Energy Electrons: Electron Transfer and Diffraction Yi Zheng, J. Richard Wagner, and Leon Sanche*
 

Summary:  of GCXTand XCATwhere X represents a stable abasic site in which the base is replaced by a hydrogen atom... of the backbone at sites that are distant from the abasic site (i.e., in the yield functions pCXT, Gp, p... , the 10 eV resonance at sites 8 and 9 associated ...

  

Source: Simons, Jack - Department of Chemistry, University of Utah

 

Collection: Chemistry

 
59 DNA base excision repair activities and pathway function in mitochondrial and cellular lysates from
 

Summary:  , followed by abasic site processing, gap-®lling and ligation of the DNA strand. Mammalian mitochondria... endonuclease IV, to ensure complete cleavage of abasic sites. Reactions were terminated by addition of 20 ml... - stranded, containing an 8-oxodG; THF = double-stranded, containing a THF ...

  

Source: Stuart, Jeffrey A. - Department of Biological Sciences, Brock University

 

Collection: Biology and Medicine

 
60 Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis
 

Summary:  in the active site is near-native. When tested with an abasic or CPD lesions, the effects of Mn2 þ on relaxing... extension. Bypass of (C) a synthetic abasic site and (D) a cis-syn CPD. (E) Terminal nucleotidyl transferase... incoming nucleotide with its preformed and open active site. ...

  

Source: Ling, Hong - Department of Biochemistry, University of Alberta

 

Collection: Biology and Medicine


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61 Genome Biology 2004, 5:211 commentreviewsreportsdepositedresearchinteractionsinformationrefereedresearch
 

Summary:  removes U, leaving an abasic site. Subsequent steps generate single-strand breaks [17], which become... endonucleases to nick the abasic site so that new DNA synthe- sis can recreate the duplex [6]. Reasoning... , and that uracil-DNA glyco- sylase removes U to produce an abasic ...

  

Source: Maizels, Nancy - Department of Biochemistry, University of Washington at Seattle

 

Collection: Biology and Medicine

 
62 Role of the Arabidopsis DNA glycosylase lyase ROS1 in active DNA demethylation
 

Summary:  - and -elimination reactions at the abasic site, after it removes the methylated cytosine base. A weak cleavage... activity then nicks the DNA backbone at the abasic site. Our results suggest that this lyase activity... removes the deoxyribose from the nicked abasic ...

  

Source: Zhu, Jian-Kang - Institute for Integrated Genome Biology, University of California at Riverside

 

Collection: Biotechnology

 
63 ALGEBRAIC L-T}~0RY III. TWISTED LAUREI~ EXTENSIONS
 

Summary:  element, of order 2. Here, we shall generalize I. by considering the intermediate 1UTn(A) If-g-proj ective... ~(~)). It is Cappell (in [I~) who first used the intermediate L-theories. I am grateful to Professor C... .ToC.Wall for sending a preprint to [IO~ (which contains an earlier account of the intermediate L

  

Source: Ranicki, Andrew - School of Mathematics, University of Edinburgh

 

Collection: Mathematics

 
64 New Concepts in Biochemistry Deoxyribose Phosphate Excision by the N-Terminal Domain of the Polymerase
 

Summary:  tripeptide of the sequence Lys-Trp(Tyr)-Lys can promote -elimination at an aldehydic abasic site in DNA... an activity for excising a 5-deoxyribose phosphate (dRP) group from preincised apurine/apyrimidine (AP) sites... model shows that the dRP group of the AP site can be stabilized in the catalytic groove ...

  

Source: Crasto, Chiquito - Department of Genetics, University of Alabama at Birmingham

 

Collection: Biology and Medicine

 
65 Molecular dynamics of B DNA Supplementary Animations
 

Summary:  entirely out of the double helical stack, thereby eliminating the (A·T)13 base pair and forming an abasic... and TTCC B half sites which together comprise the nonameric 5' AGAANTTCC3' DNA recognition element for (c

  

Source: Mura, Cameron - Department of Chemistry, University of Virginia

 

Collection: Chemistry

 
66 Formal Verification of Control Software: A Case Study
 

Summary:  to be halted while a technician travels to the site to repair the problem. The design of concurrent software... with a set of properties to Java. #12;1 SEQUENCE Handling 2 3 STEP A.Base_0: 4 Hold1.Base(); 5 Hold2.Base... (); 6 NEXT_STEP; 7 8 9 STEP A.Base_1: 10 IF Hold1.InBase() AND 11 Hold2.InBase() THEN 12 Vert.Work(); 13

  

Source: Technische Universität Graz, Institute for Software Technology

 

Collection: Computer Technologies and Information Sciences

 
67 NATURE BIOTECHNOLOGY VOL 17 JULY 1999 http://biotech.nature.com 639 When Cinderella disappeared in great haste
 

Summary:  . In their experiments, a comparison was made between incorporation efficien- cies of pyrene opposite the abasic site... -pair analog consisting of pyrene opposite an abasic site in B-form geometry (Courtesy E.T. Kool). © 1999... a template site lacking a base. This study can be viewed as ...

  

Source: Gray, Jeffrey J. - Department of Biomolecular and Chemical Engineering, Johns Hopkins University; Ostermeier, Marc - Department of Biomolecular and Chemical Engineering, Johns Hopkins University

 

Collection: Biology and Medicine ; Biotechnology ; Chemistry

 
68 Retrofitting the AutoBayes Program Synthesis System with Concrete Syntax
 

Summary:  #12;intermediate code AutoBayes model specification C / C++ code Test-data Generator Rewriting Engine... Systemutilities model gauss as '2D Gauss-Model for Nebula Analysis' intermediate code internal representation Fig... .e., template) and a set of con- straints. Code fragments are written in ABIR (AUTOBAYES Intermediate ...

  

Source: Utrecht, Universiteit - Department of Information and Computing Sciences

 

Collection: Computer Technologies and Information Sciences

 
69 Two distinct modes of RecA action are required for DNA polymerase V-catalyzed translesion synthesis
 

Summary:  in nucleotide incor- poration either directly opposite a lesion or at undamaged tem- plate sites... , and subsequently at a site immediately downstream of the lesion, where RecA mode 2 cocatalyzes lesion bypass. We... to a site of DNA damage and to stabilize the pol V-RecA interaction at the lesion. However, it is only a Rec

  

Source: Cox, Michael M. - Department of Biochemistry, University of Wisconsin at Madison

 

Collection: Biology and Medicine

 
70 Coumarin base-pair replacement as a fluorescent probe of ultrafast DNA dynamics
 

Summary:  was covalently attached in silico via C4 to the C10 position of an opposed abasic-site tetrahydro- furan analog... Figure 1. Structure of photoprobe Coumarin 102. O O O O O O NOO -C-glycoside abasic site 4 1 Figure 2... . Coumarin C-glycoside/abasic-site tetrahydrofuran. 3451R. S. Coleman et al. / Tetrahedron ...

  

Source: Coleman, Robert S. - Department of Chemistry, Ohio State University

 

Collection: Chemistry

 
71 Supporting On-line Materials Conformational Analysis of DNA Repair Intermediates by
 

Summary:  EL, et al. (2001) Conformation and dynamics of abasic sites in DNA investigated by time... 1 Supporting On-line Materials Conformational Analysis of DNA Repair Intermediates by Time

  

Source: Szostak, Jack W. - Department of Genetics, Harvard University

 

Collection: Environmental Sciences and Ecology ; Biology and Medicine

 
72 Comparison of the hammerhead cleavage reactions stimulated by monovalent
 

Summary:  - nisms+ Thirteen derivatives of HH16 containing single abasic sites throughout the catalytic core... are described by acronyms analogous to protein mutations; e+g+, C3X refers to a ribozyme with an abasic residue... Sribosomalsubunithasrevealedthattherearenopro- tein residues in the vicinity of the peptidyl transfer active ...

  

Source: Herschlag, Dan - Department of Biochemistry, Stanford University

 

Collection: Biology and Medicine

 
73 In vivo Recombination After Chronic Damage Exposure Falls to Below Spontaneous Levels in ``Recombomice''
 

Summary:  established that conditions that result in increased levels of BER intermediates, such as abasic sites... of recombinogenic strand breaks and abasic sites. As a first step toward revealing the molecular basis... #12;yield abasic sites that are ...

  

Source: Engelward, Bevin - Division of Bioengineering, Massachusetts Institute of Technology (MIT)

 

Collection: Biology and Medicine

 
74 AID in antibody perfection A.C. Vallura
 

Summary:  an abasic site intermediate generated by excision of the uracil produced by AID-mediated deoxycytidine deam... an abasic site for further repair. Neuberger and colleagues reasoned that if AID deaminates DNA directly... opposite U, at abasic ...

  

Source: Maizels, Nancy - Department of Biochemistry, University of Washington at Seattle

 

Collection: Biology and Medicine

 
75 The Coupling of Tight DNA Binding and Base Flipping IDENTIFICATION OF A CONSERVED STRUCTURAL MOTIF IN BASE FLIPPING ENZYMES*
 

Summary:  for the binary structure with AdoMet and the tertiary structure with an abasic target site (see red and black... -crystal structure of the cognate cytosine target site (3MHT) and the abasic target site (9MHT), and this net... 3 Ala mutant and the tight binding of ...

  

Source: Reich, Norbert O. - Department of Chemistry and Biochemistry, University of California at Santa Barbara

 

Collection: Chemistry ; Biology and Medicine

 
76 2000 Macmillan Magazines Ltd letters to nature
 

Summary:  abasic site analogs and site-directed mutagenesis. J. Mol. Biol. 290, 447±457 (1999). 13. Izumi, T. et al... . & Grollman, A. P. Oligodeoxynucleotides containing synthetic abasic sites. Model substrates for DNA... , J. P., Barsky, D., Scharer, O. D., Colvin, M. E. & Wilson, D. M. ...

  

Source: Engelman, Donald M.- Department of Molecular Biophysics and Biochemistry, Yale University

 

Collection: Biology and Medicine

 
77 Optimiza.tion Shtegics for Spatial Query Processing* Walid G. href
 

Summary:  al11101)- timizat,ion techniques in the conl ext. of an in t.egril.t fvl spatial dat,abase... is stored in sepi3rat.e spalial da1.a st-ructures and their non-spat#ial inrormation is stored in dat.abase... to the DBMS for efficient handling of complex objects. At the intermediate level, new ways for mapping the ext

  

Source: Samet, Hanan - Institute for Advanced Computer Studies & Department of Computer Science, University of Maryland at College Park

 

Collection: Computer Technologies and Information Sciences

 
78 Measurement of Local DNA Reorganization on the Picosecond and Nanosecond Time Scales
 

Summary:  in the Experimental Section) shows that when it is positioned opposite the abasic-site analogue 2 in helical B... and abasic-site analogue 2 that form a base-pair analogue with good photophysical properties. Measurement... strand has the abasic site 2 complementary to the fluorophore. Scheme 1 Scheme 2 11646 ...

  

Source: Coleman, Robert S. - Department of Chemistry, Ohio State University

 

Collection: Chemistry

 
79 Conformational Analysis of DNA Repair Intermediates by Time-Resolved Fluorescence Spectroscopy
 

Summary:  Conformational Analysis of DNA Repair Intermediates by Time-Resolved Fluorescence Spectroscopy Su... to adopt multiple individual conformations. We show that DNA repair intermediates that contain a one... and dynamics of abasic lesions and single-base mismatches,3 no systematic analysis of other DNA repair

  

Source: Szostak, Jack W. - Department of Genetics, Harvard University

 

Collection: Environmental Sciences and Ecology ; Biology and Medicine

 
80 Proteinnucleic acid interactions: unlocking mysteries old and new
 

Summary:  generated abasic sites -- derived from the recent structures of T7 and RB69 DNA polymerases in complex... at a single origin site through binding of the DnaA initiator protein to several repetitive, non... to its DNA target site reveal two different mechanisms by which cells control replication initiation

  

Source: Doudna, Jennifer A. - Department of Molecular and Cell Biology, University of California at Berkeley

 

Collection: Biology and Medicine


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81 Water in the Active Site of an All-RNA Hairpin Ribozyme and Effects of Gua8 Base Variants on the Geometry of Phosphoryl Transfer,
 

Summary:  Water in the Active Site of an All-RNA Hairpin Ribozyme and Effects of Gua8 Base Variants... that contribute to catalysis within the hairpin ribozyme active site, structures for five base variants were... members catalyze a reversible, site-specific phosphodiester bond cleavage reaction within a complementary

  

Source: Wedekind, Joseph E. - Department of Biochemistry and Biophysics, University of Rochester

 

Collection: Biology and Medicine

 
82 Sodium-Ion Binding to DNA: Detection by Ultrafast Time-Resolved Stokes-Shift Spectroscopy
 

Summary:  ) coumarin, which is paired with an abasic-site analogue in the complement.) We have reported results... ions is unresolved, as is the exact position of the important binding sites. Do ions bind in the minor... prevent close approach of the TBA to sites on the DNA. It is reasonable to regard these strong specific

  

Source: Coleman, Robert S. - Department of Chemistry, Ohio State University

 

Collection: Chemistry

 
83 1468 VOLUME 29J O U R N A L O F P H Y S I C A L O C E A N O G R A P H Y 1999 American Meteorological Society
 

Summary:  , a site (50 N, 145 W in the Pacific Ocean) where advection is comparatively weak (Gill and Niiler 1973... reaches a max- imum magnitude for some intermediate density with a large isopycnal area. The gradient... - integrated entrainment flux D ( ) w [ (x) ] dA. (20)ent e A base Here Abase {x : m(x) (x)} is the area where

  

Source: Williams, Ric - Department of Earth Sciences, University of Liverpool

 

Collection: Geosciences ; Environmental Sciences and Ecology

 
84 Berkeley Lab Accident Statistics Through April 30, 2009
 

Summary:  09 #12;8 Berkeley Lab Site-Wide TRC & DART Rates (Includes all Construction and Service Contractors... Berkeley Lab Site Accident Rates 5.70 4.95 3.79 2.92 2. 93 3.27 3.63 2.44 2.17 2.51 1.17 1.81 1.28 1.65 1... Fiscal Year Casesper200,000hoursworked Site Total Recordable Case Rate Site DART (Days Away, ...

  

Source: Lawrence Berkeley National Laboratory, High Redshift Supernova Search

 

Collection: Physics

 
85 Berkeley Lab Accident Statistics Through September 30, 2009
 

Summary:  Lab Site-Wide TRC & DART Rates (Includes all Construction and Service Contractors) Through September... , Restricted or Transferred) TRC Goal DART Goal 1.17 #12;8 LBNL vs DOE Contractor Rates Berkeley Lab Site... ,000hoursworked Site Total Recordable Case Rate Site DART (Days Away, Restricted, Transferred) ...

  

Source: Lawrence Berkeley National Laboratory, High Redshift Supernova Search

 

Collection: Physics

 
86 Berkeley Lab Accident Statistics Through March 31, 2009
 

Summary:  09 #12;9 Berkeley Lab Site-Wide TRC & DART Rates (Includes all Construction and Service Contractors... Berkeley Lab Site Accident Rates 5.70 4.95 3.79 2.92 2. 93 3.27 3.63 2.44 2.17 2.51 1.17 1.81 1.28 1.65 1... Fiscal Year Casesper200,000hoursworked Site Total Recordable Case Rate Site DART (Days Away, ...

  

Source: Lawrence Berkeley National Laboratory, High Redshift Supernova Search

 

Collection: Physics

 
87 TheElectronMicroscopyCore(EMC) UniversityofMissouriColumbia,MO65211
 

Summary:  OptimizingFESEMandEDSPerformance (BasictoAdvanced) CourseDates:TuesdayMarch29­FridayApril1,2011 TuesdayMarch29 900to1030 LectureABasic... 1030 LectureIntermediateScanningElectronMicroscopy 1030to1100 Coffee 1100to1230 Intermediate

  

Source: Noble, James S. - Department of Industrial and Manufacturing Systems Engineering, University of Missouri-Columbia

 

Collection: Engineering

 
88 JOURNAL OF BACTERIOLOGY, 0021-9193/01/$04.00 0 DOI: 10.1128/JB.183.1.131138.2001
 

Summary:  of abasic sites is critical for defense against NO. In addition, recA mutant cells were exquisitely... /apurinic (AP) endonucleases at the abasic site. This results in a 3 -OH terminus, which can act as a primer... - nates, with a half-life of 4 h, to form abasic sites ...

  

Source: Engelward, Bevin - Division of Bioengineering, Massachusetts Institute of Technology (MIT)

 

Collection: Biology and Medicine

 
89 Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2
 

Summary:  of 10-3 to 10-4 when synthesizing undamaged DNA and can traverse various lesions, such as abasic sites... - plex with an abasic site (Ling et al. 2004a). While recent pre-steady-state kinetic data (Fiala and Suo... of Dpo4 with DNA and incoming nucleotide ddATP opposite an abasic ...

  

Source: Schlick, Tamar - Department of Chemistry, New York University

 

Collection: Chemistry

 
90 Molecular basis for discriminating between normal and damaged bases by the human alkyladenine
 

Summary:  be distinguished from normal DNA bases in the enzyme active site. Mutational analyses of residues contacting... , and the resulting abasic nucleotide is excised and replaced with a normal nucleotide by the sequential action... , the pyrrolidine abasic nucleotide (pyr; PDB ID code 1bnk; refs. 15 and 16). In the AAG pyr-DNA complex, ...

  

Source: Lau, Albert Y. - Department of Biophysics and Biophysical Chemistry, Johns Hopkins University

 

Collection: Biology and Medicine

 
91 Nucleic Acids Research doi:10.1093/nar/gkn309
 

Summary:  into undamaged DNA (35,36) and (ii) the mechanistic basis of Dpo4 bypassing an abasic site, which is a prototype... , the significant accumulation of intermediate products revealed two distinct pause sites (23- and 24-mers... ' pause sites were observable in the running start assay as a ...

  

Source: Suo, Zucai - Department of Biochemistry, Ohio State University

 

Collection: Biology and Medicine

 
92 Enzyme-Activated, Hypoxia-Selective DNA Damage by 3-Amino-2-quinoxalinecarbonitrile 1,4-Di-N-oxide
 

Summary:  and catalyzes strand cleavage at the result- ing abasic site (31-33). We find that treatment of the damaged DNA... of the damaged DNA with the enzyme endo IV, which catalyzes strand cleavage at abasic sites and oxidized abasic... to excision of oxidized base lesions and not the enzyme's ...

  

Source: Gates, Kent. S. - Departments of Chemistry & Biochemistry, University of Missouri-Columbia

 

Collection: Chemistry

 
93 A Base Change in the Catalytic Core of the Hairpin Ribozyme Perturbs Function but Not Domain Docking
 

Summary:  Institute. 1 Abbreviations: ab, abasic site with 2-deoxyribose; AP, 2-ami- nopurine; dT, deoxythymidine... (Table 1). When converting the +2 position into an abasic site with a 2-deoxyribose (ab), however, the 8... values to 10% or less. b dT ) 2-deoxythymidine; ab ) abasic ...

  

Source: Walter, Nils G. - Department of Chemistry, University of Michigan

 

Collection: Chemistry ; Biotechnology ; Biology and Medicine

 
94 Nucleobase catalysis in ribozyme mechanism Philip C Bevilacqua1,2
 

Summary:  . In addition, the structure revealed four ordered waters in the active site of the pre-cleavage state... , and are therefore better able to accommodate charge development and avoid unstable intermediates... flanking the cleavage site stack on two guanosines, G8 and G12, in a transient conformation

  

Source: Bevilacqua, Philip C.- Department of Chemistry, Pennsylvania State University

 

Collection: Chemistry

 
95 Power-Law Solvation Dynamics in DNA over Six Decades in Time Daniele Andreatta, J. Louis Perez Lustres, Sergey A. Kovalenko, Nikolaus P. Ernsting,*,
 

Summary:  complement (abasic site analogue opposite coumarin) in pH 7, 100 mM sodium phosphate buffer. Figure 1 shows... with the complex DNA structure surrounding the reaction site. Charge transfer between DNA bases is one example... , extrapolation - dotted): red - logarithmic fit at long times;13 green - biexponential fit at ...

  

Source: Coleman, Robert S. - Department of Chemistry, Ohio State University

 

Collection: Chemistry

 
96 Single cell trapping and DNA damage analysis using microwell arrays
 

Summary:  be detected when converted to abasic sites or single strand breaks with the addition of purified DNA repair... molecules, the findings agree well with the observa- tion of abasic site accumulation by Simeonov et al. (43... - sylase, and APE1 cleaves the backbone 5 to the resulting abasic ...

  

Source: Bhatia, Sangeeta - Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT)

 

Collection: Biotechnology ; Biology and Medicine

 
97 Single cell trapping and DNA damage analysis using microwell arrays
 

Summary:  be detected when converted to abasic sites or single strand breaks with the addition of purified DNA repair... is removed by a monofunctional glyco- sylase, and APE1 cleaves the backbone 5 to the resulting abasic site... ), as well as alkali sensitive sites. Although most base lesions are ...

  

Source: Engelward, Bevin - Division of Bioengineering, Massachusetts Institute of Technology (MIT)

 

Collection: Biology and Medicine

 
98 Mitochondrial and nuclear DNA base excision repair are affected differently by caloric restriction1
 

Summary:  at a defined position in the oligonucleotide), processing of the abasic site, incorporation of the new... ) and processing of the resulting abasic site by AP endonuclease. These activities were measured as percent... of oligonucleotide containing the lesion of interest at a defined site ...

  

Source: Stuart, Jeffrey A. - Department of Biological Sciences, Brock University

 

Collection: Biology and Medicine

 
99 Using the PAC-Amodeus Model and Design Patterns to Make Interactive an Existing Object-Oriented Kernel
 

Summary:  is achieved by using the PAC-Amodeus model and extending the existing objects to create intermediate... methods, it is this way we implement here the "Template Method" pattern, · ABasic, AErratic, ASniffer... the CBug interface and they extend respectively ABasic, AErratic, AS- niffer, AHungry, ALong

  

Source: Ecole Polytechnique, Centre de mathématiques

 

Collection: Mathematics

 
100 DNA Bending by EcoRI DNA Methyltransferase Accelerates Base Flipping but Compromises Specificity*
 

Summary:  for the binding of H235N M.EcoRI to DNA containing base analogs or an abasic site incorporated at the target base... determined for the binding of H235N M.EcoRI to DNA containing an abasic site or function- ally modified... kinetic studies overlook any conformational intermediates. We ...

  

Source: Reich, Norbert O. - Department of Chemistry and Biochemistry, University of California at Santa Barbara

 

Collection: Chemistry ; Biology and Medicine


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