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Purine-Derived Nitroxides for Noncovalent Spin-Labeling of Abasic Sites in Duplex Nucleic Acids

Nilesh R. Kamble, Snorri Th. Sigurdsson
2018 Chemistry - A European Journal  
Adenine-derived spin label 28 was also bound fully at low temperature (-30 °C) to abasic sites in both DNA and RNA duplexes when paired with T and U, respectively, but showed only minor binding at 20 °  ...  Our approach is based on ligand-receptor interactions, where the spin label binds to an abasic site of nucleic acids through formation of Watson-Crick base pairing with an orphan base on the opposing strand  ...  Acknowledgements First of all, I would like to express my deep sense of thanks and gratitude to my PhD supervisor Prof.  ... 
doi:10.1002/chem.201705410 pmid:29451325 fatcat:4hz32ufa2jd35m56qpylkztwhm

The Role of Active-Site Residues Phe98, His239, and Arg243 in DNA Binding and in the Catalysis of Human Uracil–DNA Glycosylase SMUG1

Danila A. Iakovlev, Irina V. Alekseeva, Yury N. Vorobjev, Nikita A. Kuznetsov, Olga S. Fedorova
2019 Molecules  
It was shown that substitutions F98W and H239A disrupt specific contacts generated by the respective wild-type residues, namely stacking with a flipped out Ura base in the damaged base-binding pocket or  ...  electrostatic interactions with DNA in cases of Phe98 and His239, respectively.  ...  The interactions of WT hSMUG1 or of the mutants with DNA duplexes containing an Ura base or a stable abasic-site analog [(2R,3S)-2-(hydroxymethyl)-3-hydroxytetrahydrofuran: F-site] were recorded by means  ... 
doi:10.3390/molecules24173133 pmid:31466351 pmcid:PMC6749576 fatcat:i2xi2nd3dbdv5k6fvhw2pn4enu

Energy Landscapes of Dynamic Ensembles of Rolling Triplet Repeat Bulge Loops: Implications for DNA Expansion Associated with Disease States

Jens Völker, Vera Gindikin, Horst H. Klump, G. Eric Plum, Kenneth J. Breslauer
2012 Journal of the American Chemical Society  
We further demonstrate that destabilizing abasic lesions alter the loop distributions so as to favor "rollamers" with the lesion positioned at the duplex/loop junction, sites where the flexibility of the  ...  Another strategic siting of an abasic site induces directed loop migration toward denaturing domains, a phenomenon that merges destabilizing domains.  ...  This interpretation is consistent with the impact of additional unpaired bases and abasic sites in three-way junctions. 107 Activation Energy for Loop Migration.  ... 
doi:10.1021/ja3010896 pmid:22397401 pmcid:PMC3318849 fatcat:lwfp6roktng57ky24a7usow35q

Interactions of non-polar and "Click-able" nucleotides in the confines of a DNA polymerase active site

Samra Obeid, Holger Bußkamp, Wolfgang Welte, Kay Diederichs, Andreas Marx
2012 Chemical Communications  
However, the small free energy barriers between machted and mismachted base pairs showed that the selectivity of DNA polymerases depends not primarily on hydrogen bonding capability.  ...  --binary) To investigate the incorporation of dCMP opposite an abasic site KlenTaq was crystallized in the presence of a DNA duplex containing an abasic site analog F and ddCTP.  ... 
doi:10.1039/c2cc34181f pmid:22766607 fatcat:5baeagt4yrf2pmxjtqvxud2eua

Thermodynamics of the multi-stage DNA lesion recognition and repair by formamidopyrimidine-DNA glycosylase using pyrrolocytosine fluorescence—stopped-flow pre-steady-state kinetics

Nikita A. Kuznetsov, Yuri N. Vorobjev, Lev N. Krasnoperov, Olga S. Fedorova
2012 Nucleic Acids Research  
abasic site analog) and non-specific (G) DNA-ligand based on stopped-flow kinetic data.  ...  Formamidopyrimidine-DNA glycosylase, Fpg protein from Escherichia coli, initiates base excision repair in DNA by removing a wide variety of oxidized lesions.  ...  The 'melting' of DNA structure was shown in our previous work using undamaged duplex with 2-aPu residue (17) .  ... 
doi:10.1093/nar/gks423 pmid:22584623 pmcid:PMC3424566 fatcat:2hoshilaevfvtau4nr5fjtffj4

5-Formyluracil-Induced Perturbations of DNA Function†

Daniel K. Rogstad, Jiyoung Heo, Nagarajan Vaidehi, William A. Goddard, Artur Burdzy, Lawrence C. Sowers
2004 Biochemistry  
with adenine lies in the plane of the pyrimidine base and is well protected from solvent on one face and only partially accessible on the other.  ...  Oxidation of the thymine methyl group can generate 5-formyluracil (FoU), which is known to be both mutagenic and chemically unstable in DNA.  ...  Wet gels were wrapped in plastic and exposed on a phosphor screen, and the radioactivity was visualized by use of a PhosphorImager (Molecular Dynamics).  ... 
doi:10.1021/bi030247j pmid:15134443 fatcat:lvihums3rzh4vhtxtruwaudama

Synthesis, characterization and solution structure of tethered oligonucleotides containing an internal 3'-phosphoglycolate, 5'-phosphate gapped lesion

H.-D. Junker
2002 Nucleic Acids Research  
Duplex DNAs (13mers containing tethered hexaethylene glycol linkers) with GTAC and GGCC cleavage sites have been synthesized in which gaps containing 3¢-PG and 5¢-P ends at the sites of BLM cleavage have  ...  The studies reveal that the lesioned DNAs are B-form and the 3¢-PG and 5¢-P are extrahelical. The base opposite the gap and the base pairs adjacent to the gap remain well stacked in the DNA duplex.  ...  Alternatively, under low O 2 tensions, a 4¢-ketoabasic site with an intact DNA strand and a free nucleic acid base results (2±4).  ... 
doi:10.1093/nar/gkf681 pmid:12490718 pmcid:PMC140059 fatcat:z42ux5wa4feepjlh6wq2osb7om

Thermodynamics of the DNA Damage Repair Steps of Human 8-Oxoguanine DNA Glycosylase

Nikita A. Kuznetsov, Alexandra A. Kuznetsova, Yuri N. Vorobjev, Lev N. Krasnoperov, Olga S. Fedorova, Fenfei Leng
2014 PLoS ONE  
In this study a thermodynamic analysis of the interaction of hOGG1 with specific and nonspecific DNA-substrates is performed based on stopped-flow kinetic data.  ...  The three steps which are accompanied with changes in the DNA conformations were detected via 2-aminopurine fluorescence in the process of binding and recognition of damaged oxoG base by hOGG1.  ...  Alexander A. Ishchenko and Dr. Murat K. Saparbaev, Groupe «Réparation de l'ADN», Université Paris-Sud XI, UMR8200 CNRS, Institute Gustave Roussy, Villejuif Cedex F-94805, France, for  ... 
doi:10.1371/journal.pone.0098495 pmid:24911585 pmcid:PMC4049573 fatcat:kev5avmcnnbrboi2jtwhi7qhl4

Multidisciplinary Experimental Approaches to Characterizing Biomolecular Dynamics

Floyd E. Romesberg
2003 ChemBioChem  
The accommodation of the model base pair within a native-like duplex was also supported by molecular dynamics simulations, which indicated that HBO packs within duplex DNA with the phototautomerizable  ...  The duplex was virtually as stable to thermal denaturation as the corresponding duplex with a dA:dT base pair (melting temperatures, T m 38 and 39 8C, respectively).  ... 
doi:10.1002/cbic.200300572 pmid:12851924 fatcat:niyt3laa4bbfrmk63pupycx6k4

Energetic signatures of single base bulges: thermodynamic consequences and biological implications

Conceição A. S. A. Minetti, David P. Remeta, Rian Dickstein, Kenneth J. Breslauer
2009 Nucleic Acids Research  
Conversely, strongly destabilized duplexes melt in a non-twostate manner and exhibit ""G Bulge values consistent with perturbations exceeding nearest-neighbor expectations that are enthalpic in origin.  ...  Calorimetric and spectroscopic characterizations of defectcontaining duplexes reveal systematic patterns of sequence-context dependent bulge-induced destabilizations.  ...  We previously have used this 'reference' duplex to systematically characterize the thermodynamic impacts of a range of adducts/lesions, including abasic sites (32, 42, 44) , exocyclic guanine (41) ,  ... 
doi:10.1093/nar/gkp1036 pmid:19946018 pmcid:PMC2800203 fatcat:2ukbv32hdzf7pnpxn574murxqa

Cleavage of DNA without loss of genetic information by incorporation of a disaccharide nucleoside

K. Nauwelaerts
2003 Nucleic Acids Research  
A ribose residue inserted between the 3¢-OH of one nucleotide and the 5¢-phosphate group of the next nucleotide, functions as a site-speci®c cleavage site within DNA.  ...  As a result of this, an intact natural oligodeoxynucleotide is obtained after ligation reaction, which means that site-speci®c cleavage and recovering of intact DNA occurs without loss of genetic information  ...  K.N. is a research assistant of the FWO and E.L. is a postdoctoral fellow of the FWO. K.V. and V.K. are recipients of an IWT fellowship.  ... 
doi:10.1093/nar/gkg911 pmid:14627809 pmcid:PMC290278 fatcat:bj25do7bafa45jsrn4j2j67q2a

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

Sobhan Sen, Nicole A. Paraggio, Latha A. Gearheart, Ellen E. Connor, Ala Issa, Robert S. Coleman, David M. Wilson, Michael D. Wyatt, Mark A. Berg
2005 Biophysical Journal  
This result is consistent with modeling, which shows that the complex accommodates coumarin at the site of the orphaned base with little distortion of the native structure.  ...  Thus, the modified oligonucleotide retains substantial biological activity and serves as a useful model of native DNA.  ...  We thank Leslie Lovelace and Dr. Salvatore Profeta for help with the modeling, and Joseph Stember for the fluorescence quenching data.  ... 
doi:10.1529/biophysj.105.062695 pmid:16199493 pmcid:PMC1366978 fatcat:2nxpsbucqncfxbgdjrut57ywbe

Structure and Stability of Duplex DNA Containing (5′S)-5′,8-Cyclo-2′-deoxyadenosine: An Oxidatively Generated Lesion Repaired by NER

Tatiana Zaliznyak, Mark Lukin, Carlos de los Santos
2012 Chemical Research in Toxicology  
Using solution state NMR spectroscopy and restrained molecular dynamics simulations, we have determined the structure of an undecameric DNA duplex having a centrally located (5'S)-5',8-cyclo-2'-deoxyadenosine  ...  The S-cdA•T duplex structure shows many similarities and some intriguing differences with the recently reported structure of an S-cdG•dC duplex 31 that suggest different lesion site dynamics.  ...  Herein, we describe the NMR characterization, thermodynamic parameters and restrained molecular dynamics (rMD) structure of an undecameric DNA duplex having a centrally located S-cdA•T base-pair.  ... 
doi:10.1021/tx300193k pmid:22928555 pmcid:PMC3472033 fatcat:amncgic74zcy5oj4szqj2fccba

Mechanisms of Base Selection by theEscherichia coliMispaired Uracil Glycosylase

Pingfang Liu, Jacob A. Theruvathu, Agus Darwanto, Victoria Valinluck Lao, Tod Pascal, William Goddard, Lawrence C. Sowers
2008 Journal of Biological Chemistry  
The relative rates of glycosylase cleavage have been correlated with the free energy of helix formation and with the size and electronic inductive properties of a series of uracil 5-substituents.  ...  A series of parameters have been obtained that allow prediction of relative MUG cleavage rates that correlate well with observed relative rates that vary over 5 orders of magnitude for the series of base  ...  Cleaved DNA fragments were separated from intact DNA by 20% denaturing polyacrylamide gels (8 M urea), and subsequently quantified using a PhosphorImager (Molecular Dynamics, Sunnyvale, CA) and ImageQuant  ... 
doi:10.1074/jbc.m707174200 pmid:18208817 pmcid:PMC2276368 fatcat:rfenhsnx7bawvd7ey7ixpxmwsi

Enthalpy−Entropy Contribution to Carcinogen-Induced DNA Conformational Heterogeneity

Fengting Liang, Bongsup P. Cho
2010 Biochemistry  
In contrast, FAF stacks better and exists as a mixture of B and S conformers, thus contributing to large enthalpy (ΔΔH 13.4 kcal/mol)/entropy (ΔΔS 34.2 eu) compensation. van't Hoff analysis of dynamic  ...  DNA damage by adduct formation is a critical step for the initiation of carcinogenesis. Aromatic amines are strong inducers of environmental carcinogenesis.  ...  The molecular contacts between lesion bound-DNA and nearby amino acid residues, such as those in the active site of a polymerase or a repair protein, can also alter the conformational dynamics at the lesion  ... 
doi:10.1021/bi901629p pmid:19961237 pmcid:PMC2805757 fatcat:3vvuxwj4evbjvf64p33ejqh7ui
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