1
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Ashwood B, Jones MS, Lee Y, Sachleben JR, Ferguson AL, Tokmakoff A. Molecular insight into how the position of an abasic site modifies DNA duplex stability and dynamics. Biophys J 2024; 123:118-133. [PMID: 38006207 PMCID: PMC10808028 DOI: 10.1016/j.bpj.2023.11.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/19/2023] [Accepted: 11/22/2023] [Indexed: 11/26/2023] Open
Abstract
Local perturbations to DNA base-pairing stability from lesions and chemical modifications can alter the stability and dynamics of an entire oligonucleotide. End effects may cause the position of a disruption within a short duplex to influence duplex stability and structural dynamics, yet this aspect of nucleic acid modifications is often overlooked. We investigate how the position of an abasic site (AP site) impacts the stability and dynamics of short DNA duplexes. Using a combination of steady-state and time-resolved spectroscopy and molecular dynamics simulations, we unravel an interplay between AP-site position and nucleobase sequence that controls energetic and dynamic disruption to the duplex. The duplex is disrupted into two segments by an entropic barrier for base-pairing on each side of the AP site. The barrier induces fraying of the short segment when an AP site is near the termini. Shifting the AP site inward promotes a transition from short-segment fraying to fully encompassing the barrier into the thermodynamics of hybridization, leading to further destabilization of the duplex. Nucleobase sequence determines the length scale for this transition by tuning the barrier height and base-pair stability of the short segment, and certain sequences enable out-of-register base-pairing to minimize the barrier height.
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Affiliation(s)
- Brennan Ashwood
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois
| | - Michael S Jones
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois
| | - Yumin Lee
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois
| | - Joseph R Sachleben
- Biomolecular NMR Core Facility, Biological Sciences Division, The University of Chicago, Chicago, Illinois
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois.
| | - Andrei Tokmakoff
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois.
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2
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Ashwood B, Jones MS, Lee Y, Sachleben JR, Ferguson AL, Tokmakoff A. Molecular insight into how the position of an abasic site and its sequence environment influence DNA duplex stability and dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.22.550182. [PMID: 37546925 PMCID: PMC10401965 DOI: 10.1101/2023.07.22.550182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Local perturbations to DNA base-pairing stability from lesions and chemical modifications can alter the stability and dynamics of an entire oligonucleotide. End effects may cause the position of a disruption within a short duplex to influence duplex stability and structural dynamics, yet this aspect of nucleic acid modifications is often overlooked. We investigate how the position of an abasic site (AP site) impacts the stability and dynamics of short DNA duplexes. Using a combination of steady-state and time-resolved spectroscopy and molecular dynamics simulations, we unravel an interplay between AP-site position and nucleobase sequence that controls energetic and dynamic disruption to the duplex. The duplex is disrupted into two segments by an entropic barrier for base pairing on each side of the AP site. The barrier induces fraying of the short segment when an AP site is near the termini. Shifting the AP site inward promotes a transition from short-segment fraying to fully encompassing the barrier into the thermodynamics of hybridization, leading to further destabilization the duplex. Nucleobase sequence determines the length scale for this transition by tuning the barrier height and base-pair stability of the short segment, and certain sequences enable out-of-register base pairing to minimize the barrier height.
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Affiliation(s)
- Brennan Ashwood
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, 929 East 57 Street, Chicago, Illinois 60637, United States
| | - Michael S. Jones
- Pritzker School of Molecular Engineering, The University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Yumin Lee
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, 929 East 57 Street, Chicago, Illinois 60637, United States
| | - Joseph R. Sachleben
- Biomolecular NMR Core Facility, Biological Sciences Division, The University of Chicago, Chicago, IL 60637, United States
| | - Andrew L. Ferguson
- Pritzker School of Molecular Engineering, The University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Andrei Tokmakoff
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, 929 East 57 Street, Chicago, Illinois 60637, United States
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3
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Ashwood B, Jones MS, Ferguson AL, Tokmakoff A. Disruption of energetic and dynamic base pairing cooperativity in DNA duplexes by an abasic site. Proc Natl Acad Sci U S A 2023; 120:e2219124120. [PMID: 36976762 PMCID: PMC10083564 DOI: 10.1073/pnas.2219124120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/27/2023] [Indexed: 03/29/2023] Open
Abstract
DNA duplex stability arises from cooperative interactions between multiple adjacent nucleotides that favor base pairing and stacking when formed as a continuous stretch rather than individually. Lesions and nucleobase modifications alter this stability in complex manners that remain challenging to understand despite their centrality to biology. Here, we investigate how an abasic site destabilizes small DNA duplexes and reshapes base pairing dynamics and hybridization pathways using temperature-jump infrared spectroscopy and coarse-grained molecular dynamics simulations. We show how an abasic site splits the cooperativity in a short duplex into two segments, which destabilizes small duplexes as a whole and enables metastable half-dissociated configurations. Dynamically, it introduces an additional barrier to hybridization by constraining the hybridization mechanism to a step-wise process of nucleating and zipping a stretch on one side of the abasic site and then the other.
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Affiliation(s)
- Brennan Ashwood
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL60637
| | - Michael S. Jones
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL60637
| | - Andrew L. Ferguson
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL60637
| | - Andrei Tokmakoff
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL60637
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4
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5
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Stabilization of an abasic site paired against an unnatural triazolyl nitrobenzene nucleoside. Biophys Chem 2020; 264:106428. [DOI: 10.1016/j.bpc.2020.106428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 07/03/2020] [Accepted: 07/03/2020] [Indexed: 11/22/2022]
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6
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Dayanidhi DPE, Malapati RP, Vaidyanathan Ganesan V. Selective recognition of DNA defects by cyclometalated Ir(iii) complexes. Dalton Trans 2019; 48:13536-13540. [DOI: 10.1039/c9dt01225g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Three different cyclometalated Ir(iii) complexes selectively bind to DNA defects.
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Affiliation(s)
- David Paul Elisa Dayanidhi
- Academy of Scientific and Innovative Research (AcSIR), Advanced Materials Laboratory
- CSIR-Central Leather Research Institute
- Chennai 600 020
| | - Rozaria Pinky Malapati
- Academy of Scientific and Innovative Research (AcSIR), Advanced Materials Laboratory
- CSIR-Central Leather Research Institute
- Chennai 600 020
| | - Vaidyanathan Vaidyanathan Ganesan
- Academy of Scientific and Innovative Research (AcSIR), Advanced Materials Laboratory
- CSIR-Central Leather Research Institute
- Chennai 600 020
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7
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Sagi J. In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids? J Nucleic Acids 2017; 2017:1641845. [PMID: 29181193 PMCID: PMC5664352 DOI: 10.1155/2017/1641845] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/15/2017] [Indexed: 01/03/2023] Open
Abstract
Synthetic analogs of natural nucleotides have long been utilized for structural studies of canonical and noncanonical nucleic acids, including the extensively investigated polymorphic G-quadruplexes (GQs). Dependence on the sequence and nucleotide modifications of the folding landscape of GQs has been reviewed by several recent studies. Here, an overview is compiled on the thermodynamic stability of the modified GQ folds and on how the stereochemical preferences of more than 70 synthetic and natural derivatives of nucleotides substituting for natural ones determine the stability as well as the conformation. Groups of nucleotide analogs only stabilize or only destabilize the GQ, while the majority of analogs alter the GQ stability in both ways. This depends on the preferred syn or anti N-glycosidic linkage of the modified building blocks, the position of substitution, and the folding architecture of the native GQ. Natural base lesions and epigenetic modifications of GQs explored so far also stabilize or destabilize the GQ assemblies. Learning the effect of synthetic nucleotide analogs on the stability of GQs can assist in engineering a required stable GQ topology, and exploring the in vitro action of the single and clustered natural base damage on GQ architectures may provide indications for the cellular events.
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Affiliation(s)
- Janos Sagi
- Rimstone Laboratory, RLI, Carlsbad, CA 92010, USA
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8
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Gamboa Varela J, Gates KS. Simple, High-Yield Syntheses of DNA Duplexes Containing Interstrand DNA-DNA Cross-Links Between an N(4) -Aminocytidine Residue and an Abasic Site. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2016; 65:5.16.1-5.16.15. [PMID: 27248783 PMCID: PMC5000854 DOI: 10.1002/cpnc.3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The protocol describes the preparation and purification of interstrand DNA-DNA cross-links derived from the reaction of an N(4) -aminocytidine residue with an abasic site in duplex DNA. The procedures employ inexpensive, commercially available chemicals and enzymes to carry out post-synthetic modification of commercially available oligodeoxynucleotides. The yield of cross-linked duplex is typically better than 90%. If purification is required, the cross-linked duplex can be readily separated from single-stranded DNA starting materials by denaturing gel electrophoresis. The resulting covalent hydrazone-based cross-links are stable under physiologically relevant conditions and may be useful for biophysical studies, structural analyses, DNA repair studies, and materials science applications. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
| | - Kent S Gates
- Department of Chemistry, University of Missouri, Columbia, Missouri
- Department of Biochemistry, University of Missouri, Columbia, Missouri
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9
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Braunlin W, Völker J, Plum GE, Breslauer KJ. DNA meter: Energy tunable, quantitative hybridization assay. Biopolymers 2016; 99:408-17. [PMID: 23529692 DOI: 10.1002/bip.22213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 01/15/2013] [Indexed: 11/06/2022]
Abstract
We describe a novel hybridization assay that employs a unique class of energy tunable, bulge loop-containing competitor strands (C*) that hybridize to a probe strand (P). Such initial "pre-binding" of a probe strand modulates its effective "availability" for hybridizing to a target site (T). More generally, the assay described here is based on competitive binding equilibria for a common probe strand (P) between such tunable competitor strands (C*) and a target strand (T). We demonstrate that loop variable, energy tunable families of C*P complexes exhibit enhanced discrimination between targets and mismatched targets, thereby reducing false positives/negatives. We refer to a C*P complex between a C* competitor single strand and the probe strand as a "tuning fork," since the C* strand exhibits branch points (forks) at the duplex-bulge interfaces within the complex. By varying the loop to create families of such "tuning forks," one can construct C*P "energy ladders" capable of resolving small differences within the target that may be of biological/functional consequence. The methodology further allows quantification of target strand concentrations, a determination heretofore not readily available by conventional hybridization assays. The dual ability of this tunable assay to discriminate and quantitate targets provides the basis for developing a technology we refer to as a "DNA Meter." Here we present data that establish proof-of-principle for an in solution version of such a DNA Meter. We envision future applications of this tunable assay that incorporate surface bound/spatially resolved DNA arrays to yield enhanced discrimination and sensitivity.
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Affiliation(s)
- William Braunlin
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Rd., Piscataway, NJ, 08854; Rational Affinity Devices, LLC
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10
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Babinský M, Fiala R, Kejnovská I, Bednářová K, Marek R, Sagi J, Sklenář V, Vorlíčková M. Loss of loop adenines alters human telomere d[AG3(TTAG3)3] quadruplex folding. Nucleic Acids Res 2014; 42:14031-41. [PMID: 25428355 PMCID: PMC4267657 DOI: 10.1093/nar/gku1245] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abasic (AP) lesions are the most frequent type of damages occurring in cellular DNA. Here we describe the conformational effects of AP sites substituted for 2′-deoxyadenosine in the first (ap7), second (ap13) or third (ap19) loop of the quadruplex formed in K+ by the human telomere DNA 5′-d[AG3(TTAG3)3]. CD spectra and electrophoresis reveal that the presence of AP sites does not hinder the formation of intramolecular quadruplexes. NMR spectra show that the structural heterogeneity is substantially reduced in ap7 and ap19 as compared to that in the wild-type. These two (ap7 and ap19) sequences are shown to adopt the hybrid-1 and hybrid-2 quadruplex topology, respectively, with AP site located in a propeller-like loop. All three studied sequences transform easily into parallel quadruplex in dehydrating ethanol solution. Thus, the AP site in any loop region facilitates the formation of the propeller loop. Substitution of all adenines by AP sites stabilizes the parallel quadruplex even in the absence of ethanol. Whereas guanines are the major determinants of quadruplex stability, the presence or absence of loop adenines substantially influences quadruplex folding. The naturally occurring adenine-lacking sites in the human telomere DNA can change the quadruplex topology in vivo with potentially vital biological consequences.
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Affiliation(s)
- Martin Babinský
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Radovan Fiala
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Iva Kejnovská
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-612 65 Brno, Czech Republic
| | - Klára Bednářová
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-612 65 Brno, Czech Republic
| | - Radek Marek
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Janos Sagi
- Rimstone Laboratory, RLI, 29 Lancaster Way, Cheshire, CT 06410, USA
| | - Vladimír Sklenář
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Michaela Vorlíčková
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-612 65 Brno, Czech Republic
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11
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Malina J, Brabec V. Thermodynamic impact of abasic sites on simulated translesion DNA synthesis. Chemistry 2014; 20:7566-70. [PMID: 24863756 DOI: 10.1002/chem.201402600] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Indexed: 12/20/2022]
Abstract
Loss of a base in DNA and the creation of an abasic (apurinic/apyrimidinic, AP) site is a frequent lesion that may occur spontaneously, or as a consequence of the action of DNA-damaging agents. The AP lesion is mutagenic or lethal if not repaired. We report a systematic thermodynamic investigation by differential scanning calorimetry on the evolution, during primer extension, of a model AP site in chemically simulated DNA translesion synthesis. Incorporation of dAMP (deoxyadenosine monophosphate), as well as dTMP (deoxythymidine monophosphate), opposite an AP site is enthalpically unfavorable, although incorporation of dTMP is more enthalpically unfavorable than that of dAMP. This finding is in a good agreement with experimental data showing that AP sites block various DNA polymerases of eukaryotic and prokaryotic origin and that, if bypassed, dAMP is preferentially inserted, whereas insertion of dTMP is less likely. The results emphasize the importance of thermodynamic contributions to the insertion of nucleotides opposite an AP site by DNA polymerases.
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Affiliation(s)
- Jaroslav Malina
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i. Kralovopolska 135, 61265 Brno, (Czech Republic), Fax: (+420) 541240499
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12
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Bag SS, Kundu R, Talukdar S. Unnatural triazolyl nucleoside stabilizes an abasic site containing DNA duplex equally as the stabilization of a natural A–T pair. RSC Adv 2013. [DOI: 10.1039/c3ra44120b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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13
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Menoni H, Hoeijmakers JHJ, Vermeulen W. Nucleotide excision repair-initiating proteins bind to oxidative DNA lesions in vivo. ACTA ACUST UNITED AC 2012; 199:1037-46. [PMID: 23253478 PMCID: PMC3529521 DOI: 10.1083/jcb.201205149] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In vivo imaging reveals that CSB and XPC promote the repair of oxidative DNA lesions independent of the canonical nucleotide excision repair process. Base excision repair (BER) is the main repair pathway to eliminate abundant oxidative DNA lesions such as 8-oxo-7,8-dihydroguanine. Recent data suggest that the key transcription-coupled nucleotide excision repair factor (TC-NER) Cockayne syndrome group B (CSB) and the global genome NER-initiating factor XPC are implicated in the protection of cells against oxidative DNA damages. Our novel live-cell imaging approach revealed a strong and very rapid recruitment of XPC and CSB to sites of oxidative DNA lesions in living cells. The absence of detectable accumulation of downstream NER factors at the site of local oxidative DNA damage provide the first in vivo indication of the involvement of CSB and XPC in the repair of oxidative DNA lesions independent of the remainder of the NER reaction. Interestingly, CSB exhibited different and transcription-dependent kinetics in the two compartments studied (nucleolus and nucleoplasm), suggesting a direct transcription-dependent involvement of CSB in the repair of oxidative lesions associated with different RNA polymerases but not involving other NER proteins.
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Affiliation(s)
- Hervé Menoni
- Department of Genetics, Erasmus MC, 3015 GE Rotterdam, Netherlands.
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14
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Fujimoto T, Nakano SI, Miyoshi D, Sugimoto N. The effects of molecular crowding on the structure and stability of g-quadruplexes with an abasic site. J Nucleic Acids 2011; 2011:857149. [PMID: 21949901 PMCID: PMC3178115 DOI: 10.4061/2011/857149] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 06/23/2011] [Accepted: 06/24/2011] [Indexed: 12/17/2022] Open
Abstract
Both cellular environmental factors and chemical modifications critically affect the properties of nucleic acids. However, the structure and stability of DNA containing abasic sites under cell-mimicking molecular crowding conditions remain unclear. Here, we investigated the molecular crowding effects on the structure and stability of the G-quadruplexes including a single abasic site. Structural analysis by circular dichroism showed that molecular crowding by PEG200 did not affect the topology of the G-quadruplex structure with or without an abasic site. Thermodynamic analysis further demonstrated that the degree of stabilization of the G-quadruplex by molecular crowding decreased with substitution of an abasic site for a single guanine. Notably, we found that the molecular crowding effects on the enthalpy change for G-quadruplex formation had a linear relationship with the abasic site effects depending on its position. These results are useful for predicting the structure and stability of G-quadruplexes with abasic sites in the cell-mimicking conditions.
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Affiliation(s)
- Takeshi Fujimoto
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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15
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Guza R, Kotandeniya D, Murphy K, Dissanayake T, Lin C, Giambasu GM, Lad RR, Wojciechowski F, Amin S, Sturla SJ, Hudson RH, York DM, Jankowiak R, Jones R, Tretyakova NY. Influence of C-5 substituted cytosine and related nucleoside analogs on the formation of benzo[a]pyrene diol epoxide-dG adducts at CG base pairs of DNA. Nucleic Acids Res 2011; 39:3988-4006. [PMID: 21245046 PMCID: PMC3089471 DOI: 10.1093/nar/gkq1341] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 12/17/2010] [Accepted: 12/20/2010] [Indexed: 01/13/2023] Open
Abstract
Endogenous 5-methylcytosine ((Me)C) residues are found at all CG dinucleotides of the p53 tumor suppressor gene, including the mutational 'hotspots' for smoking induced lung cancer. (Me)C enhances the reactivity of its base paired guanine towards carcinogenic diolepoxide metabolites of polycyclic aromatic hydrocarbons (PAH) present in cigarette smoke. In the present study, the structural basis for these effects was investigated using a series of unnatural nucleoside analogs and a representative PAH diolepoxide, benzo[a]pyrene diolepoxide (BPDE). Synthetic DNA duplexes derived from a frequently mutated region of the p53 gene (5'-CCCGGCACCC GC[(15)N(3),(13)C(1)-G]TCCGCG-3', + strand) were prepared containing [(15)N(3), (13)C(1)]-guanine opposite unsubstituted cytosine, (Me)C, abasic site, or unnatural nucleobase analogs. Following BPDE treatment and hydrolysis of the modified DNA to 2'-deoxynucleosides, N(2)-BPDE-dG adducts formed at the [(15)N(3), (13)C(1)]-labeled guanine and elsewhere in the sequence were quantified by mass spectrometry. We found that C-5 alkylcytosines and related structural analogs specifically enhance the reactivity of the base paired guanine towards BPDE and modify the diastereomeric composition of N(2)-BPDE-dG adducts. Fluorescence and molecular docking studies revealed that 5-alkylcytosines and unnatural nucleobase analogs with extended aromatic systems facilitate the formation of intercalative BPDE-DNA complexes, placing BPDE in a favorable orientation for nucleophilic attack by the N(2) position of guanine.
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MESH Headings
- 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide/analogs & derivatives
- 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide/chemistry
- Base Pairing
- Chromatography, High Pressure Liquid
- Cytosine/analogs & derivatives
- DNA Adducts/chemistry
- Deoxyguanosine/analogs & derivatives
- Deoxyguanosine/chemistry
- Genes, p53
- Guanine/chemistry
- Isotope Labeling
- Models, Molecular
- Oligodeoxyribonucleotides/chemical synthesis
- Oligodeoxyribonucleotides/chemistry
- Spectrometry, Fluorescence
- Spectrometry, Mass, Electrospray Ionization
- Tandem Mass Spectrometry
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Affiliation(s)
- Rebecca Guza
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Delshanee Kotandeniya
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Kristopher Murphy
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Thakshila Dissanayake
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Chen Lin
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - George Madalin Giambasu
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Rahul R. Lad
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Filip Wojciechowski
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shantu Amin
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shana J. Sturla
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Robert H.E. Hudson
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Darrin M. York
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Ryszard Jankowiak
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Roger Jones
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Natalia Y. Tretyakova
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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16
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Školáková P, Bednářová K, Vorlíčková M, Sagi J. Quadruplexes of human telomere dG3(TTAG3)3 sequences containing guanine abasic sites. Biochem Biophys Res Commun 2010; 399:203-8. [DOI: 10.1016/j.bbrc.2010.07.055] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 07/15/2010] [Indexed: 12/20/2022]
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17
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Hydrolysis of DNA and its molecular components in the dry state. Forensic Sci Int Genet 2010; 4:168-77. [DOI: 10.1016/j.fsigen.2009.08.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Revised: 08/09/2009] [Accepted: 08/11/2009] [Indexed: 11/19/2022]
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18
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Völker J, Plum G, Klump HH, Breslauer KJ. Energetic coupling between clustered lesions modulated by intervening triplet repeat bulge loops: allosteric implications for DNA repair and triplet repeat expansion. Biopolymers 2010; 93:355-69. [PMID: 19890964 PMCID: PMC3902826 DOI: 10.1002/bip.21343] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Clusters of closely spaced oxidative DNA lesions present challenges to the cellular repair machinery. When located in opposing strands, base excision repair (BER) of such lesions can lead to double strand DNA breaks (DSB). Activation of BER and DSB repair pathways has been implicated in inducing enhanced expansion of triplet repeat sequences. We show here that energy coupling between distal lesions (8oxodG and/or abasic sites) in opposing DNA strands can be modulated by a triplet repeat bulge loop located between the lesion sites. We find this modulation to be dependent on the identity of the lesions (8oxodG vs. abasic site) and the positions of the lesions (upstream vs. downstream) relative to the intervening bulge loop domain. We discuss how such bulge loop-mediated lesion crosstalk might influence repair processes, while favoring DNA expansion, the genotype of triplet repeat diseases.
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Affiliation(s)
- Jens Völker
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Rd, Piscataway, NJ 08854
| | - G.Eric Plum
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Rd, Piscataway, NJ 08854
- IBET Inc, 1507 Chambers Road, Suite 301, Columbus, OH 43212
| | - Horst H. Klump
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch 7800, South Africa
| | - Kenneth J. Breslauer
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Rd, Piscataway, NJ 08854
- The Cancer Institute of New Jersey, New Brunswick, NJ 08901
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19
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Nakano SI, Oka H, Uotani Y, Uenishi K, Fujii M, Sugimoto N. Dynamics and Energetics of the Base Flipping Conformation Studied with Base Pair-Mimic Nucleosides. Biochemistry 2009; 48:11304-11. [DOI: 10.1021/bi901496q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Shu-ichi Nakano
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST)
- Frontier Institute for Biomolecular Engineering Research (FIBER)
| | - Hirohito Oka
- Department of Chemistry, Faculty of Science and Engineering
| | - Yuuki Uotani
- Department of Chemistry, Faculty of Science and Engineering
| | | | - Masayuki Fujii
- Molecular Engineering Institute (MEI)
- Department of Environmental and Biological Chemistry
| | - Naoki Sugimoto
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST)
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Department of Chemistry, Faculty of Science and Engineering
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20
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Völker J, Plum GE, Klump HH, Breslauer KJ. DNA repair and DNA triplet repeat expansion: the impact of abasic lesions on triplet repeat DNA energetics. J Am Chem Soc 2009; 131:9354-60. [PMID: 19566100 PMCID: PMC2705181 DOI: 10.1021/ja902161e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Indexed: 11/29/2022]
Abstract
Enhanced levels of DNA triplet expansion are observed when base excision repair (BER) of oxidative DNA base damage (e.g., 8-oxo-dG) occurs at or near CAG repeat sequences. This observation suggests an interplay between processing mechanisms required for DNA repair and expansion pathways that yield genotypes associated with many neurological/developmental disorders. It has been proposed that DNA expansion involves the transient formation within the triplet repeat domains of non-native slipped DNA structures that are incorrectly processed by the BER machinery of repair during DNA synthesis. We show here that replacement within a triplet repeat bulge loop domain of a guanosine residue by an abasic site, the universal BER intermediate, increases the population of slipped/looped DNA structures relative to the corresponding lesion-free construct. Such abasic lesion-induced energetic enhancement of slipped/looped structures provides a linkage between BER and DNA expansion. We discuss how the BER machinery of repair may be influenced by abasic-induced energetic alterations in the properties of regions proximal to and/or within triplet repeat domains, thereby potentially modulating levels of DNA expansion.
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21
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Meneni SR, D'Mello R, Norigian G, Baker G, Gao L, Chiarelli MP, Cho BP. Sequence effects of aminofluorene-modified DNA duplexes: thermodynamic and circular dichroism properties. Nucleic Acids Res 2006; 34:755-63. [PMID: 16449208 PMCID: PMC1356535 DOI: 10.1093/nar/gkj480] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Revised: 01/14/2005] [Accepted: 01/14/2005] [Indexed: 11/12/2022] Open
Abstract
Circular dichroism (CD) and UV-melting experiments were conducted with 16 oligodeoxynucleotides modified by the carcinogen 2-aminofluorene, whose sequence around the lesion was varied systematically [d(CTTCTNG[AF]NCCTC), N = G, A, C, T], to gain insight into the factors that determine the equilibrium between base-displaced stacked (S) and external B-type (B) duplex conformers. Differing stabilities among the duplexes can be attributed to different populations of S and B conformers. The AF modification always resulted in sequence-dependent thermal (T(m)) and thermodynamic (-DeltaG degrees ) destabilization. The population of B-type conformers derived from eight selected duplexes (i.e. -AG*N- and -CG*N-) was inversely proportional to the -DeltaG degrees and T(m) values, which highlights the importance of carcinogen/base stacking in duplex stabilization even in the face of disrupted Watson-Crick base pairing in S-conformation. CD studies showed that the extent of the adduct-induced negative ellipticities in the 290-350 nm range is correlated linearly with -DeltaG degrees and T(m), but inversely with the population of B-type conformations. Taken together, these results revealed a unique interplay between the extent of carcinogenic interaction with neighboring base pairs and the thermodynamic properties of the AF-modified duplexes. The sequence-dependent S/B heterogeneities have important implications in understanding how arylamine-DNA adducts are recognized in nucleotide excision repair.
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Affiliation(s)
- Srinivasa Rao Meneni
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode IslandKingston, RI 02881, USA
- Department of Chemistry, Loyola UniversityChicago, IL 60626, USA
| | - Rhijuta D'Mello
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode IslandKingston, RI 02881, USA
- Department of Chemistry, Loyola UniversityChicago, IL 60626, USA
| | - Gregory Norigian
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode IslandKingston, RI 02881, USA
- Department of Chemistry, Loyola UniversityChicago, IL 60626, USA
| | - Gregory Baker
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode IslandKingston, RI 02881, USA
- Department of Chemistry, Loyola UniversityChicago, IL 60626, USA
| | - Lan Gao
- Department of Chemistry, Loyola UniversityChicago, IL 60626, USA
| | | | - Bongsup P. Cho
- To whom correspondence should be addressed at Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 41 Lower College Road, Kingston, RI 02881, USA. Tel: +1 401 874 5024; Fax: +1 401 874 5766;
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22
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Nakano SI, Uotani Y, Uenishi K, Fujii M, Sugimoto N. DNA base flipping by a base pair-mimic nucleoside. Nucleic Acids Res 2005; 33:7111-9. [PMID: 16361269 PMCID: PMC1316115 DOI: 10.1093/nar/gki1018] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
On the basis of non-covalent bond interactions in nucleic acids, we synthesized the deoxyadenosine derivatives tethering a phenyl group (X) and a naphthyl group (Z) by an amide linker, which mimic a Watson–Crick base pair. Circular dichroism spectra indicated that the duplexes containing X and Z formed a similar conformation regardless of the opposite nucleotide species (A, G, C, T and an abasic site analogue F), which was not observed for the natural duplexes. The ΔG370 values among the natural duplexes containing the A/A, A/G, A/C, A/T and A/F pairs differed by 5.2 kcal mol−1 while that among the duplexes containing X or Z in place of the adenine differed by only 1.9 or 2.8 kcal mol−1, respectively. Fluorescence quenching experiments confirmed that 2-amino purine opposite X adopted an unstacked conformation. The structural and thermodynamic analyses suggest that the aromatic hydrocarbon group of X and Z intercalates into a double helix, resulting in the opposite nucleotide base flipping into an unstacked position regardless of the nucleotide species. This observation implies that modifications at the aromatic hydrocarbon group and the amide linker may expand the application of the base pair-mimic nucleosides for molecular biology and biotechnology.
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Affiliation(s)
- Shu-ichi Nakano
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan
| | - Yuuki Uotani
- Department of Chemistry, Faculty of Science and Engineering, Konan University8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan
| | - Kazuya Uenishi
- Molecular Engineering Institute, Kinki University11-6 Kayanomori, Iizuka, Fukuoka 820-8555, Japan
| | - Masayuki Fujii
- Molecular Engineering Institute, Kinki University11-6 Kayanomori, Iizuka, Fukuoka 820-8555, Japan
- Department of Environmental and Biological Chemistry, Kinki University11-6 Kayanomori, Iizuka, Fukuoka 820-8555, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan
- Department of Chemistry, Faculty of Science and Engineering, Konan University8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan
- To whom correspondence should be addressed. Tel: +81 78 435 2497; Fax: +81 78 435 2539;
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23
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Douki T. Effect of denaturation on the photochemistry of pyrimidine bases in isolated DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2005; 82:45-52. [PMID: 16243533 DOI: 10.1016/j.jphotobiol.2005.08.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2005] [Revised: 08/11/2005] [Accepted: 08/22/2005] [Indexed: 10/25/2022]
Abstract
The influence of denaturation on DNA photochemistry was studied by quantifying the yield of formation of all possible bipyrimidine photolesions within isolated genomic DNA samples exposed to UVC radiation. Effects of DNA melting was studied either by carrying out irradiation over a wide range of temperature (0-90 degrees C) or by decreasing the ionic strength of the solution at 30 degrees C. A first observation was a much larger decrease in the photoreactivity upon increasing the temperature in single-stranded than in double-stranded DNA. Secondly, formation of trans,syn cyclobutane dimers and, to a lesser extent, modification in the ratio between the yields of cyclobutane dimers and (6-4) photoproducts, were found to be other main features associated with denaturation. These results emphasize the modulating role of structure in the yield and nature of UV-induced DNA damage.
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Affiliation(s)
- Thierry Douki
- Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique UMR-E 3 CEA-UJF, CEA/DSM/Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, 38054 Grenoble Cedex 9, France.
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24
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Abstract
DNA mismatch repair (MMR) is an evolutionarily conserved process that corrects mismatches generated during DNA replication and escape proofreading. MMR proteins also participate in many other DNA transactions, such that inactivation of MMR can have wide-ranging biological consequences, which can be either beneficial or detrimental. We begin this review by briefly considering the multiple functions of MMR proteins and the consequences of impaired function. We then focus on the biochemical mechanism of MMR replication errors. Emphasis is on structure-function studies of MMR proteins, on how mismatches are recognized, on the process by which the newly replicated strand is identified, and on excision of the replication error.
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Affiliation(s)
- Thomas A Kunkel
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA.
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25
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Nakano SI, Sugimoto N. Central Dogma for a Molecular Design Based on DNA: DNB (Databasing/Designable Nanobio) → ENB (Engineering Nanobio) → FNB (Functional Nanobio). CHEM LETT 2005. [DOI: 10.1246/cl.2005.1206] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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26
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Collini M, D'Alfonso L, Baldini G, Oldani A, Cellai L, Giordano C, Barone F, Mazzei F, Chirico G. Fluorescence anisotropy in the frequency domain by an optical microscope. APPLIED SPECTROSCOPY 2004; 58:160-165. [PMID: 15000709 DOI: 10.1366/000370204322842887] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Fluorescence anisotropy decay spectroscopy is a suitable tool for investigating the size and the shape of biological molecules. We coupled this technique to an optical microscope in order to reduce the excitation volume and to allow its application to spatially inhomogeneous samples. Phase modulated measurements of the fluorescence anisotropy decay were performed by feeding an intensity modulated linearly polarized laser beam to the epifluorescence port of a microscope. Here we report the test of the dynamic response of the microscope by comparing the lifetime and fluorescence polarization anisotropy decays obtained in cuvettes in a standard phase modulation fluorometer and on tiny drops on the microscope stage. We show that once a correction factor for the objective depolarization is introduced in the best-fit functions for the data analysis of the decays, the results obtained on the two setups are comparable. Some applications are reported here on long DNA tracts as well on short DNA fragments containing structural anomalies.
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Affiliation(s)
- Maddalena Collini
- Istituto Nazionale per la Fisica della Materia, Dipartimento di Fisica, Università di Milano Bicocca, Piazza della Scienza 3, Milano 20126 Italy
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27
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Barone F, Dogliotti E, Cellai L, Giordano C, Bjørås M, Mazzei F. Influence of DNA torsional rigidity on excision of 7,8-dihydro-8-oxo-2'-deoxyguanosine in the presence of opposing abasic sites by human OGG1 protein. Nucleic Acids Res 2003; 31:1897-903. [PMID: 12655006 PMCID: PMC152805 DOI: 10.1093/nar/gkg289] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2002] [Revised: 02/05/2003] [Accepted: 02/05/2003] [Indexed: 11/14/2022] Open
Abstract
The human protein OGG1 (hOGG1) targets the highly mutagenic base 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxodG) and shows a high specificity for the opposite DNA base. Abasic sites can arise in DNA in close opposition to 8-oxodG either during repair of mismatched bases (i.e. 8-oxodG/A mismatches) or, more frequently, as a consequence of ionizing radiation exposure. Bistranded DNA lesions may remain unrepaired and lead to cell death via double-strand break formation. In order to explore the role of damaged-DNA dynamics in recognition/excision by the hOGG1 repair protein, specific oligonucleotides containing an 8-oxodG opposite an abasic site, at different relative distances on the complementary strand, were synthesized. Rotational dynamics were studied by means of fluorescence polarization anisotropy decay experiments and the torsional elastic constant as well as the hydrodynamic radius of the DNA fragments were evaluated. Efficiency of excision of 8-oxodG was tested using purified human glycosylase. A close relation between the twisting flexibility of the DNA fragment and the excision efficiency of the oxidative damage by hOGG1 protein within a cluster was found.
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Affiliation(s)
- F Barone
- Laboratorio di Fisica, Istituto Superiore di Sanità, Viale Regina Elena 299, I-00161 Roma, Italy
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