51
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Manoj P, Min CK, Aravindakumar C, Joo T. Ultrafast charge transfer dynamics in 2-aminopurine modified double helical DNA. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.07.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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52
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Osakada Y, Kawai K, Fujitsuka M, Majima T. Kinetics of charge transfer in DNA containing a mismatch. Nucleic Acids Res 2008; 36:5562-70. [PMID: 18757889 PMCID: PMC2553589 DOI: 10.1093/nar/gkn505] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Charge transfer (CT) in DNA offers a unique approach for the detection of a single-base mismatch in a DNA molecule. While the single-base mismatch would significantly affect the CT in DNA, the kinetic basis for the drastic decrease in the CT efficiency through DNA containing mismatches still remains unclear. Recently, we determined the rate constants of the CT through the fully matched DNA, and we can now estimate the CT rate constant for a certain fully matched sequence. We assumed that further elucidating of the kinetics in mismatched sequences can lead to the discrimination of the DNA single-base mismatch based on the kinetics. In this study, we investigated the detailed kinetics of the CT through DNA containing mismatches and tried to discriminate a mismatch sequence based on the kinetics of the CT in DNA containing a mismatch.
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Affiliation(s)
- Yasuko Osakada
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki Osaka 567-0047, Japan
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53
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Ballin JD, Prevas JP, Bharill S, Gryczynski I, Gryczynski Z, Wilson GM. Local RNA conformational dynamics revealed by 2-aminopurine solvent accessibility. Biochemistry 2008; 47:7043-52. [PMID: 18543944 DOI: 10.1021/bi800487c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acrylamide quenching is widely used to monitor the solvent exposure of fluorescent probes in vitro. Here, we tested the utility of this technique to discriminate local RNA secondary structures using the fluorescent adenine analogue 2-aminopurine (2-AP). Under native conditions, the solvent accessibilities of most 2-AP-labeled RNA substrates were poorly resolved by classical single-population models; rather, a two-state quencher accessibility algorithm was required to model acrylamide-dependent changes in 2-AP fluorescence in structured RNA contexts. Comparing 2-AP quenching parameters between structured and unstructured RNA substrates permitted the effects of local RNA structure on 2-AP solvent exposure to be distinguished from nearest neighbor effects or environmental influences on intrinsic 2-AP photophysics. Using this strategy, the fractional accessibility of 2-AP for acrylamide ( f a) was found to be highly sensitive to local RNA structure. Base-paired 2-AP exhibited relatively poor accessibility, consistent with extensive shielding by adjacent bases. 2-AP in a single-base bulge was uniformly accessible to solvent, whereas the fractional accessibility of 2-AP in a hexanucleotide loop was indistinguishable from that of an unstructured RNA. However, these studies also provided evidence that the f a parameter reflects local conformational dynamics in base-paired RNA. Enhanced base pair dynamics at elevated temperatures were accompanied by increased f a values, while restricting local RNA breathing by adding a C-G base pair clamp or positioning 2-AP within extended RNA duplexes significantly decreased this parameter. Together, these studies show that 2-AP quenching studies can reveal local RNA structural and dynamic features beyond those that can be measured by conventional spectroscopic approaches.
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Affiliation(s)
- Jeff D Ballin
- Department of Biochemistry and Molecular Biology and Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
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54
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Grozema FC, Tonzani S, Berlin YA, Schatz GC, Siebbeles LDA, Ratner MA. Effect of Structural Dynamics on Charge Transfer in DNA Hairpins. J Am Chem Soc 2008; 130:5157-66. [DOI: 10.1021/ja078162j] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Ferdinand C. Grozema
- Opto-electronic Materials Section, DelftChemTech, Delft University of Technology, Julianalaan 136, 2628 BL, Delft, The Netherlands, and Center for Nanofabrication and Molecular Self-Assembly, Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113
| | - Stefano Tonzani
- Opto-electronic Materials Section, DelftChemTech, Delft University of Technology, Julianalaan 136, 2628 BL, Delft, The Netherlands, and Center for Nanofabrication and Molecular Self-Assembly, Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113
| | - Yuri A. Berlin
- Opto-electronic Materials Section, DelftChemTech, Delft University of Technology, Julianalaan 136, 2628 BL, Delft, The Netherlands, and Center for Nanofabrication and Molecular Self-Assembly, Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113
| | - George C. Schatz
- Opto-electronic Materials Section, DelftChemTech, Delft University of Technology, Julianalaan 136, 2628 BL, Delft, The Netherlands, and Center for Nanofabrication and Molecular Self-Assembly, Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113
| | - Laurens D. A. Siebbeles
- Opto-electronic Materials Section, DelftChemTech, Delft University of Technology, Julianalaan 136, 2628 BL, Delft, The Netherlands, and Center for Nanofabrication and Molecular Self-Assembly, Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113
| | - Mark A. Ratner
- Opto-electronic Materials Section, DelftChemTech, Delft University of Technology, Julianalaan 136, 2628 BL, Delft, The Netherlands, and Center for Nanofabrication and Molecular Self-Assembly, Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113
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55
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Khan A. Reorganization energy, activation energy, and mechanism of hole transfer process in DNA: A theoretical study. J Chem Phys 2008; 128:075101. [DOI: 10.1063/1.2828513] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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56
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Cornicchi E, Capponi S, Marconi M, Onori G, Paciaroni A. Thermal fluctuations of DNA enclosed by glycerol–water glassy matrices: an elastic neutron scattering investigation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:583-90. [DOI: 10.1007/s00249-008-0268-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Revised: 12/28/2007] [Accepted: 01/08/2008] [Indexed: 11/25/2022]
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57
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Sandin P, Börjesson K, Li H, Mårtensson J, Brown T, Wilhelmsson LM, Albinsson B. Characterization and use of an unprecedentedly bright and structurally non-perturbing fluorescent DNA base analogue. Nucleic Acids Res 2007; 36:157-67. [PMID: 18003656 PMCID: PMC2248743 DOI: 10.1093/nar/gkm1006] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
This article presents the first evidence that the DNA base analogue 1,3-diaza-2-oxophenoxazine, tC(O), is highly fluorescent, both as free nucleoside and incorporated in an arbitrary DNA structure. tC(O) is thoroughly characterized with respect to its photophysical properties and structural performance in single- and double-stranded oligonucleotides. The lowest energy absorption band at 360 nm (epsilon = 9000 M(-1) cm(-1)) is dominated by a single in-plane polarized electronic transition and the fluorescence, centred at 465 nm, has a quantum yield of 0.3. When incorporated into double-stranded DNA, tC(O) shows only minor variations in fluorescence intensity and lifetime with neighbouring bases, and the average quantum yield is 0.22. These features make tC(O), on average, the brightest DNA-incorporated base analogue so far reported. Furthermore, it base pairs exclusively with guanine and causes minimal perturbations to the native structure of DNA. These properties make tC(O) a promising base analogue that is perfectly suited for e.g. photophysical studies of DNA interacting with macromolecules (proteins) or for determining size and shape of DNA tertiary structures using techniques such as fluorescence anisotropy and fluorescence resonance energy transfer (FRET).
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Affiliation(s)
- Peter Sandin
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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58
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Ballin JD, Bharill S, Fialcowitz-White EJ, Gryczynski I, Gryczynski Z, Wilson GM. Site-specific variations in RNA folding thermodynamics visualized by 2-aminopurine fluorescence. Biochemistry 2007; 46:13948-60. [PMID: 17997580 DOI: 10.1021/bi7011977] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The fluorescent base analogue 2-aminopurine (2-AP) is commonly used to study specific conformational and protein binding events involving nucleic acids. Here, combinations of steady-state and time-resolved fluorescence spectroscopy of 2-AP were employed to monitor conformational transitions within a model hairpin RNA from diverse structural perspectives. RNA substrates adopting stable, unambiguous secondary structures were labeled with 2-AP at an unpaired base, within the loop, or inside the base-paired stem. Steady-state fluorescence was monitored as the RNA hairpins made the transitions between folded and unfolded conformations using thermal denaturation, urea titration, and cation-mediated folding. Unstructured control RNA substrates permitted the effects of higher-order RNA structures on 2-AP fluorescence to be distinguished from stimulus-dependent changes in intrinsic 2-AP photophysics and/or interactions with adjacent residues. Thermodynamic parameters describing local conformational changes were thus resolved from multiple perspectives within the model RNA hairpin. These data provided energetic bases for construction of folding mechanisms, which varied among different folding-unfolding stimuli. Time-resolved fluorescence studies further revealed that 2-AP exhibits characteristic signatures of component fluorescence lifetimes and respective fractional contributions in different RNA structural contexts. Together, these studies demonstrate localized conformational events contributing to RNA folding and unfolding that could not be observed by approaches monitoring only global structural transitions.
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Affiliation(s)
- Jeff D Ballin
- Department of Biochemistry and Molecular Biology and Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
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59
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Affiliation(s)
- Adam P Silverman
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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60
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Pal C, Hüttermann J. Postirradiation electron transfer vs differential radical decay in X-irradiated DNA and its mixtures with additives. Electron spin resonance spectroscopy in LiBr glass at low temperatures. J Phys Chem B 2007; 110:14976-87. [PMID: 16869613 DOI: 10.1021/jp0583086] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Free radical formation in DNA and in colyophilized mixtures of DNA with the additives mitoxantrone and riboflavin was monitored after X-ray irradiation in frozen aqueous glasses (7 M LiBr/D2O) at 77 K by electron spin resonance (ESR) spectroscopy. Specifically, the postirradiation time course at 77 K of the respective free radical intensity residing on DNA or on the additive was probed in order to test the hypothesis of electron transfer from DNA, e.g., to mitoxantrone after irradiation under these conditions (e.g., Messer, A.; Carpenter, K.; Forzley, K.; Buchanan, J.; Yang, S.; Razskazovskii, Y.; Cai, Z.; Sevilla, M. D. J. Phys. Chem. B 2000, 104, 1128). For both additives, different additive loadings and irradiation doses were employed. The observed relative change in contributions of DNA and of additive radical components to the experimental spectra with time could be ascribed, for both additives, unequivocally to independent, differential fading of component radicals. Transfer from DNA to the additive, e.g., by electron tunneling as proposed before could be ruled out to occur by a detailed, quantitative analysis of the experimental spectra using reconstruction techniques. Additional studies were performed with the nucleotides TMP and dCMP and its mixtures with mitoxantrone in order to describe the time course in systems which are expected to behave independently; the results supported the conclusions arrived at from the analysis of the DNA/additive system. A model was proposed to describe the postirradiation radical fading mechanisms which involve liberation of radiation-induced matrix-trapped defects with time. It was assumed that these defects are ESR-mute and react with radicals by net radical destruction. Some experimental observations are presented concerning influence of temperature and of the matrix on the fading processes. These seem to argue in favor of such a model although a detailed, quantitative description is still not possible.
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Affiliation(s)
- Chandrima Pal
- Fachrichtung Biophysik, Universität des Saarlandes, Klinikum Bau 76, 66421 Homburg, Germany
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61
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Augustyn K, Genereux J, Barton J. Distance-Independent DNA Charge Transport across an Adenine Tract. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200701522] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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62
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Augustyn KE, Genereux JC, Barton JK. Distance-Independent DNA Charge Transport across an Adenine Tract. Angew Chem Int Ed Engl 2007; 46:5731-3. [PMID: 17607671 DOI: 10.1002/anie.200701522] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Katherine E Augustyn
- Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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63
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Chen XJ, Schramm J, Tuohy C, Skiff H, Hummel K, Szklarski AR, Vacirca N, Wolf BA, Hirsh DJ. Progress towards a DNA-based model system for the study of electron spin-spin interactions. Biophys Chem 2007; 129:148-62. [PMID: 17574723 DOI: 10.1016/j.bpc.2007.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Revised: 05/22/2007] [Accepted: 05/23/2007] [Indexed: 10/23/2022]
Abstract
A DNA-based model system is described for studying electron spin-spin interactions between a paramagnetic metal ion and a nitroxide spin label. The modified base deoxythymidine-EDTA (dT-EDTA) chelates the divalent or trivalent metal ion and produces a new feature in the circular dichroism (CD) spectra that makes it possible to monitor local DNA melting. Based on the results of optical and electron paramagnetic resonance (EPR) experiments, we find that the terminus of the DNA duplex that incorporates dT-EDTA and the spin-label melts at a higher temperature than the rest of the DNA duplex. EPR microwave progressive power saturation experiments performed at 77 K are consistent with the specific binding of Dy(III) at the EDTA site and an intramolecular dipole-dipole interaction between the nitroxide spin-label and the chelated Dy(III). This model system should be suitable for studying the relaxation properties of metal ions by saturation-recovery EPR.
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Affiliation(s)
- Xi Jun Chen
- Department of Chemistry, The College of New Jersey, PO Box 7718, Ewing, NJ 08628, USA
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64
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Neely RK, Magennis SW, Parsons S, Jones AC. Photophysics and X-ray Structure of Crystalline 2-Aminopurine. Chemphyschem 2007; 8:1095-102. [PMID: 17385756 DOI: 10.1002/cphc.200600593] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
To explore the effect of intermolecular interactions on the photophysics of 2-aminopurine (2AP) in a well-defined environment, we have investigated the fluorescence properties of single 2AP crystals, having determined their X-ray structure. In the crystal, 2AP is subject to base-stacking and hydrogen-bonding interactions similar to those found in DNA. The crystal shows dual fluorescence: pi-stacked molecules in the bulk of the lattice have redshifted excitation and emission spectra, while molecules at defect sites have spectra similar to those of 2AP in solution or in DNA. Heterogeneous intermolecular interactions in the crystal give rise to multiexponential fluorescence decay characteristics similar to those observed for 2AP-labelled DNA. The presence of about 13 % of the 7H tautomer in the crystal confirms that 9H-7H tautomerisation of 2AP occurs in the ground state. Long-wavelength excitation of a 2AP-labelled oligonucleotide duplex produced redshifted emission similar to that observed in the crystal, indicating that pi-stacking interaction of 2AP with nucleobases gives rise to a low energy excited state.
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Affiliation(s)
- Robert K Neely
- School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
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65
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Ramreddy T, Rao BJ, Krishnamoorthy G. Site-specific dynamics of strands in ss- and dsDNA as revealed by time-domain fluorescence of 2-aminopurine. J Phys Chem B 2007; 111:5757-66. [PMID: 17469866 DOI: 10.1021/jp068818f] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It is well recognized that structure and dynamics of DNA strands guide proteins toward their cognate sites in DNA. While the dynamics is controlled primarily by the nucleotide sequence, the context of a particular sequence in relation to an open end could also play a significant role. In this work we have used the fluorescent analogue of adenine, 2-aminopurine (2-AP), to extract information on site-specific dynamics of DNA strands associated with 30-70 nucleotides length. Measurement of fluorescence lifetime and anisotropy decay kinetics in various types of DNA strands in which 2-AP was located in specific positions revealed novel insights into the dynamics of strands. We find that in single-stranded (ss) DNA, the extent of motional dynamics of the bases falls off sharply from the very end toward the middle of the strand. In contrast, the flexibility of the backbone decreases more gradually in the same direction. In double-stranded (ds) DNA, the level of base-pair fraying increases toward the ends in a graded manner. Surprisingly, the same is countered by the presence of ss-overhangs emanating from dsDNA ends. Moreover, the extent of concerted motion of bases in duplex DNA increased from the end to the middle of the duplex, a result which is both striking and counterintuitive. Most surprisingly, the two complementary strands of a duplex that were unequal in length exhibited differential dynamics: the longer one with overhangs showed a distinctly higher level of flexibility than the recessed shorter strand in the same duplex. All these results, taken together, provoke newer insights in our understanding of how different bases in DNA strands are endowed with specific dynamic properties as a function of their positions. These properties are likely to be used in facilitating specific recognitions of DNA bases by proteins during various DNA-protein interaction systems.
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Affiliation(s)
- T Ramreddy
- Department of Chemical Science and Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
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66
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Lin X, Kang G, Lu L. DNA/Poly(p-aminobenzensulfonic acid) composite bi-layer modified glassy carbon electrode for determination of dopamine and uric acid under coexistence of ascorbic acid. Bioelectrochemistry 2007; 70:235-44. [DOI: 10.1016/j.bioelechem.2006.02.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2005] [Revised: 02/18/2006] [Accepted: 02/20/2006] [Indexed: 11/26/2022]
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67
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Kawai K, Osakada Y, Sugimoto A, Fujitsuka M, Majima T. Hole Transfer Rates in A-Form DNA/2′-OMeRNA Hybrid. Chemistry 2007; 13:2386-91. [PMID: 17163564 DOI: 10.1002/chem.200601210] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The hole transfer rates in the DNA/DNA B-form duplex and DNA/2'-OMeRNA A-form duplex were measured which occurred in the time range of approximately 100 micros. The hole transfer rates in the A-form duplexes were slower and more strongly dependent on the temperature compared to those in the B-form duplexes, suggesting that the A-form is more rigid than the B-form duplex in this time scale.
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Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan.
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68
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Somsen OJG, Keukens LB, de Keijzer MN, van Hoek A, van Amerongen H. Structural heterogeneity in DNA: temperature dependence of 2-aminopurine fluorescence in dinucleotides. Chemphyschem 2007; 6:1622-7. [PMID: 16082664 DOI: 10.1002/cphc.200400648] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The fluorescent base analogue 2-aminopurine is a sensitive probe for local dynamics of DNA. Its fluorescence is quenched by interaction with the neighboring bases, but the underlying mechanisms are still under investigation. We studied 2-aminopurine fluorescence in dinucleotides with each of the natural bases. Consistently, two of the four fluorescence-decay components depend strongly on temperature. Our results indicate that these components are due to the excited-state dynamics of a single conformational state. We propose a variation of the gating model in which transient unstacking occurs in the excited state.
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Affiliation(s)
- Oscar J G Somsen
- Wageningen University, Laboratory of Biophysics, P.O. Box 8128, 6700 ET Wageningen, The Netherlands.
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69
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Neely RK, Jones AC. Influence of Base Dynamics on the Conformational Properties of DNA: Observation of Static Conformational States in Rigid Duplexes at 77 K. J Am Chem Soc 2006; 128:15952-3. [PMID: 17165705 DOI: 10.1021/ja064390m] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Time-resolved fluorescence of 2-aminopurine-labeled DNA duplexes at 77 K reveals the relationship between base dynamics and the conformational heterogeneity that results in the well-known multiexponential fluorescence decay at room temperature. The conformation that exhibits rapid interbase charge transfer at room temperature is not populated in the frozen duplex at 77 K; this geometry is accessed by thermal motion of the bases, it is not a minimum energy structure of the duplex. Three photophysically distinct conformational states persist in the frozen duplex; these are minimum energy structures and do not interconvert at room temperature on the time scale of the 2-aminopurine excited-state lifetime.
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Affiliation(s)
- Robert K Neely
- School of Chemistry and the Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre (COSMIC), The University of Edinburgh, Edinburgh EH9 3JJ, UK
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70
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Osakada Y, Kawai K, Fujitsuka M, Majima T. Charge transfer through DNA nanoscaled assembly programmable with DNA building blocks. Proc Natl Acad Sci U S A 2006; 103:18072-6. [PMID: 17116889 PMCID: PMC1838708 DOI: 10.1073/pnas.0607148103] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA nanostructures based on programmable DNA molecular recognition have been developed, but the nanoelectronics of using DNA is still challenging. A more rapid charge-transfer (CT) process through the DNA nanoassembly is required for further development of programmable DNA nanoelectronics. In this article, we present direct absorption measurements of the long-range CT over a 140-A DNA assembly based on a GC repetitive sequence constructed by simply mixing DNA building blocks. We show that a CT through DNA nanoscale assembly is possible and programmable with the designed DNA sequence.
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Affiliation(s)
- Yasuko Osakada
- Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Kiyohiko Kawai
- Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
- *To whom correspondence may be addressed. E-mail: or
| | - Mamoru Fujitsuka
- Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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71
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72
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Abstract
Nature has specifically designed proteins, as opposed to DNA, for electron transfer. There is no doubt about the electron transfer within proteins compared with the uncertain and continuing debate about charge transfer through DNA. However, the exact mechanism of electron transfer within peptide systems has been a source of controversy. Two different mechanisms for electron transfer between a donor and an acceptor, electron hopping and bridge-assisted superexchange, have been proposed, and are supported by experimental evidence and theoretical calculations. Several factors were found to affect the kinetics of this process, including peptide chain length, secondary structure and hydrogen bonding. Electrochemical measurements of surface-supported peptides have contributed significantly to the debate. Here we summarize the current approaches to the study of electron transfer in peptides with a focus on surface measurements and comment on these results in light of the current and often controversial debate on electron transfer mechanisms in peptides.
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Affiliation(s)
- Yi-Tao Long
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan, S7N 5C9, Canada
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73
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Adhikary A, Becker D, Collins S, Koppen J, Sevilla MD. C5'- and C3'-sugar radicals produced via photo-excitation of one-electron oxidized adenine in 2'-deoxyadenosine and its derivatives. Nucleic Acids Res 2006; 34:1501-11. [PMID: 16537838 PMCID: PMC1401510 DOI: 10.1093/nar/gkl026] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report that photo-excitation of one-electron-oxidized adenine [A(-H)•] in dAdo and its 2′-deoxyribonucleotides leads to formation of deoxyribose sugar radicals in remarkably high yields. Illumination of A(-H)• in dAdo, 3′-dAMP and 5′-dAMP in aqueous glasses at 143 K leads to 80-100% conversion to sugar radicals at C5′ and C3′. The position of the phosphate in 5′- and 3′-dAMP is observed to deactivate radical formation at the site of substitution. In addition, the pH has a crucial influence on the site of sugar radical formation; e.g. at pH ∼5, photo-excitation of A(-H)• in dAdo at 143 K produces mainly C5′• whereas only C3′• is observed at high pH ∼12. 13C substitution at C5′ in dAdo yields 13C anisotropic couplings of (28, 28, 84) G whose isotropic component 46.7 G identifies formation of the near planar C5′•. A β-13C 16 G isotropic coupling from C3′• is also found. These results are found to be in accord with theoretically calculated 13C couplings at C5′ [DFT, B3LYP, 6-31(G) level] for C5′• and C3′•. Calculations using time-dependent density functional theory [TD-DFT B3LYP, 6-31G(d)] confirm that transitions in the near UV and visible induce hole transfer from the base radical to the sugar group leading to sugar radical formation.
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Affiliation(s)
| | | | | | | | - Michael D. Sevilla
- To whom correspondence should be addressed. Tel: +1 248 370 2328; Fax: +1 248 370 2321;
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74
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Shih CC, Georghiou S. Large-amplitude fast motions in double-stranded DNA driven by solvent thermal fluctuations. Biopolymers 2006; 81:450-63. [PMID: 16419073 DOI: 10.1002/bip.20444] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The nature of the internal dynamics of double-stranded DNA in aqueous environment remains to be established. We consider the motions to stem from thermal fluctuations/dissipations of the harmonic modes of beads (bases and sugars) in a cylindrical geometry that are tracked through the stochastic Langevin trajectories; these are characterized by parameters obtained from published data. The present approach has allowed a comparative study of the dynamics for DNA lengths in the range of 20-600 base pairs. For this range, we find that rotational motions about directions parallel to the helix axis (opening, twist) and perpendicular to it (propeller-twist, roll) contribute significantly to the dynamics. For a 20-mer at a solvent viscosity of 1 cP, the calculated fluorescence anisotropy profile exhibits a fast decay in the subnanosecond range due to large-amplitude fluctuations at the mesoscopic level. This feature reproduces the experimental behavior well, and suggests a possible way for the initiation of biological processes: they may be suddenly triggered on this scale through the occurrence of favorable thermal fluctuations. This analysis also reveals that, as is the case for a 20-mer, the dynamics of longer N-mers are dominated by internal motions, and are modulated by the viscosity of the solvent, in agreement with our previous experimental observations. Moreover, the model indicates that occurrence of partially concerted rotations of the bases due to thermal fluctuations can possibly be sustained over a DNA length of the order of 100 A at 1 ns, suggesting a possible mechanism for action-at-a-distance in transcription.
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Affiliation(s)
- Chia C Shih
- Department of Physics, University of Tennessee, Knoxville, TN 37996-1200, USA.
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75
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Wagenknecht HA. Electron transfer processes in DNA: mechanisms, biological relevance and applications in DNA analytics. Nat Prod Rep 2006; 23:973-1006. [PMID: 17119642 DOI: 10.1039/b504754b] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In principle, DNA-mediated charge transfer processes can be categorized as oxidative hole transfer and reductive electron transfer. With respect to the routes of DNA damage most of the past research has been focused on the investigation of oxidative hole transfer or transport. On the other hand, the transport or transfer of excess electrons has a large potential for biomedical applications, mainly for DNA chip technology.
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Affiliation(s)
- Hans-Achim Wagenknecht
- University of Regensburg, Institute for Organic Chemistry, D-93040, Regensburg, Germany.
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76
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Neely RK, Daujotyte D, Grazulis S, Magennis SW, Dryden DTF, Klimašauskas S, Jones AC. Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes. Nucleic Acids Res 2005; 33:6953-60. [PMID: 16340006 PMCID: PMC1310896 DOI: 10.1093/nar/gki995] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
DNA base flipping is an important mechanism in molecular enzymology, but its study is limited by the lack of an accessible and reliable diagnostic technique. A series of crystalline complexes of a DNA methyltransferase, M.HhaI, and its cognate DNA, in which a fluorescent nucleobase analogue, 2-aminopurine (AP), occupies defined positions with respect the target flipped base, have been prepared and their structures determined at higher than 2 Å resolution. From time-resolved fluorescence measurements of these single crystals, we have established that the fluorescence decay function of AP shows a pronounced, characteristic response to base flipping: the loss of the very short (∼100 ps) decay component and the large increase in the amplitude of the long (∼10 ns) component. When AP is positioned at sites other than the target site, this response is not seen. Most significantly, we have shown that the same clear response is apparent when M.HhaI complexes with DNA in solution, giving an unambiguous signal of base flipping. Analysis of the AP fluorescence decay function reveals conformational heterogeneity in the DNA–enzyme complexes that cannot be discerned from the present X-ray structures.
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Affiliation(s)
- Robert K. Neely
- School of Chemistry, The University of EdinburghWest Mains Road, Edinburgh EH9 3JJ, UK
- Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre (COSMIC), The University of EdinburghWest Mains Road, Edinburgh EH9 3JZ, UK
| | - Dalia Daujotyte
- Laboratory of Biological DNA Modification, Institute of BiotechnologyLT-02241 Vilnius, Lithuania
| | - Saulius Grazulis
- Laboratory of DNA–Protein Interactions, Institute of BiotechnologyLT-02241 Vilnius, Lithuania
| | - Steven W. Magennis
- Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre (COSMIC), The University of EdinburghWest Mains Road, Edinburgh EH9 3JZ, UK
| | - David T. F. Dryden
- School of Chemistry, The University of EdinburghWest Mains Road, Edinburgh EH9 3JJ, UK
- Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre (COSMIC), The University of EdinburghWest Mains Road, Edinburgh EH9 3JZ, UK
| | - Saulius Klimašauskas
- Laboratory of Biological DNA Modification, Institute of BiotechnologyLT-02241 Vilnius, Lithuania
- Department of Biochemistry and Biophysics, Faculty of Natural Sciences, Vilnius UniversityLT-2009 Vilnius, Lithuania
| | - Anita C. Jones
- School of Chemistry, The University of EdinburghWest Mains Road, Edinburgh EH9 3JJ, UK
- Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre (COSMIC), The University of EdinburghWest Mains Road, Edinburgh EH9 3JZ, UK
- To whom correspondence should be addressed. Tel: +44 131 6506449; Fax: +44 131 6504743;
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77
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Sen S, Paraggio NA, Gearheart LA, Connor EE, Issa A, Coleman RS, Wilson DM, Wyatt MD, Berg MA. Effect of protein binding on ultrafast DNA dynamics: characterization of a DNA:APE1 complex. Biophys J 2005; 89:4129-38. [PMID: 16199493 PMCID: PMC1366978 DOI: 10.1529/biophysj.105.062695] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Synthetic oligonucleotides with a fluorescent coumarin group replacing a basepair have been used in recent time-resolved Stokes-shift experiments to measure DNA dynamics on the femtosecond to nanosecond timescales. Here, we show that the APE1 endonuclease cleaves such a modified oligonucleotide at the abasic site opposite the coumarin with only a fourfold reduction in rate. In addition, a noncatalytic mutant (D210N) binds tightly to the same oligonucleotide, albeit with an 85-fold reduction in binding constant relative to a native oligonucleotide containing a guanine opposite the abasic site. Thus, the modified oligonucleotide retains substantial biological activity and serves as a useful model of native DNA. In the complex of the coumarin-containing oligonucleotide and the noncatalytic APE1, the dye's absorption spectrum is shifted relative to its spectrum in either water or within the unbound oligonucleotide. Thus the dye occupies a site within the DNA:protein complex. 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. Stokes-shift measurements of the complex show surprisingly little change in the dynamics within the 40 ps-40 ns time range.
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Affiliation(s)
- Sobhan Sen
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
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78
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Wettig SD, Wood DO, Aich P, Lee JS. M-DNA: A novel metal ion complex of DNA studied by fluorescence techniques. J Inorg Biochem 2005; 99:2093-101. [PMID: 16185768 DOI: 10.1016/j.jinorgbio.2005.07.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2005] [Revised: 07/18/2005] [Accepted: 07/26/2005] [Indexed: 10/25/2022]
Abstract
M-DNA, a complex formed in solution between divalent metal ions (M) and duplex DNA, has been studied extensively using fluorescence quenching. This review examines the methods used to examine the formation of M-DNA, and its ability to serve as a pathway for electron transfer between donor and acceptor chromaphores. A mass action model for M-DNA formation is presented based upon the results of fluorescence quenching studies using fluorescein/QSY-7 labeled duplexes. From the mass action analysis, it was determined that approximately 1.4 protons are released per base pair, with k(eq) on the order of 10(-8), indicative of a strong interaction. As resonance energy transfer is shown to be unlikely over the distances involved in this work, the observed quenching in M-DNA is discussed in terms of an electron hopping mechanism for electron transfer, with k(hop)=2.5 x 10(11)s(-1).
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Affiliation(s)
- Shawn D Wettig
- College of Pharmacy and Nutrition, University of Saskatchewan, 110 Science Place, Saskatoon, Sasketchewan, Canada S7N 5C9
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79
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Liu T, Barton JK. DNA Electrochemistry through the Base Pairs Not the Sugar−Phosphate Backbone. J Am Chem Soc 2005; 127:10160-1. [PMID: 16028914 DOI: 10.1021/ja053025c] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using intercalated, covalently bound daunomycin as a redox probe, ground state charge transport in DNA films with a perturbation in base pair stacking was examined in comparison with breaks in the sugar-phosphate backbone. While the introduction of one or even two nicks in the sugar-phosphate backbone yields no detectable effect on electron transfer, a CA mismatch significantly attenuates the electron transfer yield. These results confirm that the base pair stack is the pathway for DNA-mediated charge transfer, not the sugar-phosphate backbone.
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Affiliation(s)
- Tao Liu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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80
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Yavin E, Boal AK, Stemp EDA, Boon EM, Livingston AL, O'Shea VL, David SS, Barton JK. Protein-DNA charge transport: redox activation of a DNA repair protein by guanine radical. Proc Natl Acad Sci U S A 2005; 102:3546-51. [PMID: 15738421 PMCID: PMC553321 DOI: 10.1073/pnas.0409410102] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2004] [Accepted: 01/19/2005] [Indexed: 11/18/2022] Open
Abstract
DNA charge transport (CT) chemistry provides a route to carry out oxidative DNA damage from a distance in a reaction that is sensitive to DNA mismatches and lesions. Here, DNA-mediated CT also leads to oxidation of a DNA-bound base excision repair enzyme, MutY. DNA-bound Ru(III), generated through a flash/quench technique, is found to promote oxidation of the [4Fe-4S](2+) cluster of MutY to [4Fe-4S](3+) and its decomposition product [3Fe-4S](1+). Flash/quench experiments monitored by EPR spectroscopy reveal spectra with g = 2.08, 2.06, and 2.02, characteristic of the oxidized clusters. Transient absorption spectra of poly(dGC) and [Ru(phen)(2)dppz](3+) (dppz = dipyridophenazine), generated in situ, show an absorption characteristic of the guanine radical that is depleted in the presence of MutY with formation instead of a long-lived species with an absorption at 405 nm; we attribute this absorption also to formation of the oxidized [4Fe-4S](3+) and [3Fe-4S](1+) clusters. In ruthenium-tethered DNA assemblies, oxidative damage to the 5'-G of a 5'-GG-3' doublet is generated from a distance but this irreversible damage is inhibited by MutY and instead EPR experiments reveal cluster oxidation. With ruthenium-tethered assemblies containing duplex versus single-stranded regions, MutY oxidation is found to be mediated by the DNA duplex, with guanine radical as an intermediate oxidant; guanine radical formation facilitates MutY oxidation. A model is proposed for the redox activation of DNA repair proteins through DNA CT, with guanine radicals, the first product under oxidative stress, in oxidizing the DNA-bound repair proteins, providing the signal to stimulate DNA repair.
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Affiliation(s)
- Eylon Yavin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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81
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Abstract
Charge transport (CT) through DNA has been found to occur over long molecular distances in a reaction that is sensitive to intervening structure. The process has been described mechanistically as involving diffusive charge-hopping among low-energy guanine sites. Using a kinetically fast electron hole trap, N(4)-cyclopropylcytosine ((CP)C), here we show that hole migration must involve also the higher-energy pyrimidine bases. In DNA assemblies containing either [Rh(phi)(2)(bpy')](3+) or an anthraquinone derivative, two high-energy photooxidants, appreciable oxidative damage at a distant (CP)C is observed. The damage yield is modulated by lower-energy guanine sites on the same or complementary strand. Significantly, the efficiency in trapping at (CP)C is equivalent to that at N(2)-cyclopropylguanosine ((CP)G). Indeed, even when (CP)G and (CP)C are incorporated as neighboring bases on the same strand, their efficiency of photodecomposition is comparable. Thus, CT is not simply a function of the relative energies of the isolated bases but instead may require orbital mixing among the bases. We propose that charge migration through DNA involves occupation of all of the DNA bases with radical delocalization within transient structure-dependent domains. These delocalized domains may form and break up transiently, facilitating and limiting CT. This dynamic delocalized model for DNA CT accounts for the sensitivity of the process to sequence-dependent DNA structure and provides a basis to reconcile and exploit DNA CT chemistry and physics.
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Affiliation(s)
- Fangwei Shao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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