501
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Bhattacharya PK, Cha J, Barton JK. 1H NMR determination of base-pair lifetimes in oligonucleotides containing single base mismatches. Nucleic Acids Res 2002; 30:4740-50. [PMID: 12409465 PMCID: PMC135820 DOI: 10.1093/nar/gkf601] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Proton nuclear magnetic resonance (NMR) spectroscopy is employed to characterize the kinetics of base-pair opening in a series of 9mer duplexes containing different single base mismatches. The imino protons from the different mismatched, as well as fully matched, duplexes are assigned from the imino-imino region in the WATERGATE NOESY spectra. The exchange kinetics of the imino protons are measured from selective longitudinal relaxation times. In the limit of infinite exchange catalyst concentration, the exchange times of the mismatch imino protons extrapolate to much shorter lifetimes than are commonly observed for an isolated GC base pair. Different mismatches exhibit different orders of base-pair lifetimes, e.g. a TT mismatch has a shorter base-pair lifetime than a GG mismatch. The effect of the mismatch was observed up to a distance of two neighboring base pairs. This indicates that disruption in the duplex caused by the mismatch is quite localized. The overall order of base-pair lifetimes in the selected sequence context of the base pair is GC > GG > AA > CC > AT > TT. Interestingly, the fully matched AT base pair has a shorter base-pair lifetime relative to many of the mismatches. Thus, in any given base pair, the exchange lifetime can exhibit a strong dependence on sequence context. These findings may be relevant to the way mismatch recognition is accomplished by proteins and small molecules.
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Affiliation(s)
- Pratip K Bhattacharya
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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502
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Fahlman RP, Sharma RD, Sen D. The charge conduction properties of DNA holliday junctions depend critically on the identity of the tethered photooxidant. J Am Chem Soc 2002; 124:12477-85. [PMID: 12381189 DOI: 10.1021/ja020495n] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism for electrical charge conduction in DNA has been the subject of much recent interest and debate. Many of the measurements of DNA conductivity have been made in aqueous solution, with an aromatic photooxidant moiety such as anthraquinone or a rhodium(III) complex covalently tethered to the DNA. Such studies, however, have given discrepant results, for instance, regarding the relative ability of AT- and GC-rich sequences to conduct charge and the possibility of thymine cyclobutane dimer repair through the DNA from a distance. A recent paper on conduction in DNA immobile four-way junctions using the rhodium photooxidant reported conduction in all four helical arms, contrary to what is known about the three-dimensional structure and stacking of 4-way junctions. We have reexamined conduction in such junctions using rhodium [Rh(phi)(2)(byp)Cl(3)] as well as the anthraquinone photooxidants, and find that although our rhodium data agree with the previously published work, the anthraquinone data reveal conduction in only two of the four helical arms, consistent with the known tertiary structure of four-way junctions. An electrophoretic investigation revealed the formation of intermolecular aggregates in the rhodium-derivatized junctions, but not in the anthraquinone-labeled junctions. Rhodium-specific aggregation was also observed with simple DNA duplexes under the same experimental conditions. A characteristic property of aggregation was that all participating DNA molecules required the rhodium derivatization, and underivatized molecules did not aggregate with the derivatized ones. It is conceivable that the results reported here will help reconcile the various discrepancies that have been reported from charge conduction experiments carried out on DNA utilizing different photooxidants.
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Affiliation(s)
- Richard P Fahlman
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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503
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Starikov E. Quantum chemistry of nucleic acids: how it could help and when it is necessary. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2002. [DOI: 10.1016/s1389-5567(02)00024-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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504
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Lewis FD, Liu J, Weigel W, Rettig W, Kurnikov IV, Beratan DN. Donor-bridge-acceptor energetics determine the distance dependence of electron tunneling in DNA. Proc Natl Acad Sci U S A 2002; 99:12536-41. [PMID: 12228728 PMCID: PMC130495 DOI: 10.1073/pnas.192432899] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2002] [Accepted: 07/22/2002] [Indexed: 11/18/2022] Open
Abstract
Electron transfer (ET) processes in DNA are of current interest because of their involvement in oxidative strand cleavage reactions and their relevance to the development of molecular electronics. Two mechanisms have been identified for ET in DNA, a single-step tunneling process and a multistep charge-hopping process. The dynamics of tunneling reactions depend on both the distance between the electron donor and acceptor and the nature of the molecular bridge separating the donor and acceptor. In the case of protein and alkane bridges, the distance dependence is not strongly dependent on the properties of the donor and acceptor. In contrast, we show here that the distance decay of DNA ET rates varies markedly with the energetics of the donor and acceptor relative to the bridge. Specifically, we find that an increase in the energy of the bridge states by 0.25 eV (1 eV = 1.602 x 10(-19) J) relative to the donor and acceptor energies for photochemical oxidation of nucleotides, without changing the reaction free energy, results in an increase in the characteristic exponential distance decay constant for the ET rates from 0.71 to 1.1 A(-1). These results show that, in the small tunneling energy gap regime of DNA ET, the distance dependence is not universal; it varies strongly with the tunneling energy gap. These DNA ET reactions fill a "missing link" or transition regime between the large barrier (rapidly decaying) tunneling regime and the (slowly decaying) hopping regime in the general theory of bridge-mediated ET processes.
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Affiliation(s)
- Frederick D Lewis
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA.
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505
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Abstract
Electrons migrate over long distances along the DNA in a multistep hopping process where the rate of each step depends strongly upon its length. The efficiency of this process is not only determined by the electron transfer rates but also by competing reactions with water, in which the charge carriers are trapped. Because electron transfer through DNA can occur under the conditions of oxidative stress, biological consequences are highly likely. In addition, it has been observed that some DNA-binding enzymes influence this charge transport. The question of whether DNA is a suitable material for nanolelectronic devices remains unanswered.
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Affiliation(s)
- Bernd Giese
- Department of chemistry, University of Basel, St Johanns Ring 19, Switzerland.
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506
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Kanvah S, Schuster GB. Long-range oxidative damage to DNA: protection of guanines by a nonspecifically bound disulfide. J Am Chem Soc 2002; 124:11286-7. [PMID: 12236740 DOI: 10.1021/ja027259x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One-electron oxidation of DNA generates a base radical cation ("hole") that migrates through the duplex and causes damage at guanines. Unrepaired damage may lead to mutations. It has been suggested that "sacrificial guanines" in intron regions of DNA might serve to protect genes from damage. We have investigated the ability of a noncovalently bound sacrificial reagent to protect DNA from damage. Irradiation of an anthraquinone (AQ)-linked DNA duplex injects a radical cation into the DNA that causes reactions at GG steps close to and farther from the AQ. Bis[2-(3-(aminopropyl)amino)ethyl]disulfide, an analogue of spermine, binds to duplex DNA. Irradiation of the AQ-linked DNA in the presence of this disulfide suppresses the reaction at both GG steps and protects the DNA from damage. It is suggested that evolutionary pressure for the preservation of genomic integrity would yield disulfide-containing compounds optimized to bind to DNA and neutralize base radical cations.
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Affiliation(s)
- Sriram Kanvah
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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507
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Lewis FD, Liu X, Miller SE, Hayes RT, Wasielewski MR. Dynamics of electron injection in DNA hairpins. J Am Chem Soc 2002; 124:11280-1. [PMID: 12236737 DOI: 10.1021/ja026751d] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dynamics of electron injection has been investigated in DNA hairpins possessing a stilbenediether electron donor linker by means of femtosecond transient absorption spectroscopy. Ultrafast electron injection and charge recombination are observed with neighboring cytosine or thymine bases; however, guanine-guanine base pairs are not reduced, permitting the investigation of the distance dependence of charge injection.
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Affiliation(s)
- Frederick D Lewis
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, USA.
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508
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Voityuk AA, Rösch N. Fragment charge difference method for estimating donor–acceptor electronic coupling: Application to DNA π-stacks. J Chem Phys 2002. [DOI: 10.1063/1.1502255] [Citation(s) in RCA: 260] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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509
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Santhosh U, Schuster GB. long-range charge transport in duplex DNA: anthraquinone sensitization results are independent of terminal ionic distribution. J Am Chem Soc 2002; 124:10986-7. [PMID: 12224939 DOI: 10.1021/ja026932f] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Irradiation of an anthraquinone (AQ) derivative linked to a 5'-terminus of duplex DNA results in the formation of a base radical cation ("hole") that can migrate through the DNA. Reaction of the radical cation occurs primarily at the 5'-G of GG sequences. This reaction results in the formation of strand breaks when the irradiated DNA is treated with piperidine. The strand breaks are detected by polyacrylamide gel electrophoresis of samples that are labeled at the 3'- or 5'-terminus with (32)P. In contrast to a previous report in which a linked rhodium metallointercalator is used as the sensitizer to oxidize the DNA (Williams, T. T.; Barton, J. K. J. Am. Chem. Soc. 2002, 124, 1840-1841), we find that the position of the label does not affect the relative reactivity of the GG steps when AQ is the sensitizer.
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Affiliation(s)
- U Santhosh
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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510
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Li X, Cai Z, Sevilla MD. Energetics of the Radical Ions of the AT and AU Base Pairs: A Density Functional Theory (DFT) Study. J Phys Chem A 2002. [DOI: 10.1021/jp021322n] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Xifeng Li
- Department of Chemistry, Oakland University, Rochester, Michigan 48309
| | - Zhongli Cai
- Department of Chemistry, Oakland University, Rochester, Michigan 48309
| | - M. D. Sevilla
- Department of Chemistry, Oakland University, Rochester, Michigan 48309
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511
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Affiliation(s)
- Xi Hu
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
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512
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Pascaly M, Yoo J, Barton JK. DNA mediated charge transport: characterization of a DNA radical localized at an artificial nucleic acid base. J Am Chem Soc 2002; 124:9083-92. [PMID: 12149012 DOI: 10.1021/ja0202210] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA assemblies containing 4-methylindole incorporated as an artificial base provide a chemically well-defined system in which to explore the oxidative charge transport process in DNA. Using this artificial base, we have combined transient absorption and EPR spectroscopies as well as biochemical methods to test experimentally current mechanisms for DNA charge transport. The 4-methylindole radical cation intermediate has been identified using both EPR and transient absorption spectroscopies in oxidative flash-quench studies using a dipyridophenazine complex of ruthenium as the intercalating oxidant. The 4-methylindole radical cation intermediate is particularly amenable to study given its strong absorptivity at 600 nm and EPR signal measured at 77 K with g = 2.0065. Both transient absorption and EPR spectroscopies show that the 4-methylindole is well incorporated in the duplex; the data also indicate no evidence of guanine radicals, given the low oxidation potential of 4-methylindole relative to the nucleic acid bases. Biochemical studies further support the irreversible oxidation of the indole moiety and allow the determination of yields of irreversible product formation. The construction of these assemblies containing 4-methylindole as an artificial base is also applied in examining long-range charge transport mediated by the DNA base pair stack as a function of intervening distance and sequence. The rate of formation of the indole radical cation is >/=10(7) s(-)(1) for different assemblies with the ruthenium positioned 17-37 A away from the methylindole and with intervening A-T base pairs primarily composing the bridge. In these assemblies, methylindole radical formation at a distance is essentially coincident with quenching of the ruthenium excited state to form the Ru(III) oxidant; charge transport is not rate limiting over this distance regime. The measurements here of rates of radical cation formation establish that a model of G-hopping and AT-tunneling is not sufficient to account for DNA charge transport. Instead, these data are viewed mechanistically as charge transport through the DNA duplex primarily through hopping among well stacked domains of the helix defined by DNA sequence and dynamics.
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Affiliation(s)
- Matthias Pascaly
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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513
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514
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515
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Fu PKL, Bradley PM, van Loyen D, Dürr H, Bossmann SH, Turro C. DNA photocleavage by a supramolecular Ru(II)-viologen complex. Inorg Chem 2002; 41:3808-10. [PMID: 12132903 DOI: 10.1021/ic020136t] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A novel Ru(II) complex possessing two sequentially linked viologen units, Ru-V(1)-V(2)(6+), was synthesized and characterized. Upon excitation of the Ru(II) unit (lambda(exc) = 532 nm, fwhm approximately 10 ns), a long-lived charge-separated (CS) state is observed (tau = 1.7 micros) by transient absorption spectroscopy. Unlike Ru(bpy)(3)(2+), which cleaves DNA upon photolysis through the formation of reactive oxygen species, such as (1)O(2) and O(2)(-), the photocleavage of plasmid DNA by Ru-V(1)-V(2)(6+) is observed both in air and under N(2) atmosphere (lambda(irr) > 395 nm).
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Affiliation(s)
- Patty K-L Fu
- Department of Chemistry, The Ohio State University, Columbus, OH 43210, USA
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516
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Rak J, Voityuk AA, Marquez A, Rösch N. The Effect of Pyrimidine Bases on the Hole-Transfer Coupling in DNA†. J Phys Chem B 2002. [DOI: 10.1021/jp014261m] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Janusz Rak
- Institut für Physikalische und Theoretische Chemie, Technische Universität München, 85747 Garching, Germany, Department of Chemistry, University of Gdañsk, Sobieskiego 18, 80−353 Gdañsk, Poland, and Departamento de Química Física, Facultad de Química, Universitad de Sevilla, CL/Prof. García González s/n, 41012-Sevilla, Spain
| | - Alexander A. Voityuk
- Institut für Physikalische und Theoretische Chemie, Technische Universität München, 85747 Garching, Germany, Department of Chemistry, University of Gdañsk, Sobieskiego 18, 80−353 Gdañsk, Poland, and Departamento de Química Física, Facultad de Química, Universitad de Sevilla, CL/Prof. García González s/n, 41012-Sevilla, Spain
| | - Antonio Marquez
- Institut für Physikalische und Theoretische Chemie, Technische Universität München, 85747 Garching, Germany, Department of Chemistry, University of Gdañsk, Sobieskiego 18, 80−353 Gdañsk, Poland, and Departamento de Química Física, Facultad de Química, Universitad de Sevilla, CL/Prof. García González s/n, 41012-Sevilla, Spain
| | - Notker Rösch
- Institut für Physikalische und Theoretische Chemie, Technische Universität München, 85747 Garching, Germany, Department of Chemistry, University of Gdañsk, Sobieskiego 18, 80−353 Gdañsk, Poland, and Departamento de Química Física, Facultad de Química, Universitad de Sevilla, CL/Prof. García González s/n, 41012-Sevilla, Spain
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517
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Jortner J, Bixon M, Voityuk AA, Rösch N. Superexchange Mediated Charge Hopping in DNA. J Phys Chem A 2002. [DOI: 10.1021/jp014232b] [Citation(s) in RCA: 136] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joshua Jortner
- School of Chemistry, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel, and Institut für Physikalische und Theoretische Chemie, Technische Universität München, 85747 Garching, Germany
| | - M. Bixon
- School of Chemistry, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel, and Institut für Physikalische und Theoretische Chemie, Technische Universität München, 85747 Garching, Germany
| | - Alexander A. Voityuk
- School of Chemistry, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel, and Institut für Physikalische und Theoretische Chemie, Technische Universität München, 85747 Garching, Germany
| | - Notker Rösch
- School of Chemistry, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel, and Institut für Physikalische und Theoretische Chemie, Technische Universität München, 85747 Garching, Germany
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518
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Boon EM, Pope MA, Williams SD, David SS, Barton JK. DNA-mediated charge transport as a probe of MutY/DNA interaction. Biochemistry 2002; 41:8464-70. [PMID: 12081496 DOI: 10.1021/bi012068c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MutY is an Escherichia coli DNA repair enzyme that binds to 8-oxo-G:A and G:A mismatches and catalyzes the deglycosylation of the mismatched 2'-deoxyadenosine. We have applied DNA-mediated charge transport to probe the interaction of MutY with its DNA substrate. Oligonucleotides synthesized with a tethered rhodium intercalator and guanine doublets placed before and after the MutY binding site are used to assay for base flipping activity by MutY. On the basis of this assay, we find no evidence that MutY uses progressive base flipping as a means to find its binding site; protein binding does not perturb long-range DNA charge transport. DNA-mediated charge transport can be utilized to promote protein-DNA cross-linking from a distance. Long-range oxidation of 8-oxo-G within the MutY binding site using tethered rhodium intercalators promoted cross-linking and yielded information on MutY side chains that interact with this base. On the basis of photooxidative cross-linking of the wild type but not K142A mutant, it is evident that, within the protein complex, lysine 142 makes important contacts with 8-oxo-G.
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Affiliation(s)
- Elizabeth M Boon
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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519
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Nakatani K, Dohno C, Saito I. N(2)-phenyldeoxyguanosine: modulation of the chemical properties of deoxyguanosine toward one-electron oxidation in DNA. J Am Chem Soc 2002; 124:6802-3. [PMID: 12059182 DOI: 10.1021/ja025781d] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have shown here that (1) substitution of an exocyclic amino group of dG is effective in modulating the chemical properties of dG toward one-electron oxidation and (2) decomposition of the guanine radical cation was effectively suppressed near dPhG. These results indicate that dPhG is a prototype of nucleosides functioning as an intrinsic antioxidant of duplex DNA toward one-electron oxidation.
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Affiliation(s)
- Kazuhiko Nakatani
- Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, and CREST and PRESTO, Japan Science and Technology Corporation, Kyoto 606-8501, Japan.
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520
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Komineas S, Kalosakas G, Bishop AR. Effects of intrinsic base-pair fluctuations on charge transport in DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2002; 65:061905. [PMID: 12188757 DOI: 10.1103/physreve.65.061905] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2002] [Indexed: 05/23/2023]
Abstract
We investigate propagation of a charge carrier along intrinsically dynamically disordered double-stranded DNA. This is realized by the semiclassical coupling of the charge with a nonlinear lattice model that can accurately describe the statistical mechanics of the large amplitude fluctuations of the base pairs leading to the thermal denaturation transition of DNA. We find that the fluctuating intrinsic disorder can trap the charge and inhibit polaronic charge transport. The dependence of the mean distance covered by the charge carrier until its trapping, as a function of the energy of the fluctuations of the base pairs is also presented.
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Affiliation(s)
- S Komineas
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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521
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Effect of hydrogen bonding on the photo-oxidation of DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2002. [DOI: 10.1016/s1389-5567(02)00005-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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522
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Basko DM, Conwell EM. Self-trapping versus trapping: application to hole transport in DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2002; 65:061902. [PMID: 12188754 DOI: 10.1103/physreve.65.061902] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2002] [Indexed: 05/23/2023]
Abstract
We address the problem of interplay between self-trapping effects and effects of an external potential, which may be relevant for many physical systems, such as polarons in solids or a Bose-Einstein condensate with attraction. If the potential consists of two different wells, the system initially localized in the shallower well may relax into the deeper well, or may not if stabilized by the self-trapping effect. We show how this picture can be applied to interpret results of recent experiments on electron transfer in the DNA molecule [Giese et al., Nature 412, 318 (2001)]. The results of our calculations agree well with the experimental findings, giving evidence that hole transport in DNA involves polaronic effects.
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Affiliation(s)
- D M Basko
- Department of Chemistry, University of Rochester, Rochester, New York 14627, USA.
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523
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524
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Reid GD, Whittaker DJ, Day MA, Turton DA, Kayser V, Kelly JM, Beddard GS. Femtosecond electron-transfer reactions in mono- and polynucleotides and in DNA. J Am Chem Soc 2002; 124:5518-27. [PMID: 11996595 DOI: 10.1021/ja0172363] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quenching of redox active, intercalating dyes by guanine bases in DNA can occur on a femtosecond time scale both in DNA and in nucleotide complexes. Notwithstanding the ultrafast rate coefficients, we find that a classical, nonadiabatic Marcus model for electron transfer explains the experimental observations, which allows us to estimate the electronic coupling (330 cm(-1)) and reorganization (8070 cm(-1)) energies involved for thionine-[poly(dG-dC)](2) complexes. Making the simplifying assumption that other charged, pi-stacked DNA intercalators also have approximately these same values, the electron-transfer rate coefficients as a function of the driving force, DeltaG, are derived for similar molecules. The rate of electron transfer is found to be independent of the speed of molecular reorientation. Electron transfer to the thionine singlet excited state from DNA obtained from calf thymus, salmon testes, and the bacterium, micrococcus luteus (lysodeikticus) containing different fractions of G-C pairs, has also been studied. Using a Monte Carlo model for electron transfer in DNA and allowing for reaction of the dye with the nearest 10 bases in the chain, the distance dependence scaling parameter, beta, is found to be 0.8 +/- 0.1 A(-1). The model also predicts the redox potential for guanine dimers, and we find this to be close to the value for isolated guanine bases. Additionally, we find that the pyrimidine bases are barriers to efficient electron transfer within the superexchange limit, and we also infer from this model that the electrons do not cross between strands on the picosecond time scale; that is, the electronic coupling occurs predominantly through the pi-stack and is not increased substantially by the presence of hydrogen bonding within the duplex. We conclude that long-range electron transfer in DNA is not exceptionally fast as would be expected if DNA behaved as a "molecular wire" but nor is it as slow as is seen in proteins, which do not benefit from pi-stacking.
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Affiliation(s)
- Gavin D Reid
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
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525
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Lewis FD, Zuo X, Liu J, Hayes RT, Wasielewski MR. Dynamics of inter- and intrastrand hole transport in DNA hairpins. J Am Chem Soc 2002; 124:4568-9. [PMID: 11971697 DOI: 10.1021/ja0177859] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dynamics of photoinduced electron transfer has been investigated in DNA hairpins possessing a stilbenedicarboxamide (Sa) electron acceptor, a guanine (G) primary donor, and two adjacent guanines (GG) as secondary donors. Hole transport from G to GG across a single A is more rapid than across AA or T by factors of 20 +/- 7 and 40 +/- 15, respectively. Intrastrand hole transport across a single A is more rapid than interstrand transport by a factor of 7 +/- 3.
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Affiliation(s)
- Frederick D Lewis
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, USA.
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526
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Fahlman RP, Sen D. DNA conformational switches as sensitive electronic sensors of analytes. J Am Chem Soc 2002; 124:4610-6. [PMID: 11971708 DOI: 10.1021/ja012618u] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The electrical conductivity of DNA is dependent on its conformational state. We demonstrate here that such a dependence may be harnessed for the electronic sensing of external analytes, for instance, adenosine. Such a DNA sensor incorporates an analyte "receptor", whose altered conformation in the presence of bound analyte switches the conformation, and hence, the conductive path between two DNA double-helical stems. Two distinct designs for such sensors are described here, that permit significant electrical conduction through a "detector" double-helical stem only in the presence of the bound analyte. In the first design, current flows through the analyte receptor itself, whereas in the second, current flows in a path adjacent to the receptor. The former design may be especially suitable for certain categories of analytes, including heterocycle-containing compounds such as adenosine, whereas the latter design should be generally applicable to the detection of any molecular analyte, large or small. Since analyte detection in these DNA sensors is electronic, the potential exists for their application in rapid and automated chip-based detection of small molecules as well as of proteins and other macromolecules.
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Affiliation(s)
- Richard P Fahlman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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527
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Andersson M, Linke M, Chambron JC, Davidsson J, Heitz V, Hammarström L, Sauvage JP. Long-range electron transfer in porphyrin-containing [2]-rotaxanes: tuning the rate by metal cation coordination. J Am Chem Soc 2002; 124:4347-62. [PMID: 11960464 DOI: 10.1021/ja0119907] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of [2]-rotaxanes has been synthesized in which two Zn(II)-porphyrins (ZnP) electron donors were attached as stoppers on the rod. A macrocycle attached to a Au(III)-porphyrin (AuP+) acceptor was threaded on the rod. By selective excitation of either porphyrin, we could induce an electron transfer from the ZnP to the AuP+ unit that generated the same ZnP*+-AuP* charge-transfer state irrespective of which porphyrin was excited. Although the reactants were linked only by mechanical or coordination bonds, electron-transfer rate constants up to 1.2x10(10) x s(-1) were obtained over a 15-17 A edge-to-edge distance between the porphyrins. The resulting charge-transfer state had a relatively long lifetime of 10-40 ns and was formed in high yield (>80%) in most cases. By a simple variation of the link between the reactants, viz. a coordination of the phenanthroline units on the rotaxane rod and ring by either Ag+ or Cu+, we could enhance the electron-transfer rate from the ZnP to the excited 3AuP+. We interpret our data in terms of an enhanced superexchange mechanism with Ag+ and a change to a stepwise hopping mechanism with Cu+, involving the oxidized Cu(phen)22+ unit as a real intermediate. When the ZnP unit was excited instead, electron transfer from the excited 1ZnP to AuP+ was not affected, or even slowed, by Ag+ or Cu+. We discuss this asymmetry in terms of the different orbitals involved in mediating the reaction in an electron- and a hole-transfer mechanism. Our results show the possibility to tune the rates of electron transfer between noncovalently linked reactants by a convenient modification of the link. The different effect of Ag+ and Cu+ on the rate with ZnP and AuP+ excitation shows an additional possibility to control the electron-transfer reactions by selective excitation. We also found that coordination of the Cu+ introduced an energy-transfer reaction from 1ZnP to Cu(phen)2+ (k = 5.1x10(9) x s(-1)) that proceeded in competition with electron transfer to AuP+ and was followed by a quantitative energy transfer to give the 3ZnP state (k = 1.5x10(9) x s(-1)).
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Affiliation(s)
- Mikael Andersson
- Department of Physical Chemistry, Uppsala University, Box 532, S-751 21 Uppsala, Sweden
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528
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Pourtois G, Beljonne D, Cornil J, Ratner MA, Brédas JL. Photoinduced electron-transfer processes along molecular wires based on phenylenevinylene oligomers: a quantum-chemical insight. J Am Chem Soc 2002; 124:4436-47. [PMID: 11960473 DOI: 10.1021/ja017150+] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantum-chemical techniques are applied to model the mechanisms of photoinduced charge transfer from a pi-electron donating group (tetracene, D) to a pi-electron-acceptor moiety (pyromellitimide, A) separated by a bridge of increasing size (p-phenylenevinylene oligomers, B). Correlated Hartree-Fock semiempirical approaches are exploited to calculate the four main parameters controlling the transfer rate (k(RP)) in the framework of Marcus-Jortner-Levich's formalism: (i) the electronic coupling between the initial and final states; (ii) and (iii) the internal and external reorganization energy terms; and (iv) the variation of the free Gibbs energy. The charge transfer is shown to proceed in these compounds through two competing mechanisms, coherent (superexchange) versus incoherent (bridge-mediated) pathways. While superexchange is the dominant mechanism for short bridges, incoherent transfer through hopping along the phenylene vinylene segment takes over in longer chains (for ca. three phenylenevinylene repeat units). The influence of the chemical structure of the pi-conjugated phenylenevinylene bridge on the electronic properties and the rate of charge transfer is also investigated.
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Affiliation(s)
- G Pourtois
- Laboratory for Chemistry of Novel Materials, University of Mons-Hainaut, 20, Place du Parc, B-7000 Mons, Belgium
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529
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Kawai K, Wata Y, Hara M, Tojo S, Majima T. Regulation of one-electron oxidation rate of guanine by base pairing with cytosine derivatives. J Am Chem Soc 2002; 124:3586-90. [PMID: 11929247 DOI: 10.1021/ja016530s] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Effects of base pairing on the one-electron oxidation rate of guanine derivatives, guanine, 8-bromoguanine, and 8-oxo-7,8-dihydroguanine have been studied. The one-electron oxidation rate of guanine derivatives was determined by triplet-quenching experiments, using N,N'-dibutylnaphthaldiimide (NDI) in the triplet excited state (3NDI*) and fullerene (C(60)) in the triplet excited state ((3)C(60*)) as oxidants. In all three guanine derivatives studied here, acceleration of the one-electron oxidation was observed upon hydrogen bonding with cytosine, which demonstrates lowering of the oxidation potential of guanine derivatives by base pairing with cytosine. When a methyl or bromo group was introduced to the C5 position of cytosine, acceleration or suppression of the one-electron oxidation relative to the guanine:cytosine base pair was observed, respectively. The results demonstrate that the one-electron oxidation rate of guanine in DNA can be regulated by introducing a substituent on base pairing cytosine.
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Affiliation(s)
- Kiyohiko Kawai
- Contribution from The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan.
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530
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Delaney S, Pascaly M, Bhattacharya PK, Han K, Barton JK. Oxidative damage by ruthenium complexes containing the dipyridophenazine ligand or its derivatives: a focus on intercalation. Inorg Chem 2002; 41:1966-74. [PMID: 11925195 DOI: 10.1021/ic0111738] [Citation(s) in RCA: 200] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interactions with DNA by a family of ruthenium(II) complexes bearing the dppz (dppz = dipyridophenazine) ligand or its derivatives have been examined. The complexes include Ru(bpy)(2)(dppx)(2+) (dppx = 7,8-dimethyldipyridophenazine), Ru(bpy)(2)(dpq)(2+) (dpq = dipyridoquinoxaline), and Ru(bpy)(2)(dpqC)(2+) (dpqC = dipyrido-6,7,8,9-tetrahydrophenazine). Their ground and excited state oxidation/reduction potentials have been determined using cyclic voltammetry and fluorescence spectroscopy. An intercalative binding mode has been established on the basis of luminescence enhancements in the presence of DNA, excited state quenching, fluorescence polarization values, and enantioselectivity. Oxidative damage to DNA by these complexes using the flash/quench method has been examined. A direct correlation between the amount of guanine oxidation obtained via DNA charge transport and the strength of intercalative binding was observed. Oxidative damage to DNA through DNA-mediated charge transport was also compared directly for two DNA-tethered ruthenium complexes. One contains the dppz ligand that binds avidly by intercalation, and the other contains only bpy ligands, that, while bound covalently, can only associate with the base pairs through groove binding. Long range oxidative damage was observed only with the tethered, intercalating complex. These results, taken together, all support the importance of close association and intercalation for DNA-mediated charge transport. Electronic access to the DNA base pairs, provided by intercalation of the oxidant, is a prerequisite for efficient charge transport through the DNA pi-stack.
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Affiliation(s)
- Sarah Delaney
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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531
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Haraguchi K, Delaney MO, Wiederholt CJ, Sambandam A, Hantosi Z, Greenberg MM. Synthesis and characterization of oligodeoxynucleotides containing formamidopyrimidine lesions and nonhydrolyzable analogues. J Am Chem Soc 2002; 124:3263-9. [PMID: 11916409 DOI: 10.1021/ja012135q] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligodeoxynucleotides containing formamidopyrimidine lesions and C-nucleoside analogues at defined sites were prepared by solid-phase synthesis and in some cases enzymatic ligation. Formamidopyrimidine lesions were introduced as dinucleotides to prevent rearrangement to their pyranose isomers. Oligodeoxynucleotides containing single diastereomers of C-nucleoside analogues of Fapy.dA were introduced by using the respective phosphoramidites. The formamidopyrimidine lesions reduce the T(M) of dodecamers relative to their unmodified nucleotide counterparts when opposite the nucleotide proper base-pairing partner. However, duplexes containing Fapy.dG-dA mispairs melt significantly higher than those comprised of dG-dA. All duplexes containing Fapy.dA-dX or its C-nucleoside analogue melt lower than the respective complexes containing dA-dX. Studies of the alkaline lability of oligodeoxynucleotides containing formamidopyrimidine lesions indicate that Fapy.dA is readily identified as an alkali-labile lesion with use of piperidine (1.0 M, 90 degrees C, 20 min), but Fapy.dG is less easily identified in this manner.
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Affiliation(s)
- Kazuhiro Haraguchi
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
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532
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Núñez ME, Noyes KT, Barton JK. Oxidative charge transport through DNA in nucleosome core particles. CHEMISTRY & BIOLOGY 2002; 9:403-15. [PMID: 11983330 DOI: 10.1016/s1074-5521(02)00121-7] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Eukaryotic DNA is packaged into nucleosomes, made up of 146 bp of DNA wrapped around a core of histone proteins. We used photoexcited rhodium intercalators to explore DNA charge transport within these assemblies. Although histone proteins inhibit intercalation of the rhodium complex within the core particle, they do not prevent 5'-GG-3' oxidation, the signature of oxidative charge transport through DNA. Moreover, using rhodium intercalators tethered to the 5' terminus of the DNA, we found that guanine bases within the nucleosome can be oxidized from a distance of 24 bp. Histone binding did not affect the pattern and extent of this oxidation. Therefore, although the structure of the nucleosome core particle generally protects DNA from damage by solution-borne molecules, packaging within the nucleosome does not protect DNA from charge transfer damage through the base pair stack.
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Affiliation(s)
- Megan E Núñez
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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533
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Turro NJ. Damage control of DNA in nucleosome core particles: when a histone's loving, protective embrace is just not good enough. CHEMISTRY & BIOLOGY 2002; 9:399. [PMID: 11983328 DOI: 10.1016/s1074-5521(02)00128-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Packaging DNA into nucleosome core particles generally offers protection from damage by molecules diffusing in solution. However, on page 403 of this issue, Barton and coworkers report that although noncovalently bound, activated Rh (Rhodium) does not readily bind within nucleosomal DNA, activated Rh that is covalently tethered to the 5' terminus of a histone-associated oligonucleotide oxidizes guanine bases from a distance of up to 24 base pairs, demonstrating that histones do not protect DNA from long-range damage from the transport of charge through stacked bases. This implies that oxidative damage generated on DNA in vivo may spread from an initially damaged site to distal sites. Once created, such sites may persist and be resistant to repair because of the protective packaging by histones; they thus may result in permanent mutations.
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Affiliation(s)
- Nicholas J Turro
- Department of Chemistry, Columbia University, 3000 Broadway, MC 3119, New York, NY 10027, USA
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534
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Lewis FD, Liu J, Liu X, Zuo X, Hayes RT, Wasielewski MR. Dynamics and Energetics of Hole Trapping in DNA by 7-Deazaguanine. Angew Chem Int Ed Engl 2002. [DOI: 10.1002/1521-3757(20020315)114:6<1068::aid-ange1068>3.0.co;2-s] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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535
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Lewis FD, Liu J, Liu X, Zuo X, Hayes RT, Wasielewski MR. Dynamics and energetics of hole trapping in DNA by 7-deazaguanine. Angew Chem Int Ed Engl 2002; 41:1026-8. [PMID: 12491301 DOI: 10.1002/1521-3773(20020315)41:6<1026::aid-anie1026>3.0.co;2-t] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Frederick D Lewis
- Department of Chemistry, Northwestern University, Evanston, IL 60208-3113, USA.
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536
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Williams TT, Barton JK. The effect of varied ion distributions on long-range DNA charge transport. J Am Chem Soc 2002; 124:1840-1. [PMID: 11866582 DOI: 10.1021/ja012217e] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Long-range oxidative damage to DNA was utilized as a probe to delineate the effects of different ion distributions on DNA charge transport. DNA assemblies were constructed, containing a tethered rhodium intercalating photooxidant, spatially separated from two 5'-GG-3' sites of oxidative damage, with either an A6-tract or a mixed DNA sequence intervening between the guanine doublets; the extent of charge transport was assessed through measurements of the ratio of yields of damage at the guanine doublet distal versus that proximal to the metal binding site. The distal/proximal damage ratios were compared after photooxidation of otherwise identical Rh-tethered assemblies, except for 32P-labeling either at the 5'- or 3'-end; this labeling difference corresponds, in the absence of charge neutralization by condensed counterions, to a shift in negative charge from one end of the duplex to the other. Both with assemblies containing the mixed sequence and the A6-tract, we observed that moving the negative charges to the proximal end of the duplex significantly decreased hole transport to the distal end. We propose that these results reflect variations in the thermodynamic potential at the proximal and distal guanine sites because of the change in charges at the termini of the oligomer. High values for the internal dielectric constant of the stacked base pairs are suggested by these data. Hence, the longitudinal polarizability of DNA may be important to consider in mechanisms for long-range DNA charge transport.
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Affiliation(s)
- Tashica T Williams
- Division of Chemistry and Chemical Engineering, California Institute of Technology Pasadena, California 91125, USA
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537
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Boon EM, Salas JE, Barton JK. An electrical probe of protein-DNA interactions on DNA-modified surfaces. Nat Biotechnol 2002; 20:282-6. [PMID: 11875430 DOI: 10.1038/nbt0302-282] [Citation(s) in RCA: 190] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA charge transport chemistry is found to provide a sensitive method for probing protein-dependent changes in DNA structure and enzymatic reactions. Here we describe the development of an electrochemical assay of protein binding to DNA-modified electrodes based upon the detection of associated perturbations in DNA base stacking. Gold electrode surfaces that were modified with loosely packed DNA duplexes, covalently crosslinked to a redox-active intercalator and containing the binding site of the test protein, were constructed. Charge transport through DNA as a function of protein binding was then assayed. Substantial attenuation in current is seen in the presence of the base-flipping enzymes HhaI methylase and uracil DNA glycosylase, as well as with TATA-binding protein. When restriction endonuclease PvuII (R.PvuII) binds to its methylated target, little base-stacking perturbation occurs and little diminution in current flow is observed. Importantly, the kinetics of restriction by R.PvuII of its nonmethylated target is also easily monitored electrochemically. This approach should be generally applicable to assaying protein--DNA interactions and reactions on surfaces.
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Affiliation(s)
- Elizabeth M Boon
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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538
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Nakatani K, Dohno C, Ogawa A, Saito I. Suppression of DNA-mediated charge transport by BamHI binding. CHEMISTRY & BIOLOGY 2002; 9:361-6. [PMID: 11927261 DOI: 10.1016/s1074-5521(02)00119-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A guanine radical cation produced by one-electron DNA oxidation migrates over long distances through the DNA pi-stack. Fundamental questions regarding the likelihood of charge transport in genomic DNA, the effects of protein binding, and its biological consequences arise as the next issues of study. Electronic effects of protein binding on the efficiency of charge transport were investigated for the endonuclease BamHI-DNA complex. Direct contact of a positively charged guanidium group of BamHI to guanines in the recognition sequence 5'-GGATCC-3' completely suppressed one-electron oxidation of the guanine in the protein binding site and dramatically lowered the charge transport efficiency through the sequence. Electronically insulated guanines, by the hydrogen bonding contact of a guanidium group in BamHI, no longer function as a stepping stone in the charge transport through the DNA pi-stack.
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Affiliation(s)
- Kazuhiko Nakatani
- Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Japan.
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539
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Okamoto A, Tanabe K, Dohno C, Saito I. Modulation of remote DNA oxidation by hybridization with peptide nucleic acids (PNA). Bioorg Med Chem 2002; 10:713-8. [PMID: 11814860 DOI: 10.1016/s0968-0896(01)00320-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have examined the efficiency of DNA photooxidation in DNA/PNA duplex and DNA/(PNA)(2) triplex for the first time. DNA/PNA duplex was cleaved at GG steps by external riboflavin with high efficiency like specific GG cleavage in DNA/DNA duplex. However, the 5'G selectivity of the GG oxidation in DNA/PNA duplex was much lower than that observed in DNA/DNA duplex. Remote DNA oxidation of oxidant-tethered DNA/PNA duplex was considerably suppressed. In contrast, the formation of DNA/(PNA)(2) triplex by hybridization with two PNA strands completely inhibited the remote GG oxidation, indicating that PNA acts as an inhibition for remote oxidative DNA damage.
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Affiliation(s)
- Akimitsu Okamoto
- Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Kyoto 606-8501, Japan
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540
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Voityuk AA, Rösch N. Quantum Chemical Modeling of Electron Hole Transfer through π Stacks of Normal and Modified Pairs of Nucleobases. J Phys Chem B 2002. [DOI: 10.1021/jp013417f] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander A. Voityuk
- Institut for Physikalische and Theoretische Chemie, Technische Universität München, 85747 Garching, Germany
| | - Notker Rösch
- Institut for Physikalische and Theoretische Chemie, Technische Universität München, 85747 Garching, Germany
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541
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Tong GSM, Kurnikov IV, Beratan DN. Tunneling Energy Effects on GC Oxidation in DNA. J Phys Chem B 2002. [DOI: 10.1021/jp013387g] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Glenna S. M. Tong
- Departments of Chemistry and Biochemistry, Box 90346, Duke University, Durham, North Carolina 27708-0346
| | - Igor V. Kurnikov
- Departments of Chemistry and Biochemistry, Box 90346, Duke University, Durham, North Carolina 27708-0346
| | - David N. Beratan
- Departments of Chemistry and Biochemistry, Box 90346, Duke University, Durham, North Carolina 27708-0346
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542
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Boone E, Schuster GB. Long-range oxidative damage in duplex DNA: the effect of bulged G in a G-C tract and tandem G/A mispairs. Nucleic Acids Res 2002; 30:830-7. [PMID: 11809898 PMCID: PMC100289 DOI: 10.1093/nar/30.3.830] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Two series of duplex DNA oligomers were prepared having an anthraquinone derivative (AQ) covalently linked at a 5'-terminus. Irradiation of the AQ at 350 nm leads to injection of an electron hole (radical cation) into the DNA. The radical cation migrates through the DNA causing reaction primarily at G(n) sequences. In one series, GA tandem mispairs are inserted between GG steps to assess the effect of the mispair on the transport of the radical cation, reaction (damage) caused by the radical cation at the mispair, and repair of the resulting damage by formamidopyrimidine DNA glycosylase (Fpg). In the second series, a bulged guanine in a G3C2 sequence is interposed between the GG steps. These experiments reveal that neither G/A tandem mispairs nor bulged guanines are significant barriers to long-range charge migration in DNA. The radical cation does not cause reaction at guanines in the G/A tandem mispair. Reaction does occur at the bulged guanine, but it is repaired by Fpg.
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Affiliation(s)
- Edna Boone
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
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543
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Reynisson J, Steenken S. DFT studies on the pairing abilities of the one-electron reduced or oxidized adenine–thymine base pair. Phys Chem Chem Phys 2002. [DOI: 10.1039/b206342e] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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544
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Henderson P, Boone E, Schuster G. Bulged Guanine is Uniquely Sensitive to Damage Caused by Visible-Light Irradiation of Ethidium Bound to DNA: A Possible Role in Mutagenesis. Helv Chim Acta 2002. [DOI: 10.1002/1522-2675(200201)85:1<135::aid-hlca135>3.0.co;2-h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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545
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Kawai K, Takada T, Tojo S, Majima T. Hole transfer through DNA monitored by transient absorption of phenothiazine radical cation. Tetrahedron Lett 2002. [DOI: 10.1016/s0040-4039(01)02064-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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546
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547
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Dietrich A, Buschmann V, Müller C, Sauer M. Fluorescence resonance energy transfer (FRET) and competing processes in donor-acceptor substituted DNA strands: a comparative study of ensemble and single-molecule data. J Biotechnol 2002; 82:211-31. [PMID: 11999691 DOI: 10.1016/s1389-0352(01)00039-3] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We studied the fluorescence resonance energy transfer (FRET) efficiency of different donor-acceptor labeled model DNA systems in aqueous solution from ensemble measurements and at the single molecule level. The donor dyes: tetramethylrhodamine (TMR); rhodamine 6G (R6G); and a carbocyanine dye (Cy3) were covalently attached to the 5'-end of a 40-mer model oligonucleotide. The acceptor dyes, a carbocyanine dye (Cy5), and a rhodamine derivative (JA133) were attached at modified thymidine bases in the complementary DNA strand with donor-acceptor distances of 5, 15, 25 and 35 DNA-bases, respectively. Anisotropy measurements demonstrate that none of the dyes can be observed as a free rotor; especially in the 5-bp constructs the dyes exhibit relatively high anisotropy values. Nevertheless, the dyes change their conformation with respect to the oligonucleotide on a slower time scale in the millisecond range. This results in a dynamic inhomogeneous distribution of donor/acceptor (D/A) distances and orientations. FRET efficiencies have been calculated from donor and acceptor fluorescence intensity as well as from time-resolved fluorescence measurements of the donor fluorescence decay. Dependent on the D/A pair and distance, additional strong fluorescence quenching of the donor is observed, which simulates lower FRET efficiencies at short distances and higher efficiencies at longer distances. On the other hand, spFRET measurements revealed subpopulations that exhibit the expected FRET efficiency, even at short D/A distances. In addition, the measured acceptor fluorescence intensities and lifetimes also partly show fluorescence quenching effects independent of the excitation wavelength, i.e. either directly excited or via FRET. These effects strongly depend on the D/A distance and the dyes used, respectively. The obtained data demonstrate that besides dimerization at short D/A distances, an electron transfer process between the acceptor Cy5 and rhodamine donors has to be taken into account. To explain deviations from FRET theory even at larger D/A distances, we suggest that the pi-stack of the DNA double helix mediates electron transfer from the donor to the acceptor, even over distances as long as 35 base pairs. Our data show that FRET experiments at the single molecule level are rather suited to resolve fluorescent subpopulations in heterogeneous mixture, information about strongly quenched subpopulations gets lost.
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Affiliation(s)
- Anja Dietrich
- Physikalisch-Chemishes Institut, Universität Heidelberg, Germany
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548
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Abstract
In this contribution we advance and explore the thermally induced hopping (TIH) mechanism for long-range charge transport (CT) in DNA and in large-scale chemical systems. TIH occurs in donor-bridge-acceptor systems, which are characterized by off-resonance donor-bridge interactions (energy gap DeltaE > 0), involving thermally activated donor-bridge charge injection followed by intrabridge charge hopping. We observe a "transition" from superexchange to TIH with increasing the bridge length (i.e., the number N of the bridge constituents), which is manifested by crossing from the exponential N-dependent donor-acceptor CT rate at low N (< N(X)) to a weakly (algebraic) N-dependent CT rate at high N (>N(X)). The "critical" bridge size N(X) is determined by the energy gap, the nearest-neighbor electronic couplings, and the temperature. Experimental evidence for the TIH mechanism was inferred from our analysis of the chemical yields for the distal/proximal guanine (G) triplets in the (GGG)(+)TTXTT(GGG) duplex (X = G, azadine (zA), and adenine (A)) studied by Nakatani, Dohno and Saito [J. Am. Chem. Soc. 2000, 122, 5893]. The TIH sequential model, which involves hole hopping between (GGG) and X, is analyzed in terms of a sequential process in conjunction with parallel reactions of (GGG)(+) with water, and provides a scale of (free) energy gaps (relative to (GGG)(+)) of Delta = 0.21-0.24 eV for X = A, Delta = 0.10-0.14 eV for X = zA, and Delta = 0.05-0.10 eV for X = G. We further investigated the chemical yields for long-range TIH in (G)l(+)Xn(G)l (l = 1-3) duplexes, establishing the energetic constraints (i.e., the donor - bridge base (X) energy gap Delta), the bridge structural constraints (i.e., the intrabridge X-X hopping rates k(m)), and the kinetic constraints (i.e., the rate k(d) for the reaction of with water). Effective TIH is expected to prevail for Delta less than or approximately equal to 0.20 eV with a "fast" water reaction (k(d)/k(m) approximately 10(-3)) and for Delta < 0.30 eV with a "slow" water reaction (k(d)/k(m) approximately 10(-5)). We conclude that (T)n bridges (for which Delta approximately equals 0.6 eV) cannot act in TIH of holes. From an analysis based on the energetics of the electronic coupling matrix elements in G(+)(T-A)n(GGG) duplexes we conclude that the superexchange mechanism is expected to dominate for n = 1-4. For long (A)n bridges (n > or approximately equal to 4) the TIH prevails, provided that the water side reaction is slow, raising the issue of chemical control of TIH through long (A)n bridges in DNA attained by changing the solution composition.
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Affiliation(s)
- M Bixon
- School of Chemistry, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
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549
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Kawai K, Takada T, Tojo S, Ichinose N, Majima T. Observation of hole transfer through DNA by monitoring the transient absorption of pyrene radical cation. J Am Chem Soc 2001; 123:12688-9. [PMID: 11741438 DOI: 10.1021/ja0158152] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- K Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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550
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Kurnikov IV, Tong GSM, Madrid M, Beratan DN. Hole Size and Energetics in Double Helical DNA: Competition between Quantum Delocalization and Solvation Localization. J Phys Chem B 2001. [DOI: 10.1021/jp0132329] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- I. V. Kurnikov
- Department of Chemistry, Box 90346, Duke University, Durham, North Carolina 27708-0346, and Pittsburgh Supercomputing Center, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - G. S. M. Tong
- Department of Chemistry, Box 90346, Duke University, Durham, North Carolina 27708-0346, and Pittsburgh Supercomputing Center, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - M. Madrid
- Department of Chemistry, Box 90346, Duke University, Durham, North Carolina 27708-0346, and Pittsburgh Supercomputing Center, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - D. N. Beratan
- Department of Chemistry, Box 90346, Duke University, Durham, North Carolina 27708-0346, and Pittsburgh Supercomputing Center, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
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