Electron Transfer and Charge Transport Processes in DNA

Lewis, Frederick D.

doi:10.1002/9783527618248.ch37

Cited by 24 publications

(9 citation statements)

References 249 publications

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“…This problem is different from most ET reactions in biology studied to date, which typically occur over a distances of 10-15 Å by a tunneling mechanism and, consequently, do not involve aromatic amino acid radical intermediates. [44][45][46][47][48][49][50][51][52][53][54][55][56] The participation of tyrosine in the radical-initiation pathway of RNR steps beyond simple ET because the management of proton and electron inventories is required for charge transport involving the amino acid. In the accompanying paper, we have shown that fluorotyrosine derivatives have radical peak-reduction potentials from -50 to +270 mV relative to Y and pK a s that range from 5.6 to 7.8.…”

Section: Discussionmentioning

confidence: 99%

pH Rate Profiles of F_nY₃₅₆−R2s (n = 2, 3, 4) in Escherichia coli Ribonucleotide Reductase: Evidence that Y₃₅₆ Is a Redox-Active Amino Acid along the Radical Propagation Pathway

et al. 2006

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The Escherichia coli ribonucleotide reductase (RNR), composed of two subunits (R1 and R2), catalyzes the conversion of nucleotides to deoxynucleotides. Substrate reduction requires that a tyrosyl radical (Y(122)*) in R2 generate a transient cysteinyl radical (C(439)*) in R1 through a pathway thought to involve amino acid radical intermediates [Y(122)* --> W(48) --> Y(356) within R2 to Y(731) --> Y(730) --> C(439) within R1]. To study this radical propagation process, we have synthesized R2 semisynthetically using intein technology and replaced Y(356) with a variety of fluorinated tyrosine analogues (2,3-F(2)Y, 3,5-F(2)Y, 2,3,5-F(3)Y, 2,3,6-F(3)Y, and F(4)Y) that have been described and characterized in the accompanying paper. These fluorinated tyrosine derivatives have potentials that vary from -50 to +270 mV relative to tyrosine over the accessible pH range for RNR and pK(a)s that range from 5.6 to 7.8. The pH rate profiles of deoxynucleotide production by these F(n)()Y(356)-R2s are reported. The results suggest that the rate-determining step can be changed from a physical step to the radical propagation step by altering the reduction potential of Y(356)* using these analogues. As the difference in potential of the F(n)()Y* relative to Y* becomes >80 mV, the activity of RNR becomes inhibited, and by 200 mV, RNR activity is no longer detectable. These studies support the model that Y(356) is a redox-active amino acid on the radical-propagation pathway. On the basis of our previous studies with 3-NO(2)Y(356)-R2, we assume that 2,3,5-F(3)Y(356), 2,3,6-F(3)Y(356), and F(4)Y(356)-R2s are all deprotonated at pH > 7.5. We show that they all efficiently initiate nucleotide reduction. If this assumption is correct, then a hydrogen-bonding pathway between W(48) and Y(356) of R2 and Y(731) of R1 does not play a central role in triggering radical initiation nor is hydrogen-atom transfer between these residues obligatory for radical propagation.

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Section: Discussionmentioning

confidence: 99%

pH Rate Profiles of F_nY₃₅₆−R2s (n = 2, 3, 4) in Escherichia coli Ribonucleotide Reductase: Evidence that Y₃₅₆ Is a Redox-Active Amino Acid along the Radical Propagation Pathway

et al. 2006

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“…1 Initial studies of the mechanisms of CT in DNA employed indirect methods such as fluorescence quenching or oxidative strand cleavage at guanine bases to infer the distance and base-sequence dependence of the CT process. 2 Studies by the groups of Barton, Schuster, Giese, Saito, and others, which combined DNA base-sequence design and the principles of physical organic chemistry served to elucidate many of the basic features of DNA CT. These studies have been the subject of several collected volumes and comprehensive reviews.…”

Section: ■ Introductionmentioning

confidence: 99%

Tracking Photoinduced Charge Separation in DNA: from Start to Finish

2018

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The initial studies of the dynamics of photoinduced charge separation conducted in our laboratories 20 years ago found strongly distance-dependent rate constants over short distances but failed to detect intermediates in the transport of positive charge (holes). These observations were consistent with the single-step superexchange or tunneling mechanism that had been observed for numerous donor-bridge-acceptor systems at that time. Subsequent studies found weak distance dependence for hole transport over longer distances in DNA, characteristic of incoherent hopping of either localized or delocalized holes. The introduction of synthetic DNA capped hairpin constructs possessing hole donor and acceptor chromophores (or purine bases) at opposite ends of a base-pair domain made it possible to determine the time required for transit of charge from one chromophore to the other and, in some cases, to distinguish between the transit time and the much faster initial charge injection time. These studies eliminated conventional tunneling as a viable mechanism for charge transport in DNA except at very short donor-acceptor separations; however, they did not establish the presence or nature of intermediates in the charge separation process. Recent studies in our laboratories have succeeded in identifying key intermediates as well as untangling the dynamics and efficiency of the charge separation process from start to finish. The dynamics of the initial charge injection process is dependent upon both its free energy and the stacking of the hole donor chromophore and adjacent purine base. The transport of positive charge (holes) over multiple base pairs in duplex DNA occurs most efficiently via repeating adenine bases, known as A-tracts. The transit time across an A-tract is strongly dependent upon the free energy for hole injection, whereas the efficiency of charge separation depends on the competition between charge delocalization and charge recombination in the contact radical ion pair. The guanine cation radical has been detected both by femtosecond transient absorption and by stimulated Raman spectroscopies when the guanine is located near the chromophore employed for hole injection into an A-tract. Replacement of guanine by its derivative 8-phenylethynylguanine (EG), permits tracking of hole transport across longer poly(purine) sequences as a consequence of the stronger transient absorption and stimulated Raman scattering for EG vs G. We have recently obtained evidence based on femtosecond transient absorption spectroscopy for the formation of delocalized A-polarons in A-tracts possessing four or more A-T base pairs. Similar methods have been used to track hole transport across less-common DNA structures including diblock and triblock poly(purines), locked nucleic acids, three-way junctions, and G-quadruplexes. Similar methods are have been applied to the study of photoinduced electron transport in DNA.

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“…Electron transfer (ET) has been the focus of most studies of charge transport in biology. Proteins modified with redox-active donors and acceptors, − protein partners, − and DNA bioconjugates − reveal that electrons transfer over long distances according to the Marcus theory of ET, augmented by considerations for electron tunneling. , In functioning enzymes, however, the occurrence of isolated ET is uncommon. Many primary metabolic steps involving charge transport rely on amino acid radicals in which ET is coupled to proton transfer (PT). − For such charge-transport reactions, the problem is intrinsically more complicated because both the electron and proton tunnel and these tunneling events can be coupled to one another. , As the electron moves, the p K a of the oxidized cofactor will change; however, to predict kinetics, knowledge of the driving forces for the ET and PT reactions is insufficient.…”

Section: Introductionmentioning

confidence: 99%

“…Electron transfer (ET) has been the focus of most studies of charge transport in biology. Proteins modified with redox-active donors and acceptors, [1][2][3][4][5] protein partners, [6][7][8][9][10] and DNA bioconjugates [11][12][13][14] reveal that electrons transfer over long distances according to the Marcus theory of ET, 15 augmented by considerations for electron tunneling. 16,17 In functioning enzymes, however, the occurrence of isolated ET is uncommon.…”

Section: Introductionmentioning

confidence: 99%

Mono-, Di-, Tri-, and Tetra-Substituted Fluorotyrosines: New Probes for Enzymes That Use Tyrosyl Radicals in Catalysis

et al. 2006

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A set of N-acylated, carboxyamide fluorotyrosine (F(n)()Y) analogues [Ac-3-FY-NH(2), Ac-3,5-F(2)Y-NH(2), Ac-2,3-F(2)Y-NH(2), Ac-2,3,5-F(3)Y-NH(2), Ac-2,3,6-F(3)Y-NH(2) and Ac-2,3,5,6-F(4)Y-NH(2)] have been synthesized from their corresponding amino acids to interrogate the detailed reaction mechanism(s) accessible to F(n)()Y*s in small molecules and in proteins. These Ac-F(n)()Y-NH(2) derivatives span a pK(a) range from 5.6 to 8.4 and a reduction potential range of 320 mV in the pH region accessible to most proteins (6-9). DFT electronic-structure calculations capture the observed trends for both the reduction potentials and pK(a)s. Dipeptides of the methyl ester of 4-benzoyl-l-phenylalanyl-F(n)()Ys at pH 4 were examined with a nanosecond laser pulse and transient absorption spectroscopy to provide absorption spectra of F(n)()Y*s. The EPR spectrum of each F(n)()Y* has also been determined by UV photolysis of solutions at pH 11 and 77 K. The ability to vary systematically both pK(a) and radical reduction potential, together with the facility to monitor radical formation with distinct absorption and EPR features, establishes that F(n)()Ys will be useful in the study of biological charge-transport mechanisms involving tyrosine. To demonstrate the efficacy of the fluorotyrosine method in unraveling charge transport in complex biological systems, we report the global substitution of tyrosine by 3-fluorotyrosine (3-FY) in the R2 subunit of ribonucleotide reductase (RNR) and present the EPR spectrum along with its simulation of 3-FY122*. In the companion paper, we demonstrate the utility of F(n)()Ys in providing insight into the mechanism of tyrosine oxidation in biological systems by incorporating them site-specifically at position 356 in the R2 subunit of Escherichia coli RNR.

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Electron Transfer and Charge Transport Processes in DNA

Cited by 24 publications

References 249 publications

pH Rate Profiles of F_nY₃₅₆−R2s (n = 2, 3, 4) in Escherichia coli Ribonucleotide Reductase: Evidence that Y₃₅₆ Is a Redox-Active Amino Acid along the Radical Propagation Pathway

pH Rate Profiles of F_nY₃₅₆−R2s (n = 2, 3, 4) in Escherichia coli Ribonucleotide Reductase: Evidence that Y₃₅₆ Is a Redox-Active Amino Acid along the Radical Propagation Pathway

Tracking Photoinduced Charge Separation in DNA: from Start to Finish

Mono-, Di-, Tri-, and Tetra-Substituted Fluorotyrosines: New Probes for Enzymes That Use Tyrosyl Radicals in Catalysis

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Electron Transfer and Charge Transport Processes in DNA

Cited by 24 publications

References 249 publications

pH Rate Profiles of FnY356−R2s (n = 2, 3, 4) in Escherichia coli Ribonucleotide Reductase: Evidence that Y356 Is a Redox-Active Amino Acid along the Radical Propagation Pathway

pH Rate Profiles of FnY356−R2s (n = 2, 3, 4) in Escherichia coli Ribonucleotide Reductase: Evidence that Y356 Is a Redox-Active Amino Acid along the Radical Propagation Pathway

Tracking Photoinduced Charge Separation in DNA: from Start to Finish

Mono-, Di-, Tri-, and Tetra-Substituted Fluorotyrosines: New Probes for Enzymes That Use Tyrosyl Radicals in Catalysis

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Product

Resources

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pH Rate Profiles of F_nY₃₅₆−R2s (n = 2, 3, 4) in Escherichia coli Ribonucleotide Reductase: Evidence that Y₃₅₆ Is a Redox-Active Amino Acid along the Radical Propagation Pathway

pH Rate Profiles of F_nY₃₅₆−R2s (n = 2, 3, 4) in Escherichia coli Ribonucleotide Reductase: Evidence that Y₃₅₆ Is a Redox-Active Amino Acid along the Radical Propagation Pathway