DNA-Mediated Charge Transport Requires Conformational Motion of the DNA Bases:  Elimination of Charge Transport in Rigid Glasses at 77 K

O’Neill, Melanie A.; Barton, Jacqueline K.

doi:10.1021/ja0455897

Cited by 118 publications

(144 citation statements)

References 30 publications

Supporting

Mentioning

132

Contrasting

Order By: Relevance

“…Yet, many experiments have underscored the sensitivity of DNA CT to DNA structure and dynamics (9-11, 19, 20). Indeed, it is now apparent that conformational motions of the DNA bases are required for effective CT; increased rigidity of DNA assemblies limits CT (36). The results shown here cannot be understood through descriptions for DNA CT that are defined primarily by the energetics of individual bases.…”

Section: Discussionmentioning

confidence: 88%

Long-range oxidative damage to cytosines in duplex DNA

Shao

O’Neill²,

Barton³

2004

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

140

View full text Add to dashboard Cite

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, N4-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 highenergy 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 N2-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.charge transport ͉ delocalized domain ͉ radical trap ͉ base dynamics O xidative damage to DNA from a distance through longrange migration of charge has now been established in many DNA assemblies by using different pendant photooxidants through both biochemical and spectroscopic assays (1-8). The DNA base pair stack can mediate charge transport (CT) over at least 200 Å (2, 3), and the reaction is exquisitely sensitive to the dynamic structure and stacking within the DNA duplex (9, 10). This sensitivity to perturbations in base pair stacking has been advantageous in the development of DNA-based sensors for mutational analysis (11) and may provide a role for DNAmediated CT within the cell (12), but it has limited the application of physical techniques to explore CT mechanistically.Although not a robust molecular wire, the DNA duplex has in some experiments been characterized as a wide band gap semiconductor (13,14). More prevalent have been models of incoherent CT involving a mixture of localized charge-hopping among low-energy sites, guanines and sometimes adenines, and tunneling through higher-energy pyrimidine bases (15-18). These mechanisms do not provide a rationale, however, for the sensitivity of CT to DNA structure. We have observed that DNA CT is gated by the dynamical motions of the DNA bases (9, 19) and have described DNA CT as conformationally gated hopping through transient, well stacked DNA domains (20).Our experimental strategy to probe for hole density on pyrimidines exploits the rapid ...

show abstract

Section: Discussionmentioning

confidence: 88%

Long-range oxidative damage to cytosines in duplex DNA

Shao

O’Neill²,

Barton³

2004

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

140

View full text Add to dashboard Cite

show abstract

“…While other techniques with this capacity for localized monitoring do exist (eg: NMR, gel electrophoresis of kinetically-trapped radiolabeled products), these approaches are much more complicated and time consuming. Furthermore, the reaction time scales experimentally accessible to such strategies are limited.To promote more sophisticated analyses of 2-AP spectroscopic data, numerous model systems have been characterized to assess positional effects (32), sequence dependence (33-35), stacking dynamics (5,36-38), and fluorescence quenching (34,38,39). In general, positioning a 2-AP residue near the interior of duplex DNA strongly increases energy transfer efficiency and spectral shifts.…”

mentioning

confidence: 99%

“…To promote more sophisticated analyses of 2-AP spectroscopic data, numerous model systems have been characterized to assess positional effects (32), sequence dependence (33)(34)(35), stacking dynamics (5,(36)(37)(38), and fluorescence quenching (34,38,39). In general, positioning a 2-AP residue near the interior of duplex DNA strongly increases energy transfer efficiency and spectral shifts.…”

mentioning

confidence: 99%

Site-Specific Variations in RNA Folding Thermodynamics Visualized by 2-Aminopurine Fluorescence

et al. 2007

View full text Add to dashboard Cite

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 steadystate 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 were transitioned 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 stimulusdependent 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. Timeresolved 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.Fluorescence spectroscopy of 2-aminopurine (2-AP) has played a pivotal role in the elucidation of interactions within and between nucleic acids and other biomolecules including proteins, nucleic acids, and larger structures such as multicomponent ribonucleoprotein complexes. The use of 2-AP in fluorescence studies is attractive because it can form Watson-Crick type base pairs with either thymidine (DNA), uracil (RNA), or cytosine (RNA and DNA), has a red- † This work was supported by NIH/NCI grant CA102428 and a competitive supplement from the Division of Cancer Biology (NIH/NCI) under the Activities to Promote Research Collaborations initiative (to G.M.W.). Additional support (for S.B.) was provided by Public Health Service grant P20 MD001633. shifted absorption spectrum allowing differential excitation in the presence of nucleic acids and proteins, and because its fluorescence is strongly quenched by base stacking interactions (1-3). The fluorescence properties of 2-AP are extremely sensitive to local changes in conformation, making this base analogue nearly ideal for studies involving structural dynamics (4-7), mismatch (8,9) or abasic (10-12) sites, base flipping (2,13,14), and protein-nucleic acid association (15)(16)(17)(18). Examples include characterization of ribozyme folding (19-21) and catalysis (22,23), riboswitches (24), interactions with polymerases (25-27), and nucleic aciddrug interactions (28)(2...

show abstract

“…A phonon-assisted polaron model has also been put forth (22). Studies as a function of temperature have shown the CT process to be gated by base pair dynamics; in fact, base pair motions are required for CT (23,24). …”

mentioning

confidence: 99%

Protein–DNA charge transport: Redox activation of a DNA repair protein by guanine radical

Yavin

Boal²,

Stemp

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

117

124

View full text Add to dashboard Cite

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 flash͞ quench technique, is found to promote oxidation of the 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 rutheniumtethered 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.electron transfer ͉ iron-sulfur cluster ͉ oxidative DNA damage D NA-mediated charge transport (CT) from a distance to generate oxidative damage was first demonstrated in an assembly containing a tethered metallointercalator (1). In this assembly, photoinduced oxidative damage of the 5Ј-G of 5Ј-GG-3Ј sites was observed; this damage pattern has since become the hallmark of DNA CT chemistry, and long-range oxidative damage has been confirmed by using a variety of pendant oxidants (2-6). Long-range oxidative DNA damage has been demonstrated over a distance of at least 200 Å (7, 8). Indeed, DNA either packaged in nucleosome core particles (9) or inside the cell nucleus (10) has been found to be susceptible to long-range oxidative damage. Chemically well defined assemblies, consisting of DNA duplexes with covalently bound oxidants, have been particularly useful in establishing the sensitivity of DNA CT to base-stacking perturbation (11-16). Recently, analogous studies probing long-range reductive chemistry on DNA has been probed both in solution (17-20) and on DNAmodified surfaces (14,15,21). As with oxidation chemistry, these reactions show only small variations in rate with distance but are remarkably sensitive to perturbations in the intervening base pair stack. Mechanistic descriptions for DNA CT focused first on a mixture of hopping and tunneling. A phonon-assisted polaron model has also been put forth (22). Studies as a function of temperature have shown the CT process to be gated by base pair dynamics; in fact, base pair motions are required for CT (23, 24).We have therefore described DNA CT in the context of transport among delocalized DNA domains formed and dissolved based on sequence-dependent DNA dynamics.Given the exquisite sensitivity of DNA CT to DNA lesions and mismatches, we have recently explored a possible role for DNA CT in repair. We demonstrated that redox activity required DNA binding for MutY (25), a base excision repair (BER) enzyme fr...

show abstract

DNA-Mediated Charge Transport Requires Conformational Motion of the DNA Bases: Elimination of Charge Transport in Rigid Glasses at 77 K

Cited by 118 publications

References 30 publications

Long-range oxidative damage to cytosines in duplex DNA

Long-range oxidative damage to cytosines in duplex DNA

Site-Specific Variations in RNA Folding Thermodynamics Visualized by 2-Aminopurine Fluorescence

Protein–DNA charge transport: Redox activation of a DNA repair protein by guanine radical

Contact Info

Product

Resources

About