Electron transfer processes in DNA: mechanisms, biological relevance and applications in DNA analytics

Probing of DNA Photochemistry with C-Nucleosides of Xanthones and Triphenylene as Photosensitizers To Study the Formation of Cyclobutane Pyrimidine Dimers

The direct and sequence-dependent investigation of photochemical processes in DNA on the way to cyclobutane pyrimidine dimers (CPDs) as DNA damage requires the probing by photochemically different photosensitizers. The C-nucleosides of xanthone, thioxanthone, 3-methoxyxanthone, and triphenylene as photosensitizers were synthesized by Heck couplings and incorporated into ternary photoactive DNA architectures. This structural approach allows the site-selective excitation of the DNA by UV light. Together with a single defined site for T-T dimerization, not only the direct CPD formation but also the distance-dependent CPD formation in DNA as well as the possibility for energy transport processes could be investigated. Direct CPD formation was observed with xanthone, 3-methoxyxanthone, and triphenylene as sensitizers but not with thioxanthone. Only xanthone was able to induce CPDs remotely by a triplet energy transfer over up to six intervening A-T base pairs. Taken together, more precise information on the sequence dependence of the DNA triplet photochemistry was obtained.

The Influence of Spirodi(Iminohydantoin) on Charge Transfer through ds-DNA Containing 8-OXO-dG: A Theoretical Approach

Genetic information stored in a DNA base sequence is continuously exposed to harmful factors. It has been determined that 9 × 10⁴ different DNA damage events occur in a single human cell every 24 h. Of these, 7,8-dihydro-8-oxo-guanosine (^OXOG) is one of the most abundant and can undergo further transformations towards spirodi(iminohydantoin) (Sp). Sp is highly mutagenic in comparison to its precursor if not repaired. In this paper, the influence of both Sp diastereomers 4R and 4S as well as their anti and syn conformers on charge transfer through the double helix was taken into theoretical consideration. In addition, the electronic properties of four modelled double-stranded oligonucleotides (ds-oligos) were also discussed, i.e., d[A₁Sp₂A₃^oxoG₄A₅] * [T₅C₄T₃C₂T₁]. Throughout the study, the M06-2X/6-31++G** level theory was used. Solvent-solute non-equilibrated and equilibrated interactions were also considered. The subsequent results elucidated that the 7,8-dihydro-8-oxo-guanosine:cytidine (^OXOGC) base pair is the settled point of a migrated radical cation in each of the discussed cases, due to its low adiabatic ionization potential, i.e., _~5.55 [eV]. The opposite was noted for excess electron transfer through ds-oligos containing anti (R)-Sp or anti (S)-Sp. The radical anion was found on the ^OXOGC moiety, whereas in the presence of syn (S)-Sp or syn (R)-Sp, an excess electron was found on the distal A₁T₅ or A₅T₁ base pair, respectively. Furthermore, a spatial geometry analysis of the discussed ds-oligos revealed that the presence of syn (R)-Sp in the ds-oligo caused only a slight deformation to the double helix, while syn (S)-Sp formed an almost ideal base pair with a complementary dC. The above results are in strong agreement with the final charge transfer rate constant, as calculated according to Marcus' theory. In conclusion, DNA damage such as spirodi(iminohydantoin), especially when becoming part of clustered DNA damage, can affect the effectiveness of other lesion recognition and repair processes. This can lead to the acceleration of undesired and deleterious processes such as carcinogenesis or aging. However, in terms of anticancer radio-/chemo- or combined therapy, the slowing down of the repair machinery can result in increased effectiveness. With this in mind, the influence of clustered damage on charge transfer and its subsequent effect on single-damage recognition by glycosylases justifies future investigation.

The 2Ih and OXOG Proximity Consequences on Charge Transfer through ds-DNA: Theoretical Studies of Clustered DNA Damage

Genetic information is continuously exposed to harmful factors, both intra- and extracellular. Their activity can lead to the formation of different types of DNA damage. Clustered lesions (CDL) are problematic for DNA repair systems. In this study, the short ds-oligos with a CDL containing (R) or (S) 2Ih and OXOG in their structure were chosen as the most frequent in vitro lesions. In the condensed phase, the spatial structure was optimized at the M062x/D95**:M026x/sto-3G level of theory, while the electronic properties were optimized at the M062x/6-31++G** level. The influence of equilibrated and non-equilibrated solvent-solute interactions was then discussed. It was found that the presence of (R)2Ih in the ds-oligo structure causes a greater increase in structure sensitivity towards charge adoption than (S)2Ih, while OXOG shows high stability. Moreover, the analysis of charge and spin distribution reveals the different effects of 2Ih diastereomers. Additionally, the adiabatic ionization potential was found as follows for (R)-2Ih and (S)-2Ih in eV: 7.02 and 6.94. This was in good agreement with the AIP of the investigated ds-oligos. It was found that the presence of (R)-2Ih has a negative influence on excess electron migration through ds-DNA. Finally, according to the Marcus theory, the charge transfer constant was calculated. The results presented in the article show that both diastereomers of 5-carboxamido-5-formamido-2-iminohydantoin should play a significant role in the CDL recognition process via electron transfer. Moreover, it should be pointed out that even though the cellular level of (R and S)-2Ih has been obscured, their mutagenic potential should be at the same level as other similar guanine lesions found in different cancer cells.

Robust ΔSCF calculations with direct energy functional minimization methods and STEP for molecules and materials

The direct energy functional minimization method using the orbital transformation (OT) scheme in the program package CP2K has been employed for Δ self-consistent field (ΔSCF) calculations. The OT method for non-uniform molecular orbitals occupations allows us to apply the ΔSCF method for various kinds of molecules and periodic systems. Vertical excitation energies of heteroaromatic molecules and condensed phase systems, such as solvated ethylene and solvated uracil obeying periodic boundary conditions, are reported using the ΔSCF method. In addition, a Re-phosphate molecule attached to the surface of anatase (TiO₂) has been investigated. Additionally, we have implemented a recently proposed state-targeted energy projection ΔSCF algorithm [K. Carter-Fenk and J. M. Herbert, J. Chem. Theory Comput. 16(8), 5067-5082 (2020)] for diagonalization based SCF in CP2K. It is found that the OT scheme provides a smooth and robust SCF convergence for all investigated excitation energies and (non-)periodic systems.

Remote Photodamaging of DNA by Photoinduced Energy Transport

Local DNA photodamaging by light is well-studied and leads to a number of structurally identified direct damage, in particular cyclobutane pyrimidine dimers, and indirect oxidatively generated damage, such as 8-oxo-7,8-hydroxyguanine. Similar damages have now been found at remote sites, at least more than 105 Å (30 base pairs) away from the site of photoexcitation. In contrast to the established mechanisms of local DNA photodamaging, the processes of remote photodamage are only partially understood. Known pathways include those to remote oxidatively generated DNA photodamages, which were elucidated by studying electron hole transport through the DNA about 20 years ago. Recent studies with DNA photosensitizers and mechanistic proposals on photoinduced DNA-mediated energy transport are summarized in this minireview. These new mechanisms to a new type of remote DNA photodamaging provide an important extension to our general understanding to light-induced DNA damage and their mutations.

Visible light-induced charge injection and migration in self-assembled carbon dot-DNA-carbon dot nano-dumbbell obtained through controlled stoichiometric conjugation

The potential of carbon dots (CDs) for photonic conversion to charged states, together with the ability of DNA to transport such charge for extensive charge separation, offers an opportunity to control directionality of migration for photo-induced radical cations in CD-DNA based nano-assemblies. This is achieved through engineering the reaction valency of CDs whereby one CD is covalently conjugated with one ssDNA strand. Subsequently, a CD-DNA-CD nano-dumbbell architecture was created through hybridization mediated self-assembly. The time and intensity-dependent transduction of visible light photonic energy to chemical potential in DNA was achieved through irradiation of 1,4-diaminoathraquinone and glyoxal derived CD with 100 W tungsten source and natural sunlight. Following charge injection by CD, the radical cation migration in DNA was perceived through trapping of the hole in repeated GG steps in the DNA. Overall, a breakthrough in visible-light-induced charge transfer by CD into DNA was achieved, potentially applicable to optobioelectronics.

The Binding Pocket at the Interface of Multimeric Telomere G-quadruplexes: Myth or Reality?

Human telomeric DNA with hundreds of repeats of the 5'-TTAGGG-3' motif plays a crucial role in several biological processes. It folds into G-quadruplex (G4) structures and features a pocket at the interface of two contiguous G4 blocks. Up to now no structural NMR and crystallographic data are available for ligands interacting with contiguous G4s. Naphthalene diimide monomers and dyads were investigated as ligands of a dimeric G4 of human telomeric DNA comparing the results with those of the model monomeric G4. Time-resolved fluorescence, circular dichroism, isothermal titration calorimetry and molecular modeling were used to elucidate binding features. Ligand fluorescence lifetime and induced circular dichroism unveiled occupancy of the binding site at the interface. Thermodynamic parameters confirmed the hypothesis as they remarkably change for the dyad complexes of the monomeric and dimeric telomeric G4. The bi-functional ligand structure of the dyads is a fundamental requisite for binding at the G4 interface as only the dyads engage in complexes with 1 : 1 stoichiometry, lodging in the pocket at the interface and establishing multiple interactions with the DNA skeleton. In the absence of NMR and crystallographic data, our study affords important proofs of binding at the interface pocket and clues on the role played by the ligand structure.

Recent Achievements in Electrochemical and Surface Plasmon Resonance Aptasensors for Mycotoxins Detection

Mycotoxins are secondary metabolites of fungi that contaminate agriculture products. Their release in the environment can cause severe damage to human health. Aptasensors are compact analytical devices that are intended for the fast and reliable detection of various species able to specifically interact with aptamers attached to the transducer surface. In this review, assembly of electrochemical and surface plasmon resonance (SPR) aptasensors are considered with emphasis on the mechanism of signal generation. Moreover, the properties of mycotoxins and the aptamers selected for their recognition are briefly considered. The analytical performance of biosensors developed within last three years makes it possible to determine mycotoxin residues in water and agriculture/food products on the levels below their maximal admissible concentrations. Requirements for the development of sample treatment and future trends in aptasensors are also discussed.

Reductive Charge Transfer through an RNA Aptamer

The transfer of charges through double helical DNA is a very well investigated bioelectric phenomenon. RNA, on the contrary, has been less studied in this regard. The few available data report on charge transfer through RNA duplex structures mainly composed of homonucleotide sequences. In the light of the RNA world scenarios, it is an interesting question, if charge transfer can be coupled with RNA function. Functional RNAs however, contain versatile structural motifs. Therefore, electron transport also through non‐Watson–Crick base‐paired regions might be required. We here demonstrate distance‐dependent reductive charge transfer through RNA duplexes and through the non‐Watson–Crick base‐paired region of an RNA aptamer.

Inequality in the Frequency of the Open States Occurrence Depends on Single 2H/1H Replacement in DNA

In the present study, the effect of 2H/1H isotopic exchange in hydrogen bonds between nitrogenous base pairs on occurrence and open states zones dynamics is investigated. These processes are studied using mathematical modeling, taking into account the number of open states between base pairs. The calculations of the probability of occurrence of open states in different parts of the gene were done depending on the localization of the deuterium atom. The mathematical modeling study demonstrated significant inequality (dependent on single 2H/1H replacement in DNA) among three parts of the gene similar in length of the frequency of occurrence of the open states. In this paper, the new convenient approach of the analysis of the abnormal frequency of open states in different parts of the gene encoding interferon alpha 17 was presented, which took into account both rising and decreasing of them that allowed to make a prediction of the functional instability of the specific DNA regions. One advantage of the new algorithm is diminishing the number of both false positive and false negative results in data filtered by this approach compared to the pure fractile methods, such as deciles or quartiles.

Single-molecule chemistry. Part I: monitoring oxidation of G in oligonucleotides using CY3 fluorescence

Single-molecule hybridisation of CY3 dye labelled short oligonucleotides to surface immobilised probes was investigated in zero-mode waveguide nanostructures using a modified DNA sequencer. At longer measuring times, we observed changes of the initial hybridisation fluorescence pulse pattern which we attribute to products created by chemical reactions at the nucleobases. The origin is a charge separated state created by a photoinduced electron transfer from nucleobases to the dye followed by secondary reactions with oxygen and water, respectively. The positive charge can migrate through the hybrid resulting in base modifications at distant sites. Static fluorescence spectra were recorded in order to determine the properties of CY3 stacking to different base pairs, and compared to pulse intensities. A characteristic pulse pattern change was assigned to the oxidation of G to 8-oG besides the formation of a number of secondary products that are not yet identified. Further, we present a method to visualise the degree of chemical reactions to gain an overview of ongoing processes. Our study demonstrates that CY3 is able to oxidise nucleobases in ds DNA, and also in ss overhangs. An important finding is the correlation between nucleobase oxidation potential and fluorescence quenching which explains the intensity changes observed in single molecule measurements. The analysis of fluorescence traces provides the opportunity to track complete and coherent reaction sequences enabling to follow the fate of a single molecule over a long period of time, and to observe chemical reactions in real-time. This opens up the opportunity to analyse reaction pathways, to detect new products and short-lived intermediates, and to investigate rare events due to the large number of single molecules observed in parallel.

The effect of spermidine on guanine decomposition via photoinduced electron transfer in DNA

The addition of spermidine caused the attenuation of guanine decomposition via photoinduced electron transfer in pyrene-modified DNA, and higher added concentrations of spermidine resulted in the promotion of decomposition in condensed DNA.

Electron Transfer in DNA at Electrified Interfaces

The ability of the DNA double helix to transport electrons underlies many life-centered biological processes and bio-electronic applications. However, there is little consensus on how efficiently the base pair π-stacks of DNA mediate electron transport. This minireview scrutinizes the current state-of-the-art knowledge on electron transfer (ET) properties of DNA and its long-range ability to transfer (mediate) electrical signals at electrified interfaces, without being oxidized or reduced. Complex changes an electric field induces in the DNA structure and its electronic properties govern the efficiency of DNA-mediated ET at electrodes and allow addressing the existing phenomenological riddles, while recently discovered rectifying properties of DNA contribute both to our understanding of DNA's ET in living systems and to advances in molecular bioelectronics.

A DNA-based two-way thermometer to report high and low temperatures

Precise description of temperature at the microscale level is essential in many biological applications. In this study, we prepared a DNA-based thermometer that reports low and high temperatures by providing two distinct optical signals. The system is a molecular beacon that carries a loop and a stem, whose conformation is subject to change from a hairpin to a random coil when the temperature changes from low to high. A fluorophore, Cy5, and a quencher, BHQ3, are terminally labeled at the stem ends. Moreover, perylene is included in the middle of the 3'-end stem. The signaling state of Cy5 relies on the relative distance to BHQ3. However, the perylene emission is regulated by its microenvironment (i.e., the oligonucleotide or duplex state). With a temperature variation, the designed thermometer undergoes a change in conformation that leads to two signal patterns with Cy5/off and perylene/on at low temperature and Cy5/on and perylene/off at high temperature. The reversibility and biocompatibility of the thermometer design were examined for potential applications in biological systems.

Theoretical modeling of DNA electron hole transport through polypyrimidine sequences: a QM/MM study

The phenomenon of DNA hole transport (HT) has attracted of scientists for several decades, mainly due to its potential application in molecular electronics. As electron holes mostly localize on purine bases in DNA, the majority of scientific effort has been invested into chemically modifying the structures of adenine and guanine in order to increase their HT-mediating properties. In this work we examine an alternative, never yet explored, way of affecting the HT efficiency by forcing electron holes to localize on pyrimidine bases and move between them. Using an enhanced and revised version of our previously developed QM/MM model, we perform simulations of HT through polyadenine, polycytosine, polyguanine, and polythymine stacks according to a multistep hopping mechanism. From these simulations, kinetic parameters for HT are obtained. The results indicate a particularly high efficiency of cytosine→cytosine hopping, which is about ten times higher than the G → G hopping. We also discuss possible improvement of cytosine HT by modifying the oxidoreductive properties of complementary guanine residues.

Drastic promotion of guanine oxidation via electron transfer in Ψ-type DNA

Drastic promotion of guanine oxidation was induced by not only intraduplex ET but also interduplex ET in Ψ-type DNA in a crowded environment using PEG.

Inhibiting guanine oxidation and enhancing the excess-electron-transfer efficiency of a pyrene-modified oligonucleotide by introducing an electron-donating group on pyrene

PipPyU and OMePyU enhance the reduction efficiency without oxidizing guanine in DNA-mediated electron transfer.

Attenuation of guanine oxidation via DNA-mediated electron transfer in a crowded environment using small cosolutes

Guanine oxidation induced by photoirradiation on a pyrene-modified oligonucleotide was investigated under molecular crowding using small cosolutes such as glycerol.

Thermally induced hopping model for long-range triplet excitation energy transfer in DNA

Long-range triplet excitation energy transfer in DNA occurs through hops between T bases, providing it with a shallow distance dependence. Hops over two thymines on the same strand are preferred.

Mechanistic insights into the photogeneration and quenching of guanine radical cation via one-electron oxidation of G-quadruplex DNA

Selectivity of activation site for the photogeneration and quenching of guanine radical cation was elucidated by the analysis of the relaxation paths of one-electron oxidation of G-quadruplex DNA.

Guanine-oligothiophene conjugates: liquid-crystalline properties, photoconductivities and ion-responsive emission of their nanoscale assemblies

Liquid-crystalline conjugated guanine–oligothiophene derivatives show electron or ambipolar carrier transport properties and ion-induced phase transition accompanied by a luminescence colour change.

We here report the supramolecular self-assembly of hydrogen-bonded motifs for the development of nanostructured materials that exhibit dynamic functions such as stimuli-responsive properties and molecular recognition behaviour. We have designed and synthesised new thermotropic bicontinuous and columnar liquid-crystalline (LC) guanine–oligothiophene conjugates tethered with lipophilic chains, which exhibit ionic, electronic and photoluminescence properties. Their potassium salt complexes self-assemble into thermotropic columnar LC phases. Time-of-flight photoconductivity measurements have revealed that the guanine–oligothiophene conjugates in the LC states possess charge transport abilities with either electron or ambipolar mobility values of 10^–4 to 10^–3 cm² V^–1 s^–1. Furthermore, we have found that the complexation of potassium ions with the guanine motif could lead not only to structural change and thermal stabilization of the LC phases but also to a photoluminescence colour change in the solid states. The strategy presented in this work could lead to the design of new functional LC materials that could potentially be applicable as sensors and electronic devices.

Elucidation of the Dexter-Type Energy Transfer in DNA by Thymine-Thymine Dimer Formation Using Photosensitizers as Artificial Nucleosides

C-nucleosides of 4-methylbenzophenone, 4-methoxybenzophenone, and 2'-methoxyacetophenone were synthetically incorporated as internal photosensitizers into DNA double strands. This structurally new approach makes it possible to study the distance dependence of thymidine dimer formation because the site of photoinduced triplet energy transfer injection is clearly defined. The counterstrands to these modified strands lacked the phosphodiester bond between the two adjacent thymidines that are supposed to react with each other. Their dimerization could be evidenced by gel electrophoresis because the covalent connection by cyclobutane formation between the two thymidines changes the mobility. A shallow exponential distance dependence for the formation of thymidine dimers over up to 10 A-T base pairs was observed that agrees with a Dexter-type triplet-triplet energy transfer mechanism. Concomitantly, a significant amount of photoinduced DNA crosslinking was observed.

Dynamics of Excess-Electron Transfer through Alternating Adenine:Thymine Sequences in DNA

This paper presents the results of an investigation into the sequence-dependent excess-electron transfer (EET) dynamics in DNA, which plays an important role in DNA damage/repair. There are many published studies on EET in consecutive adenine:thymine (A:T) sequences (Tn), but those in alternating A:T sequences (ATn) remain limited. Here, two series of functionalized DNA oligomers, Tn and ATn, were synthesized with a strongly electron-donating photosensitizer, a trimer of ethylenedioxythiophene (3 E), and an electron acceptor, diphenylacetylene (DPA). Laser flash photolysis experiments showed that the EET rate constant of AT3 is two times lower than that of T3 due to the lack of π-stacking of Ts in AT3. Thus, it was indicated that excess-electron hopping is affected by the interaction between LUMOs of nucleotides.

5-Nitroindole oligonucleotides with alkynyl side chains: universal base pairing, triple bond hydration and properties of pyrene "click" adducts

Oligonucleotides with 3-ethynyl-5-nitroindole and 3-octadiynyl-5-nitroindole 2'-deoxyribonucleosides were prepared by solid-phase synthesis. To this end, nucleoside phosphoramidites with clickable side chains were synthesized. The 3-ethynylated 5-nitroindole nucleoside was hydrated during automatized DNA synthesis to 3-acetyl-5-nitroindole 2'-deoxyribonucleoside. Side product formation was circumvented by triisopropylsilyl protection of the ethynyl side chain and was removed with TBAF after oligonucleotide synthesis. All compounds with a clickable 5-nitroindole skeleton show universal base pairing and can be functionalized with almost any azide in any position of the DNA chain. Functionalization of the side chain with 1-azidomethylpyrene afforded click adducts in which the fluorescence was quenched by the 5-nitroindole moieties. However, fluorescence was slightly recovered during duplex formation. Oligonucleotides with a pyrene residue and a long linker arm are stabilized over those with non-functionalized side chains. From the UV red shift of the pyrene residue in oligonucleotides and modelling studies, pyrene intercalation was established for the long linker adduct showing increased duplex stability over those with a short side chain.

How Does Guanine-Cytosine Base Pair Affect Excess-Electron Transfer in DNA?

Charge transfer and proton transfer in DNA have attracted wide attention due to their relevance in biological processes and so on. Especially, excess-electron transfer (EET) in DNA has strong relation to DNA repair. However, our understanding on EET in DNA still remains limited. Herein, by using a strongly electron-donating photosensitizer, trimer of 3,4-ethylenedioxythiophene (3E), and an electron acceptor, diphenylacetylene (DPA), two series of functionalized DNA oligomers were synthesized for investigation of EET dynamics in DNA. The transient absorption measurements during femtosecond laser flash photolysis showed that guanine:cytosine (G:C) base pair affects EET dynamics in DNA by two possible mechanisms: the excess-electron quenching by proton transfer with the complementary G after formation of C(•-) and the EET hindrance by inserting a G:C base pair as a potential barrier in consecutive thymines (T's). In the present paper, we provided useful information based on the direct kinetic measurements, which allowed us to discuss EET through oligonucleotides for the investigation of DNA damage/repair.

Acceleration of Long-Range Photoinduced Electron Transfer through DNA by Hydroxyquinolines as Artificial Base Pairs

The C-nucleoside based on the hydroxyquinoline ligand (Hq) is complementary to itself and forms stable Hq-Hq pairs in double-stranded DNA. These artificial Hq-Hq pairs may serve as artificial electron carriers for long-range photoinduced electron transfer in DNA, as elucidated by a combination of gel electrophoretic analysis of irradiated samples and time-resolved transient absorption spectroscopy. For this study, the Hq-Hq pair was combined with a DNA-based donor-acceptor system consisting of 6-N,N-dimethylaminopyrene conjugated to 2'-deoxyuridine as photoinducible electron donor, and methyl viologen attached to the 2'-position of uridine as electron acceptor. The Hq radical anion was identified in the time-resolved measurements and strand cleavage products support its role as an intermediate charge carrier. Hence, the Hq-Hq pair significantly enhances the electron hopping capability of DNA compared to natural DNA bases over long distances while keeping the self-assembly properties as the most attractive feature of DNA as a supramolecular architecture.

Driving force dependence of charge separation and recombination processes in dyads of nucleotides and strongly electron-donating oligothiophenes

Charge transfer in DNA has attracted great attention of scientists because of its importance in biological processes. However, our knowledge on excess-electron transfer in DNA still remains limited in comparison to numerous studies of hole transfer in DNA. To clarify the dynamics of excess-electron transfer in DNA by photochemical techniques, new electron-donating photosensitizers should be developed. Herein, a terthiophene and two 3,4-ethylenedioxythiophene oligomers were used as photosensitizers in dyads including natural nucleobases as electron acceptors. The charge separation and recombination processes in the dyads were investigated by femtosecond laser flash photolysis, and the driving force dependence of these rate constants was discussed on the basis of the Marcus theory. From this study, the conformation effect on charge recombination process was found. We expect that 3,4-ethylenedioxythiophene oligomers are useful in investigation of excess-electron-transfer dynamics in DNA.

Luminescence quenching by photoinduced charge transfer between metal complexes in peptide nucleic acids

A new scaffold for studying photoinduced charge transfer has been constructed by connecting a [Ru(Bpy)3](2+) donor to a bis(8-hydroxyquinolinate)2 copper [CuQ2] acceptor through a peptide nucleic acid (PNA) bridge. The luminescence of the [Ru(Bpy)3](2+*) donor is quenched by electron transfer to the [CuQ2] acceptor. Photoluminescence studies of these donor-bridge-acceptor systems reveal a dependence of the charge transfer on the length and sequence of the PNA bridge and on the position of the donor and acceptor in the PNA. In cases where the [Ru(Bpy)3](2+) can access the π base stack at the terminus of the duplex, the luminescence decay is described well by a single exponential; but if the donor is sterically hindered from accessing the π base stack of the PNA duplex, a distribution of luminescence lifetimes for the donor [Ru(Bpy)3](2+*) is observed. Molecular dynamics simulations are used to explore the donor-PNA-acceptor structure and the resulting conformational distribution provides a possible explanation for the distribution of electron transfer rates.

(DNS)C: a fluorescent, environmentally sensitive cytidine derivative for the direct detection of GGG triad sequences

With the goal of developing a fluorescent nucleoside sensitive to its environment, in this study we synthesized (DNS)C, a novel modified 2'-deoxycytidine bearing a 5-(dimethylamino)naphthalene-1-sulfonyl (dansyl) moiety at the N4 position, and tested its properties in monomeric and oligomeric states. (DNS)C undergoes intramolecular photoinduced electron transfer between its dansyl and cytosine units, resulting in remarkable changes in fluorescence that depend on the choice of solvent. In addition, the fluorescence behavior and thermal stability of oligonucleotides containing (DNS)C are dependent on the nature of the flanking and neighboring bases. Notably, (DNS)C exhibits fluorescence enhancement only in fully matched duplex DNA containing a GGG triad sequence. The environmental sensitivity of (DNS)C can be exploited as a fluorescence tool for monitoring the interactions of DNA with other biomolecules, including DNA, RNA, and proteins.

Electron transport in DNA initiated by diaminonaphthalene donors alternatively bound by non-covalent and covalent association

Non-covalent association can identify active donors for study of charge transfer in DNA but may not establish detailed correlations between donor structure and transfer efficiency.

Fluorescence quenching over short range in a donor-DNA-acceptor system

A new donor-DNA-acceptor system has been synthesized containing Nile red-modified 2'-deoxyuridine as charge donor and 6-N,N-dimethylaminopyrene-modified 2'-deoxyuridine as acceptor to investigate the charge transfer in DNA duplexes using fluorescence spectroscopy and time-resolved femtosecond pump-probe techniques. Fluorescence quenching experiments revealed that the quenching efficiency of Nile red depends on two components: 1) the presence of a charge acceptor and 2) the number of intervening CG and AT base pairs between donor and acceptor. Surprisingly, the quenching efficiency of two base pairs (73% for CG and the same for AT) is higher than that for one base pair (68% for CG and 37% for AT), while at a separation of three base pairs less than 10% quenching is observed. A comparison with the results of time-resolved measurements revealed a correlation between quenching efficiency and the first ultrafast time constant suggesting that quenching proceeds via a charge transfer from the donor to the acceptor. All transients are satisfactorily described with two decays: a rapid charge transfer with 600 fs (∼10(12) s(-1)) that depends strongly and in a non-linear fashion on the distance between donor and acceptor, and a slower time constant of a few picoseconds (∼10(11) s(-1)) with weak distance dependence. A third time constant on a nanosecond time scale represents the fluorescence lifetime of the donor molecule. According to these results and time-dependent density functional theory (TDDFT) calculations a combination of single-step superexchange and multistep hopping mechanisms can be proposed for this short-range charge transfer. Furthermore, significantly less quenching efficiency and slower charge transfer rates at very short distances indicate that the direct interaction between donor and acceptor leads to a local structural distortion of DNA duplexes which may provide some uncertainty in identifying the charge transfer rates in short-range systems.