Femtosecond direct observation of charge transfer between bases in DNA

Pathways for fluorescence quenching in 2-aminopurine π-stacked with pyrimidine nucleobases

Fluorescent analogues of nucleobases are very useful as probes to study DNA dynamics, because natural DNA does not fluoresce significantly. In many of these analogues, such as 2-aminopurine (2AP), the fluorescence is quenched when incorporated into DNA through processes that are not well understood. This work uses theoretical studies to examine fluorescence quenching pathways in 2AP-containing dimers. The singlet excited states of π-stacked dimer systems containing 2AP and a pyrimidine base, thymine or cytosine, have been studied using ab initio computational methods. Computed relaxation pathways along the excited-state surfaces reveal novel mechanisms that can lead to fluorescence quenching in the π-stacked dimers. The placement of 2AP on the 5' or 3' terminus of the dimers has different effects on the excitation energies and the relaxation pathways on the S(1) excited state. Conical intersections between the ground and first excited states exist when 2AP is placed at the 3' side, whereas the placement of 2AP at the 5' side leads to the switching of a bright state to a dark state. Both of these processes can lead to fluorescence quenching and may contribute to the fluorescence quenching observed in 2AP when incorporated in DNA.

Oxidation of 2'-deoxyadenosine 5'-monophosphate photoinduced by lumazine

UV radiation induces damages to the DNA molecule and its components through photosensitized reactions. Among these processes, photosensitized oxidations may occur through electron transfer or hydrogen abstraction (type I mechanism) and/or the production of singlet molecular oxygen ((1)O(2)) (type II mechanism). Lumazines are an important family of heterocyclic compounds present in biological systems as biosynthetic precursors and/or products of metabolic degradation. To evaluate the capability of lumazines to act as photosensitizers through type I mechanism, we have investigated the oxidation of 2'-deoxyadenosine 5'-monophosphate (dAMP) photosensitized by the specific compound called lumazine (pteridine-2,4(1,3H)-dione; Lum) in aqueous solutions under UV irradiation. The photochemical reactions were followed by UV/vis spectrophotometry, HPLC, electrochemical measurement of dissolved O(2), and an enzymatic method for H(2)O(2) determination. The effect of pH was evaluated and the participation of oxygen was investigated. In aerated solutions, oxidation of dAMP photoinduced by the acid form of Lum (pH 5.5) takes place through a type I mechanism, in which the excitation of Lum is followed by an electron transfer from dAMP molecule to the Lum triplet excited state. During the process, O(2) is consumed and H(2)O(2) is generated, whereas the photosensitizer is not consumed. In contrast, no evidence of a photochemical reaction induced by the basic form of Lum (pH 10.5) was observed.

Single-step charge transport through DNA over long distances

Quantum yields for charge transport across adenine tracts of increasing length have been measured by monitoring hole transport in synthetic oligonucleotides between photoexcited 2-aminopurine, a fluorescent analogue of adenine, and N(2)-cyclopropyl guanine. Using fluorescence quenching, a measure of hole injection, and hole trapping by the cyclopropyl guanine derivative, we separate the individual contributions of single- and multistep channels to DNA charge transport and find that with 7 or 8 intervening adenines the charge transport is a coherent, single-step process. Moreover, a transition occurs from multistep to single-step charge transport with increasing donor/acceptor separation, opposite to that generally observed in molecular wires. These results establish that coherent transport through DNA occurs preferentially across 10 base pairs, favored by delocalization over a full turn of the helix.

Heterogeneity and dynamics of the ligand recognition mode in purine-sensing riboswitches

High-resolution crystal structures and biophysical analyses of purine-sensing riboswitches have revealed that a network of hydrogen bonding interactions appear to be largey responsible for discrimination of cognate ligands against structurally related compounds. Here we report that by using femtosecond time-resolved fluorescence spectroscopy to capture the ultrafast decay dynamics of the 2-aminopurine base as the ligand, we have detected the presence of multiple conformations of the ligand within the binding pockets of one guanine-sensing and two adenine-sensing riboswitches. All three riboswitches have similar conformational distributions of the ligand-bound state. The known crystal structures represent the global minimum that accounts for 50-60% of the population, where there is no significant stacking interaction between the ligand and bases of the binding pocket, but the hydrogen-bonding cage collectively provides an electronic environment that promotes an ultrafast ( approximately 1 ps) charge transfer pathway. The ligand also samples multiple conformations in which it significantly stacks with either the adenine or the uracil bases of the A21-U75 and A52-U22 base pairs that form the ceiling and floor of the binding pocket, respectively, but favors the larger adenine bases. These alternative conformations with well-defined base stacking interactions are approximately 1-1.5 kcal/mol higher in DeltaG degrees than the global minimum and have distinct charge transfer dynamics within the picosecond to nanosecond time regime. Inside the pocket, the purine ligand undergoes dynamic motion on the low nanosecond time scale, sampling the multiple conformations based on time-resolved anisotropy decay dynamics. These results allowed a description of the energy landscape of the bound ligand with intricate details and demonstrated the elastic nature of the ligand recognition mode by the purine-sensing riboswitches, where there is a dynamic balance between hydrogen bonding and base stacking interactions, yielding the high affinity and specificity by the aptamer domain.

II. Model building: an electrical theory of control of growth and development in animals, prompted by studies of exogenous magnetic field effects (paper I), and evidence of DNA current conduction, in vitro

A theory of control of cellular proliferation and differentiation in the early development of metazoan systems, postulating a system of electrical controls "parallel" to the processes of molecular biochemistry, is presented. It is argued that the processes of molecular biochemistry alone cannot explain how a developing organism defies a stochastic universe. The demonstration of current flow (charge transfer) along the long axis of DNA through the base-pairs (the "pi-way) in vitro raises the question of whether nature may employ such current flows for biological purposes. Such currents might be too small to be accessible to direct measurement in vivo but conduction has been measured in vitro, and the methods might well be extended to living systems. This has not been done because there is no reasonable model which could stimulate experimentation. We suggest several related, but detachable or independent, models for the biological utility of charge transfer, whose scope admittedly outruns current concepts of thinking about organization, growth, and development in eukaryotic, metazoan systems. The ideas are related to explanations proposed to explain the effects demonstrated on tumors and normal tissues described in Article I (this issue). Microscopic and mesoscopic potential fields and currents are well known at sub-cellular, cellular, and organ systems levels. Not only are such phenomena associated with internal cellular membranes in bioenergetics and information flow, but remarkable long-range fields over tissue interfaces and organs appear to play a role in embryonic development (Nuccitelli, 1992 ). The origin of the fields remains unclear and is the subject of active investigation. We are proposing that similar processes could play a vital role at a "sub-microscopic level," at the level of the chromosomes themselves, and could play a role in organizing and directing fundamental processes of growth and development, in parallel with the more discernible fields and currents described.

Can charge transfer in DNA significantly be modulated by varying the pi stack conformation?

DNA is an ideal target for single-molecule manipulations. The conformation of stacked basepairs in DNA depends sensitively on various factors such as temperature, the kind of solvent and counterions, changes in the backbone, applied forces, etc. This raises the question of whether the rate of charge transfer (CT) through the stack can be considerably enhanced by tuning of "observed" DNA conformations. Using a stochastic approach to account for the effects of thermal fluctuations, we study how the efficiency of CT in poly(dA)-poly(dT) and poly(dG)-poly(dC) sequences will change by variation of the pi stack structure. The CT process is shown to be not very sensitive to the torsional angle (twist) while affected more strongly by altering translation modes (shift and slide). We conclude that the design of basepair stacks with significantly improved electrical conductivity, as compared to poly(dG)-poly(dC), appears to be quite elusive. Specific changes of the pi stack structure can increase the efficiency of CT by a factor of approximately 3 (e.g., in systems with negative shift); much stronger effects can hardly be expected. This result, formally derived for molecular ensembles, should also be applicable for single-molecule systems because of the strong effects of dynamical disordering.

DNA fragmentation in human fibroblasts under extremely low frequency electromagnetic field exposure

Extremely low frequency electromagnetic fields (ELF-EMFs) were reported to affect DNA integrity in human cells with evidence based on the Comet assay. These findings were heavily debated for two main reasons; the lack of reproducibility, and the absence of a plausible scientific rationale for how EMFs could damage DNA. Starting out from a replication of the relevant experiments, we performed this study to clarify the existence and explore origin and nature of ELF-EMF induced DNA effects. Our data confirm that intermittent (but not continuous) exposure of human primary fibroblasts to a 50 Hz EMF at a flux density of 1 mT induces a slight but significant increase of DNA fragmentation in the Comet assay, and we provide first evidence for this to be caused by the magnetic rather than the electric field. Moreover, we show that EMF-induced responses in the Comet assay are dependent on cell proliferation, suggesting that processes of DNA replication rather than the DNA itself may be affected. Consistently, the Comet effects correlated with a reduction of actively replicating cells and a concomitant increase of apoptotic cells in exposed cultures, whereas a combined Fpg-Comet test failed to produce evidence for a notable contribution of oxidative DNA base damage. Hence, ELF-EMF induced effects in the Comet assay are reproducible under specific conditions and can be explained by minor disturbances in S-phase processes and occasional triggering of apoptosis rather than by the generation of DNA damage.

Evidence of disruption of conjugation involving delta bonds in intramolecular electronic coupling

A dimer of dimers containing two quadruply bonded [Mo(2)(DAniF)(3)](+) units (DAniF = N,N'-di(p-anisyl)formamidinate) linked by the S-donor linker, dimethyldithiooxamidate was synthesized, structurally characterized, and electronic communication was probed. The core of [Mo(2)(DAniF)(3)](2)(C(2)S(2)N(2)Me(2)), 1, formed by the Mo(2)NSC(2)SNMo(2) atoms shows two fused but non planar six-membered rings, which differs from that of the beta form of dimethyloxamidate analogue that has a heteronaphthalene-type structure (Cotton, F. A.; Liu, C. Y.; Murillo, C. A.; Villagran, D.; Wang, X. J. Am. Chem. Soc. 2004, 126, 14822). For these two analogous compounds electronic coupling between the two [Mo(2)] units, as determined by electrochemical measurements, diminishes considerably upon replacement of O-donor by S-donor atoms (DeltaE(1/2) = 531 mV and 440 mV, respectively). This suggests that the non planar conformation of the linker in 1 hampers a pathway leading to pi conjugation. Density functional theory (DFT) calculations show that the highest occupied molecular orbitals HOMO-HOMO-1 energy gap of 0.12 eV for 1 is much smaller than that of 0.61 eV for the O-donor analogue, which is consistent with the electrochemical data.

Conformational analysis of DNA repair intermediates by time-resolved fluorescence spectroscopy

DNA repair enzymes are essential for maintaining the integrity of the DNA sequence. Unfortunately, very little is known about how these enzymes recognize damaged regions along the helix. Structural analysis of cellular repair enzymes bound to DNA reveals that these enzymes are able to recognize DNA in a variety of conformations. However, the prevalence of these deformations in the absence of enzymes remains unclear, as small populations of DNA conformations are often difficult to detect by NMR and X-ray crystallography. Here, we used time-resolved fluorescence spectroscopy to examine the conformational dynamics of linear, nicked, gapped, and bulged DNA in the absence of protein enzymes. This analysis reveals that damaged DNA is polymorphic in nature and able to adopt multiple individual conformations. We show that DNA repair intermediates that contain a one-nucleotide gap and bulge have a significant propensity to adopt conformations in which the orphan base resides outside the DNA helix, while DNA structures damaged by a nick or two-nucleotide gap favor intrahelical conformations. Because changes in DNA conformation appear to guide the recognition of DNA repair enzymes, we suggest that the current approach could be used to study the mechanism of DNA repair.

One-electron reduction of 2-aminopurine in the aqueous phase. A DFT and pulse radiolysis study

The electron affinity and the subsequent proton affinity of the electron adducts of 2-aminopurine (abbreviated 2AP) and adenine (A) are calculated with density functional theory (DFT). According to these calculations 2AP*- and A*- have similar thermochemical parameters leading to the conclusion that their reaction pathways should be close to analogous. Using the pulse radiolysis technique 2AP*- is formed by reaction with the hydrated electron (e(-)aq) and the resulting transient absorption spectrum is assigned to 2AP(NH)*. Additionally, it was found, employing the laser flash photolysis technique, that the excited singlet state of 2AP is incapable of oxidizing guanine in the aqueous phase. However, the one-electron oxidized 2AP (2AP*+) has sufficient energy to ionize guanine according to the DFT results in agreement with experimental data from the literature.

A DNA nanoswitch incorporating the fluorescent base analogue 2-aminopurine detects single nucleotide mismatches in unlabelled targets

DNA nanoswitches can be designed to detect unlabelled nucleic acid targets and have been shown to discriminate between targets which differ in the identity of only one base. This paper demonstrates that the fluorescent base analogue 2-aminopurine (AP) can be used to discriminate between nanoswitches with and without targets and to discriminate between matched and mismatched targets. In particular, we have used both steady-state and time-resolved fluorescence spectroscopy to determine differences in AP environment at the branchpoint of nanoswitches assembled using complementary targets and targets which incorporate single base mismatches.

Stepwise oscillatory circuits of a DNA molecule

A DNA molecule is characterized by a stepwise oscillatory circuit where every base pair is a capacitor, every phosphate bridge is an inductance, and every deoxyribose is a charge router. The circuitry accounts for DNA conductivity through both short and long distances in good agreement with experimental evidence that has led to the identification of the so-called super-exchange and multiple-step hopping mechanisms. However, in contrast to the haphazard hopping and super-exchanging events, the circuitry is a well-defined charge transport mechanism reflecting the great reliability of the genetic substance in delivering electrons. Stepwise oscillatory charge transport through a nucleotide sequence that directly modulates the oscillation frequency may have significant biological implications.

Charge transport in proteins probed by resonant photoemission

The degrees of charge localization in the highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO) of the bacterial surface layer protein of Bacillus sphaericus NCTC 9602 were studied by resonant photoemission. In agreement with a charge transport hopping mechanism that involves torsional motions of the peptide backbone, the lifetime of electrons excited into the LUMO was found to be approximately 100 fs.

2-aminopurine as a probe of RNA conformational transitions

2-aminopurine (2AP) is a fluorescent nucleobase that provides the means to probe structure and dynamics of RNA molecules. Because 2AP can base pair with Uridine, it can replace normal A:U pairs without substantial deformation of duplexes. It is best used as a probe of ostensibly single-stranded regions: its fluorescence intensity reports on base stacking and its fluorescence decay lifetimes report on its conformational dynamics. Three examples of its use are described here, illustrating how 2AP fluorescence has been used to probe RNA folding and hairpin loop dynamics.

Back-electron transfer suppresses the periodic length dependence of DNA-mediated charge transport across adenine tracts

DNA-mediated charge transport (CT) is exquisitely sensitive to the integrity of the bridging pi-stack and is characterized by a shallow distance dependence. These properties are obscured by poor coupling between the donor/acceptor pair and the DNA bridge, or by convolution with other processes. Previously, we found a surprising periodic length dependence for the rate of DNA-mediated CT across adenine tracts monitored by 2-aminopurine fluorescence. Here we report a similar periodicity by monitoring N 2-cyclopropylguanosine decomposition by rhodium and anthraquinone photooxidants. Furthermore, we find that this periodicity is attenuated by consequent back-electron transfer (BET), as observed by direct comparison between sequences that allow and suppress BET. Thus, the periodicity can be controlled by engineering the extent of BET across the bridge. The periodic length dependence is not consistent with a periodicity predicted by molecular wire theory but is consistent with a model where multiples of four to five base pairs form an ideal CT-active length of a bridging adenine domain.

Base sequence and higher-order structure induce the complex excited-state dynamics in DNA

The high photostability of DNA is commonly attributed to efficient radiationless electronic relaxation processes. We used femtosecond time-resolved fluorescence spectroscopy to reveal that the ensuing dynamics are strongly dependent on base sequence and are also affected by higher-order structure. Excited electronic state lifetimes in dG-doped d(A)20 single-stranded DNA and dG.dC-doped d(A)20.d(T)20 double-stranded DNA decrease sharply with the substitution of only a few bases. In duplexes containing d(AGA).d(TCT) or d(AG).d(TC) repeats, deactivation of the fluorescing states occurs on the subpicosecond time scale, but the excited-state lifetimes increase again in extended d(G) runs. The results point at more complex and molecule-specific photodynamics in native DNA than may be evident in simpler model systems.

Long-wavelength fluorescence from 2-aminopurine-nucleobase dimers in DNA

When 2-aminopurine (2AP) is substituted for adenine in DNA, it is widely accepted that its fluorescence spectrum is essentially unchanged from that of the free fluorophore. We show that 2AP in DNA exhibits long-wavelength emission and excitation bands, in addition to the familiar short-wavelength spectra, as a result of formation of a ground-state heterodimer with an adjacent, pi-stacked, natural base. The observation of dual emission from 2AP in a variety of oligodeoxynucleotide duplexes and single strands demonstrates the generality of this phenomenon. The photophysical and conformational properties of the long-wavelength-emitting 2AP-nucleobase dimer are examined. Analogous long-wavelength fluorescence is seen when 2AP pi-stacks with aromatic amino acid sidechains in the active sites of methyltransferase enzymes during DNA nucleotide flipping.

PNA versus DNA: effects of structural fluctuations on electronic structure and hole-transport mechanisms

The effects of structural fluctuations on charge transfer in double-stranded DNA and peptide nucleic acid (PNA) are investigated. A palindromic sequence with two guanine bases that play the roles of hole donor and acceptor, separated by a bridge of two adenine bases, was analyzed using combined molecular dynamics (MD) and quantum-chemical methods. Surprisingly, electronic structure calculations on individual MD snapshots show significant frontier orbital electronic population on the bridge in approximately 10% of the structures. Electron-density delocalization to the bridge is found to be gated by fluctuations of the covalent conjugated bond structure of the aromatic rings of the nucleic bases. It is concluded, therefore, that both thermal hopping and superexchange should contribute significantly to charge transfer even in short DNA/PNA fragments. PNA is found to be more flexible than DNA, and this flexibility is predicted to produce larger rates of charge transfer.

Time-resolved fluorescent properties of 8-vinyl-deoxyadenosine and 2-amino-deoxyribosylpurine exhibit different sensitivity to their opposite base in duplexes

8-Vinyl-deoxyadenosine (8VA) has been recently introduced as a fluorescent analogue of adenosine that is less perturbing and less quenched than the well-established 2-amino-deoxyribosylpurine (2AP) probe when inserted in oligonucleotides. To further validate 8VA as a fluorescent substitute of A, we compared the ability of 8VA and 2AP in sequences of the type d(CGT TTT XNX TTT TGC) (with N=8VA or 2AP and X=T and C) to discriminate the nature of the opposite base (Y) in duplexes. For both probes, systematic variations in the amplitudes of the short- and long-lived lifetimes of the fluorescence intensity decays as well as in the amplitude of the fast rotational correlation time of the fluorescence anisotropy decays were observed as a function of the nature of Y. From these parameters, we inferred a stability order 8VA-T > 8VA-G > 8VA-A > 8VA-C, similar to the stability order with the native A base, but different from the stability order with 2AP. Using a combination of molecular mechanics and ab initio calculations, we found that the time-resolved parameters of 8VA, but not the 2AP ones, correlate well with the geometry and the strength of the A-Y base-pairing interaction. This may be rationalized by the smaller structural and electronic perturbations induced by the vinyl group in position 8 as compared to the amino group at position 2. As a consequence, substitution of A by 8VA in a base pair was found to only minimally modify the structure and interaction energy of the base pair. Thus, 8VA can be used as a fluorescent substitute of the natural A, to straightforwardly discriminate the nature of the opposite base. This may find interesting applications notably in the elucidation of the mechanisms and dynamics of the DNA mismatch repair system.

UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases

Excited electronic states created by UV excitation of the diribonucleoside monophosphates ApA, ApG, ApC, ApU, and CpG were studied by the femtosecond transient-absorption technique. Bleach recovery signals recorded at 252 nm show that long-lived excited states are formed in all five dinucleosides. The lifetimes of these states exceed those measured in equimolar mixtures of the constituent mononucleotides by one to two orders of magnitude, indicating that electronic coupling between proximal nucleobases dramatically slows the relaxation of excess electronic energy. The decay rates of the long-lived states decrease with increasing energy of the charge-transfer state produced by transferring an electron from one base to another. The charge-transfer character of the long-lived states revealed by this analysis supports their assignment to excimer or exciplex states. Identical bleach recovery signals were seen for ApA, (A)(4), and poly(A) at delay times >10 ps after photoexcitation. This indicates that excited states localized on a stack of just two bases are the common trap states independent of the number of stacked nucleotides. The fraction of initial excitations that decay to long-lived exciplex states is approximately equal to the fraction of stacked bases determined by NMR measurements. This supports a model in which excitations associated with two stacked bases decay to exciplex states, whereas excitations in unstacked bases decay via ultrafast internal conversion. These results establish the importance of charge transfer-quenching pathways for UV-irradiated RNA and DNA in room-temperature solution.

The dynamic structural basis of differential enhancement of conformational stability by 5'- and 3'-dangling ends in RNA

Unpaired bases at the end of an RNA duplex (dangling ends) can stabilize the core duplex in a sequence-dependent manner and are important determinants of RNA folding, recognition, and functions. Using 2-aminopurine as a dangling end purine base, we have employed femtosecond time-resolved fluorescence spectroscopy, combined with UV optical melting, to quantitatively investigate the physical and structural nature of the stacking interactions between the dangling end bases and the terminal base pairs. A 3'-dangling purine base has a large subpopulation that stacks on the guanine base of the terminal GC or UG pair, either intrastrand or cross-strand depending on the orientation of the pair, thus providing stabilization of different magnitudes. On the contrary, a 5'-dangling purine base only has a marginal subpopulation that stacks on the purine of the same strand (intrastrand) but has little cross-strand stacking. Thus a 5'-dangling purine does not provide significant stabilization. These stacking structures are not static, and a dangling end base samples a range of stacked and unstacked conformations with respect to the terminal base pair. Femtosecond time-resolved anisotropy decay reveals certain hindered base conformational dynamics that occur on the picosecond to nanosecond time scales, which allow the dangling base to sample these substates. When the dangling purine is opposite to a U and is able to form a potential base pair at the end of the duplex, there is an interplay of base stacking and hydrogen-bonding interactions that depends on the orientation of the base pair relative to the adjacent GC pair. By resolving these populations that are dynamically exchanging on fast time scales, we elucidated the correlation between dynamic conformational distributions and thermodynamic stability.

Distance dependent coherence variation in DNA charge-transfer processes

We explore distance dependent variation of the coherence length relevant to DNA charge-transfer processes within 5'-GAnG3-3' DNA sequences. Recently developed on-the-fly filtered propagator functional path integral approach was employed to sort out transport trajectories with significant contribution and to analyze correlation between electronic states. In particular, the coherence length was quantitatively determined through characteristics of off-diagonal quantum trajectories. Simulated coherence lengths and experimentally observed rate constants [Nature 2001, 412, 318] were found to be consistent such that, up to n = 2, the exponential decrease of the rate constants is associated with the donor-acceptor coherence driven charge transfer. In contrast, the rate constants become insensitive to the distance for n > or = 3 in which donor and acceptor are no longer significantly correlated. It was also found that the coherence within a collective state governs the overall charge transfer, which is composed of a part of a sequence within the coherence length from the donor.

Probing dynamics of HIV-1 nucleocapsid protein/target hexanucleotide complexes by 2-aminopurine

The nucleocapsid protein (NC) plays an important role in HIV-1, mainly through interactions with the genomic RNA and its DNA copies. Though the structures of several complexes of NC with oligonucleotides (ODNs) are known, detailed information on the ODN dynamics in the complexes is missing. To address this, we investigated the steady state and time-resolved fluorescence properties of 2-aminopurine (2Ap), a fluorescent adenine analog introduced at positions 2 and 5 of AACGCC and AATGCC sequences. In the absence of NC, 2Ap fluorescence was strongly quenched in the flexible ODNs, mainly through picosecond to nanosecond dynamic quenching by its neighboring bases. NC strongly restricted the ODN flexibility and 2Ap local mobility, impeding the collisions of 2Ap with its neighbors and thus, reducing its dynamic quenching. Phe¹⁶→Ala and Trp³⁷→Leu mutations largely decreased the ability of NC to affect the local dynamics of 2Ap at positions 2 and 5, respectively, while a fingerless NC was totally ineffective. The restriction of 2Ap local mobility was thus associated with the NC hydrophobic platform at the top of the folded fingers. Since this platform supports the NC chaperone properties, the restriction of the local mobility of the bases is likely a mechanistic component of these properties.

A mechanism for stimulation of biosynthesis by electromagnetic fields: charge transfer in DNA and base pair separation

Electrons have been shown to move in DNA, and a specific DNA sequence is associated with the response to EM fields. In addition, there is evidence from biochemical reactions that EM fields can accelerate electron transfer. Interaction with electrons could displace electrons in H-bonds that hold DNA together leading to chain separation and initiating transcription. The effect of charging due to electron displacement on the energetics of DNA aggregation shows that electron transfer would favor separation of base pairs, and that DNA geometry is optimized for disaggregation under such conditions. Electrons in the H-bonds of both DNA and the surrounding water molecules fluctuate at frequencies that are much higher than the frequencies of the EM fields studied. The characteristics of the fluctuations suggest that the applied EM fields are effectively DC pulses and that interactions extend to microwave frequencies.

Ultrafast energy delocalization and electron transfer dynamics in 2-aminopurine-containing trinucleotides

The fate of electronically excited states in DNA base stacks is of tremendous importance for subsequent photochemical damage reactions in the genome. In this study we present a femtosecond broadband pump-probe study on the adenine isomer 2-aminopurine (Ap) incorporated into trinucleotides. After selective excitation of Ap we can monitor energy delocalization between neighboring Ap moieties as well as excited state electron transfer, depending on the sequence of the trinucleotide. Our results establish the time scale for intrastand excimer formation and reveal the lifetime of the excimer state.

Sequence, structure and energy transfer in DNA

Excitation energy transfer in DNA has similarities to charge transfer, but the transport is of an excited state, not of mass or charge. Use of the fluorescent, modified adenine base 2-aminopurine (2AP) as an energy trap in short (3- to 20-base) single- and double-stranded DNA oligomers is reviewed. Variation of 2AP's neighboring sequence shows (1) relatively efficient transfer from adenine compared to that from cytosine and thymine, (2) efficient transfer from guanine, but only when 2AP is at the 3' end, (3) approximate equality of efficiencies for 3' to 5' and 5' to 3' directional transfer in adenine tracks. The overall, average transfer distance at room temperature is about four adenine bases or less before de-excitation. The transfer fluorescence excitation spectral shape is similar to that of the absorption spectrum of the neighboring normal bases, confirming that initial excitation of the normal bases, followed by emission from 2AP (i.e. energy transfer), is occurring. Transfer apparently may take place both along one strand and cross-strand, depending on the oligomer sequence. Efficiency increases when the temperature is decreased, rising above 50% (overall efficiency) in decamers of adenine below -60 degrees C (frozen media). Modeling of the efficiencies of transfer from the nearest several adenine neighbors of 2AP in these oligomers suggests that the nearest two neighbors transfer with near 100% efficiency. As bases in B DNA, as well as in single-stranded DNA, are separated by less than 5 A (less than the size of a base), standard Förster transfer theory should not apply. Indeed, while both theory and experiment show efficiency decreasing with donor-acceptor distance, the experimental dependence clearly disagrees with Förster 1/r6 dependence. It is not yet clear what the best theoretical approach is, but any calculation must deal accurately with the excited states of bases, including strong base-base interactions and structural fluctuations, and should reflect the increase of efficiency with temperature decrease and the relative insensitivity to strandedness (single, double). Attempts to use DNA as a molecular "fiber optic" face three primary challenges. First, reasonable efficiency over more than a base or two occurs only in adenine stretches at temperatures well below freezing. Second, transfer in these adenine tracks is efficient in both directions. Third, absorption of UV light occurs randomly, making excitation at a specific site on this "fiber optic" a challenge.

Altered dynamics of DNA bases adjacent to a mismatch: a cue for mismatch recognition by MutS

The structural deviations as well as the alteration in the dynamics of DNA at mismatch sites are considered to have a crucial role in mismatch recognition followed by its repair utilizing mismatch repair family proteins. To compare the dynamics at a mismatch and a non-mismatch site, we incorporated 2-aminopurine, a fluorescent analogue of adenine next to a G.T mismatch, a C.C mismatch, or an unpaired T, and at several other non-mismatch positions. Rotational diffusion of 2-aminopurine at these locations, monitored by time-resolved fluorescence anisotropy, showed distinct differences in the dynamics. This alteration in the motional dynamics is largely confined to the normally matched base-pairs that are immediately adjacent to a mismatch/ unpaired base and could be used by MutS as a cue for mismatch-specific recognition. Interestingly, the enhanced dynamics associated with base-pairs adjacent to a mismatch are significantly restricted upon MutS binding, perhaps "resetting" the cues for downstream events that follow MutS binding. Recognition of such details of motional dynamics of DNA for the first time in the current study enabled us to propose a model that integrates the details of mismatch recognition by MutS as revealed by the high-resolution crystal structure with that of observed base dynamics, and unveils a minimal composite read-out involving the base mismatch and its adjacent normal base-pairs.

Ultrafast voltammetry for probing interfacial electron transfer in molecular wires

Electron transfer inside self-assembled monolayers made from complex redox-active oligophenylenevinylene molecular wires is examined by ultrafast cyclic voltammetry. Rate constants above 10(6) s(-1) are measured when the electroactive moieties are easily accessible to counterions from the electrolyte. These counterion movements are necessary to compensate the local charge created upon electron transfer. Conversely, if the redox center is buried within long hydrophobic diluents, the counterion movement towards the redox entity becomes rate limiting, thus drastically altering the rate magnitude and its physical meaning. This change in the mechanism is examined both for superexchange or when one electron-hopping step is involved.

Photosensitization of 2'-deoxyadenosine-5'-monophosphate by pterin

UV-A radiation (320-400 nm) induces damages to the DNA molecule and its components through photosensitized reactions. Pterins, heterocyclic compounds widespread in biological systems, participate in relevant biological processes and are able to act as photosensitizers. We have investigated the photosensitization of 2'-deoxyadenosine-5'-monophosphate (dAMP) by pterin (PT) in aqueous solution under UV-A radiation. The effect of pH was evaluated, the participation of oxygen was investigated and the products analyzed. Kinetic studies revealed that the reactivity of dAMP towards singlet oxygen (1O2) is very low and that this reactive oxygen species does not participate in the mechanism of photosensitization, although it is produced by PT upon UV-A excitation. In contrast, analysis of irradiated solutions by means of electrospray ionization mass spectrometry strongly suggested that 8-oxo-7,8-dihydro-2'-deoxyadenosine-5'-monophosphate (8-oxo-dAMP) was produced, indicating that the photosensitized oxidation takes place via a type I mechanism (electron transfer).

On the stability of peptide nucleic acid duplexes in the presence of organic solvents

Nucleic acid double helices are stabilized by hydrogen bonding and stacking forces (a combination of hydrophobic, dispersive and electrostatic forces) of the base pairs in the helix. One would predict the hydrogen bonding contributions to increase and the stacking contributions to decrease as the water activity in the medium decreases. Study of nucleobase paired duplexes in the absence of water and ultimately in pure aprotic, non-polar organic solvents is not possible with natural phosphodiester nucleic acids due to the ionic phosphate groups and the associated cations, but could be possible with non-ionic nucleic acid analogues or mimics such as peptide nucleic acids. We now report that peptide nucleic acid (PNA) (in contrast to DNA) duplexes show almost unaffected stability in up to 70% dimethylformamide (DMF) or dioxane, and extrapolation of the data to conditions of 100% organic solvents indicates only minor (or no) destabilization of the PNA duplexes. Our data indicate that stacking forces contribute little if at all to the duplex stability under these conditions. The differences in behaviour between the PNA and the DNA duplexes are attributed to the differences in hydration and counter ion release rather than to the differences in nucleobase interaction. These results support the possibility of having stable nucleobase paired double helices in organic solvents.

Site-specific dynamics of strands in ss- and dsDNA as revealed by time-domain fluorescence of 2-aminopurine

It is well recognized that structure and dynamics of DNA strands guide proteins toward their cognate sites in DNA. While the dynamics is controlled primarily by the nucleotide sequence, the context of a particular sequence in relation to an open end could also play a significant role. In this work we have used the fluorescent analogue of adenine, 2-aminopurine (2-AP), to extract information on site-specific dynamics of DNA strands associated with 30-70 nucleotides length. Measurement of fluorescence lifetime and anisotropy decay kinetics in various types of DNA strands in which 2-AP was located in specific positions revealed novel insights into the dynamics of strands. We find that in single-stranded (ss) DNA, the extent of motional dynamics of the bases falls off sharply from the very end toward the middle of the strand. In contrast, the flexibility of the backbone decreases more gradually in the same direction. In double-stranded (ds) DNA, the level of base-pair fraying increases toward the ends in a graded manner. Surprisingly, the same is countered by the presence of ss-overhangs emanating from dsDNA ends. Moreover, the extent of concerted motion of bases in duplex DNA increased from the end to the middle of the duplex, a result which is both striking and counterintuitive. Most surprisingly, the two complementary strands of a duplex that were unequal in length exhibited differential dynamics: the longer one with overhangs showed a distinctly higher level of flexibility than the recessed shorter strand in the same duplex. All these results, taken together, provoke newer insights in our understanding of how different bases in DNA strands are endowed with specific dynamic properties as a function of their positions. These properties are likely to be used in facilitating specific recognitions of DNA bases by proteins during various DNA-protein interaction systems.

Probing the structure of RecA-DNA filaments. Advantages of a fluorescent guanine analog

The RecA protein of Escherichia coli plays a crucial roles in DNA recombination and repair, as well as various aspects of bacterial pathogenicity. The formation of a RecA-ATP-ssDNA complex initiates all RecA activities and yet a complete structural and mechanistic description of this filament has remained elusive. An analysis of RecA-DNA interactions was performed using fluorescently labeled oligonucleotides. A direct comparison was made between fluorescein and several fluorescent nucleosides. The fluorescent guanine analog 6-methylisoxanthopterin (6MI) demonstrated significant advantages over the other fluorophores and represents an important new tool for characterizing RecA-DNA interactions.