Adenine Thymine Research Articles

Interaction of UV radiation with DNA helices

Abstract Recent experimental and theoretical investigations dealing with model DNA double helices, composed of either adenine–thymine (A–T) or guanine–cytosine (G–C) base pairs, and G quadruplexes shed some light on the excited states populated by photon absorption and their relaxation, energy transfer among bases, and one-photon ionization. These studies revealed that the Franck–Condon excited states of DNA helices cannot be considered as the sum of their monomeric constituents because electronic coupling induces delocalization of the excitation over a few bases. Energy transfer takes place via intraband scattering in less than 100 fs. The fluorescence lifetimes of DNA helices detected by fluorescence upconversion and corresponding mainly to ππ* transitions are longer than that of an equimolar mixture of nucleotides; the only exception was observed for alternating G–C polymers. Moreover, nanosecond flash photolysis experiments showed that organization of bases within single and double helices may lead to a lowering of their ionization potential. Finally, the first determination regarding the time-scale needed for the formation of T dimers, the (6–4) adducts, was determined for the single strand (dT)20.

Excited States of DNA Base Pairs Using Long-Range Corrected Time-Dependent Density Functional Theory

In this work, we present a study of the excitation energies of adenine, cytosine, guanine, thymine, and the adenine-thymine (AT) and guanine-cytosine (GC) base pairs using long-range corrected (LC) density functional theory. We compare three recent LC functionals, BNL, CAM-B3LYP, and LC-PBE0, with B3LYP and coupled cluster results from the literature. We find that the best overall performance is for the BNL functional based on LDA. However, in order to achieve this good agreement, a smaller attenuation parameter is needed, which leads to nonoptimum performance for ground-state properties. B3LYP, on the other hand, severely underestimates the charge-transfer (CT) transitions in the base pairs. Surprisingly, we also find that the CAM-B3LYP functional also underestimates the CT excitation energy for the GC base pair but correctly describes the AT base pair. This illustrates the importance of retaining the full long-range exact exchange even at distances as short as that of the DNA base pairs. The worst overall performance is obtained with the LC-PBE0 functional, which overestimates the excitations for the individual bases as well as the base pairs. It is therefore crucial to strike a good balance between the amount of local and long-range exact exchange. Thus, this work highlights the difficulties in obtained LC functionals, which provides a good description of both ground- and excited-state properties.

Effects of Hydration on the Proton Transfer Mechanism in the Adenine−Thymine Base Pair

We report the first density functional study of water catalytic effect in the double proton transfer (DPT) taking place in the adenine-thymine (AT) base pair. To gain more insight regarding the accuracy of several theoretical methods, the ability of various functionals and models for describing the geometry of this system has first been checked. According to our results, BP86/6-311++G(d,p) is the best option for describing the solvation effects in AT when applied to a two-water-molecule-featuring model. The two possible mechanisms for DPT in solution are explored: in the first one, water molecules only remain passive elements, whereas in the second one they are directly included in the reaction path. For the noncatalyzed mechanism, the stable structures constitute the canonical form of the base pair and the first proton transfer product. Nevertheless, by involving the two water molecules in the reaction, we found three stable species: canonical base pair, first proton transfer product, and double proton transfer product. Although the thermodynamic analysis confirms that AT does not contribute to spontaneous mutation through proton transfer catalyzed by surrounding water, our results suggest that microhydration may play a crucial role for DPT reaction in others DNA or RNA basis pair.

Interaction of angelicin with DNA-bases (III) DFT and ab initio second-order Moeller-Plesset study

Angelicin geometry was optimized at MP2/6-31+G(d,p) level and compared with X-ray experimental data. The highest π-electron density was found to be localized on C1C2 and on C13C14 as confirmed by the calculated bond length and bond order values. Spectrophptometric properties of angelicin were measured and compared with the computed within the TD-DFT. Quantum chemical methods were used to study the interaction of angelicin, as a nonlinear furocoumarin, with DNA bases and base pairs. The interactions with DNA bases and base pairs were studied to shade more light on the nature of the intercalation binding forces between angelicin and DNA. Comparing computed electronic properties of angelicin with that of linear psoralens show that the former is a weaker intercalator. The geometry of complexes of angelicin with adenine, thymine, adenine–thymine base pair, cytocine, guanine as well as cytocine–guanine base pair have been optimized in two main orientations, planar and stacked, at the levels of B3LYP/cc-pVDZ, MP2/6-31G(d,p) and MP2/cc-pVDZ. Effect of vertical distance and rotational angle between the stacked molecules on the interaction energy were investigated by the aforementioned methods in gas phase and water media. It was found that ab initio methods which account for the electron correlation effects are the minimum level for studying the noncovalent interactions. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010

Tunnel conductance of Watson–Crick nucleoside–base pairs from telegraph noise

The use of tunneling signals to sequence DNA is presently hampered by the small tunnelconductance of a junction spanning an entire DNA molecule. The design of a readoutsystem that uses a shorter tunneling path requires knowledge of the absolute conductanceacross base pairs. We have exploited the stochastic switching of hydrogen-bonded DNAbase–nucleoside pairs trapped in a tunnel junction to determine the conductance ofindividual molecular pairs. This conductance is found to be sensitive to the geometry of thejunction, but a subset of the data appears to come from unstrained molecular pairs. Theconductances determined from these pairs are within a factor of two of the predictions ofdensity functional calculations. The experimental data reproduces the counterintuitivetheoretical prediction that guanine–deoxycytidine pairs (3 H-bonds) have a smallerconductance than adenine–thymine pairs (2 H-bonds). A bimodal distribution ofswitching lifetimes shows that both H-bonds and molecule–metal contacts break.

Ultrafast redistribution of vibrational energy after excitation of NH stretching modes in DNA oligomers

Vibrational relaxation after spectrally selective excitation within the NH stretching band of adenine–thymine base pairs in DNA oligomers was studied by subpicosecond infrared-pump/anti-Stokes Raman-probe spectroscopy. The decay of the different NH stretching vibrations populates distinct accepting modes in the NH bending range with a rise time of 0.6 ps that is close to the NH stretching decay times. The population of thymine fingerprint modes after excitation of the adenine antisymmetric NH 2 stretching mode points to an ultrafast excitation transfer to the thymine NH stretching vibration before relaxation. The nonequilibrium fingerprint populations decay on a time scale of several picoseconds.

Ionization potential and structure relaxation of adenine, thymine, guanine and cytosine bases and their base pairs: A quantification of reactive sites

We present density functional theory (DFT) calculations using B3LYP/6-31++G∗∗ method to show relaxation in geometry of base pairs on cation radical formation. The changes in hydrogen bond length and angles show that in the cationic radical form the structure of the base pairs relaxes due to the distribution of charge. According to a recent study, it has been found that, upon excitation hole transfer from base to sugar occurs which results in sugar radical formation and leads to strand breakage [45] [A. Kumar, M.D. Sevilla, J. Phys. Chem. B 110 (2006) 24181]. One hydrogen bond increases, while the other decreases in Adenine–Thymine (AT) base pair and in case of Guanine–Cytosine (GC) base pair, one bond increases and other two decrease. Same is the case with bond angles for both the base pairs. Analysis of the electron density map of Singly Occupied Molecular Orbital (SOMO) reveals that electron is transferred mainly from adenine and guanine bases in the cationic radical formation of AT and GC base pair, respectively. The reactive sites of bases have been analyzed using condensed Fukui functions in a relaxed and frozen core approximation. The effects of relaxation on the reactivity indices are also analyzed.

Theoretical investigation of interaction between Gatifloxacin and DNA: Implications for anticancer drug design

This study is an attempt to have a better understanding of the physicochemical interaction between a novel anticancer drug, Gatifloxacin (GTFX) and its biological receptor, DNA. The eventual purpose is to design drugs which interact more with DNA. Considering the physicochemical properties of the drug as well as the mechanism by which it interacts with DNA, it should eventually allow the rational design of novel anticancer or antiviral drugs. Molecular modeling on the complex formed between Gatifloxacin and DNA presented the full ability of the drug for participating in the formation of a stable intercalation site. Besides, the molecular geometries of Gatifloxacin (GTFX) and the DNA bases (Adenine, Guanine, Cytosine and Thymine) were optimized with the aid of B3LYP/6-31G⁎ method. The properties of the isolated intercalator and its stacking interactions with the adenine⋯thymine (AT) and guanine⋯cytosine (GC) nucleic acid base pairs, were studied using DFTB method, (an approximate version of the DFT method) that was extended to cover the London dispersion energy. The B3LYP/6-31G⁎ stabilization energies of the intercalator⋯base pair complexes were found to be − 26.99 and − 37.62 kcal/mol for AT⋯GTFX and GC⋯GTFX, respectively. It was completed that the dispersion energy and the electrostatic interaction contributed to the stability of the intercalator⋯DNA base pair complexes.

Excited State, Charge Transfer, and Spin Dynamics in DNA Hairpin Conjugates with Perylenediimide Hairpin Linkers

A series of short DNA hairpins (nG) using perylene-3,4:9,10-bis(dicarboximide) (PDI) as the hairpin linker was synthesized in which the distance between the PDI and a guanine-cytosine (G-C) base pair is systematically varied by changing the number (n - 1) of adenine-thymine (A-T) base pairs between them. Due to the relatively large hydrophobic surface of PDI, the nG hairpins dimerize in buffer solutions. The photophysics and photochemistry of these hairpins were investigated using femtosecond transient absorption and time-resolved electron paramagnetic resonance (TREPR) spectroscopy. Photoexcitation of the self-assembled PDI dimer within each nG hairpin results in subpicosecond formation of its lower exciton state ((1*)PDI(2)) followed by formation of an excimer-like state ((1*X)PDI(2)) with tau = 10-28 ps. Both of these states are lower in energy than (1*)PDI, so that neither can oxidize A, C, and T. Electron transfer from G to (1*)PDI(2) is faster than formation of (1*X)PDI(2) only for 1G. Electron transfer from G to (1*X)PDI(2) for 2G-8G, occurs by the superexchange mechanism and, thus, becomes exponentially less efficient as the G-PDI(2) distance increases. Nevertheless, TREPR studies show that photoexcitation of 2G and 4G produce spin-correlated radical ion pairs having electron spin polarization patterns indicating that a low yield of charge separation proceeds from (1*X)PDI(2) by the radical pair intersystem crossing (RP-ISC) mechanism to initially yield a singlet radical ion pair. The strong spin-polarization of the radical ion pairs makes it possible to observe them, even though their concentration is low. As expected, the hairpin lacking G (0G) and that having the longest G-PDI(2) distance (8G) display no TREPR radical ion pair signals. Hairpins 0G, 2G, 4G, and 8G all exhibit triplet EPR spectra at 85 K. Simulations of the spectra show that (3*)PDI is produced mainly by a spin-orbit-induced intersystem crossing mechanism, while the spectra of 2G and 4G have 5% and 21% contributions, respectively, from (3*)PDI produced by charge recombination of radical ion pairs that originate from RP-ISC. These low percentages of RP-ISC derived (3*)PDI result mainly from the low yield of radical ion pairs in 2G and 4G.

Theoretical analysis of H/D geometric isotope effect on adenine–thymine base pair using multi-component molecular orbital method

The H/D isotope effect on adenine(A)–thymine(T) DNA base pair has been analyzed at Hartree–Fock/3-21G** level of multi-component molecular orbital (MC_MO) method, which can directly take account of the quantum effect of proton/deuteron. The difference of quantum nature between proton and deuteron in A–T base pair causes the geometric isotope effect (GIE) on the backbone structure of respective monomers, as well as the hydrogen-bonded structure (primary and secondary GIEs). Our MC_MO results clearly suggest the importance of the quantum nature in hydrogen-interacting systems.

Simultaneous determination of adenine guanine and thymine at multi-walled carbon nanotubes incorporated with poly(new fuchsin) composite film

A composite film (MWCNTs–PNF) which contains multi-walled carbon nanotubes (MWCNTs) along with the incorporation of poly(new fuchsin) (PNF) has been synthesized on glassy carbon electrode (GCE), gold (Au) and indium tin oxide (ITO) by potentiostatic methods. The presence of MWCNTs in the composite film enhances surface coverage concentration ( Γ) of PNF to ≈176.5%, and increases the electron transfer rate constant ( k s) to ≈346%. The composite film also exhibits promising enhanced electrocatalytic activity towards the mixture of biochemical compounds such as adenine (AD), guanine (GU) and thymine (THY). The surface morphology of the composite film deposited on ITO has been studied using scanning electron microscopy and atomic force microscopy. These two techniques reveal that the PNF incorporated on MWCNTs. Electrochemical quartz crystal microbalance study reveals the enhancement in the functional properties of MWCNTs and PNF. The electrocatalytic responses of analytes at MWCNTs and MWCNTs–PNF films were measured using both cyclic voltammetry (CV) and differential pulse voltammetry (DPV). From electrocatalysis studies, well separated voltammetric peaks have been obtained at the composite film for AD, GU and THY, with the peak separation of 320.3 and 132.7 mV between GU–AD and AD–THY respectively. The sensitivity of the composite film towards AD, GU and THY in DPV technique is 218.18, 12.62 and 78.22 mA M −1 cm −2 respectively, which are higher than MWCNTs film. Further, electroanalytical studies of AD, GU and THY present in single-strand deoxyribonucleic acid (ssDNA) have been carried out using semi-derivative CV and DPV.

Calculation and analysis of vibrational spectra of adenine–thymine, guanine–cytosine, and adenine–uracil complementary pairs in the condensed state

We have calculated the frequencies of the normal vibrations of the complementary nucleic acid base pairs adenine–thymine, guanine–cytosine, adenine–uracil, corresponding to the Watson–Crick structure, and the adenine–uracil pair, corresponding to the Hoogsteen structure, in condensed states and we interpret the spectra. We determine the contributions of hydrogen bonds to the vibrational modes of the complementary pairs. We have analyzed the nature of the relative displacements of the nucleic acid bases as integral molecular units along the hydrogen bonds. We show the role of hydrogen bonds in tautomeric interconversions of complementary nucleic acid base pairs.

Substantial difference between temperature dependencies of dsDNA predenaturation process obtained by voltammetry and spectroscopy

The electrooxidation of double stranded DNA has been studied in a wide temperature range by cyclic and square wave voltammetries and the results were compared with UV-Vis and CD spectroscopies. A twofold increase of dsDNA voltammetric peaks related to the conformation changes preceding the denaturation process was found to begin at a temperature lower than the well known increase of dsDNA absorbance upon denaturation (the melting point) by circa 20 degrees C. Since the dsDNA voltammetric peaks are related directly to the electrooxidation of guanine and adenine, early conformational changes in guanine-cytosine (G-C) and adenine-thymine (A-T) pairs in dsDNA are possible reasons for the increase of the voltammetric peaks. The above observations prove that the voltammetric methods are much more sensitive to the changes in guanine and adenine base-pairs conformations and indicate increased exposition of guanine and adenine in the reversible stages that precede the denaturation process of dsDNA. Interestingly, two distinct ranges of change in ellipticity in CD spectra correlate well to the changes obtained by voltammetry and UV spectroscopy, respectively. We also checked the influence of an intercalator on the dsDNA denaturation (temperature) plots. The spectroscopic measurements indicated an increase in the stability of the structure of the double stranded helix upon the addition of the intercalator, while voltammetry showed also that the exposition of guanine and adenine for the electrooxidation drops substantially in the region preceding the denaturation process.

Design of laser pulses for selective vibrational excitation of the N6-H bond of adenine and adenine-thymine base pair using optimal control theory

Time dependent quantum dynamics and optimal control theory are used for selective vibrational excitation of the N6-H (amino N-H) bond in free adenine and in the adenine-thymine (A-T) base pair. For the N6-H bond in free adenine we have used a one dimensional model while for the hydrogen bond, N6-H(A)...O4(T), present in the A-T base pair, a two mathematical dimensional model is employed. The conjugate gradient method is used for the optimization of the field dependent cost functional. Optimal laser fields are obtained for selective population transfer in both the model systems, which give virtually 100% excitation probability to preselected vibrational levels. The effect of the optimized laser field on the other hydrogen bond, N1(A)...H-N3(T), present in A-T base pair is also investigated.

Estimation of Copy Number using SYBR Green: Confounding by AT-rich DNA and by Variation in Amplicon Length

Although SYBR Green is used to estimate copy number, its fluorescence varies with amplicon length and adenine/thymine (AT) content. As a result, threshold cycle (Ct) values obtained using real-time polymerase chain reaction (PCR) are lower for longer amplicons (P<0.001) and amplicons with greater AT content (P<0.001). In contrast, neither amplicon length nor AT content affects the Ct with TaqMan probes or LUX-labeled primers. Because SYBR Green yields lower Cts with AT-rich templates and longer templates, it overestimates copy number for those templates. Therefore, sequence-specific methods such as TaqMan probes or LUX-labeled primers should be considered when using real-time PCR to estimate copy number if the amplicons generated are AT-rich or vary in length.

DNA Polymorphism as an Origin of Adenine-Thymine Tract Length-Dependent Threading Intercalation Rate

Binuclear ruthenium complexes that bind DNA by threading intercalation have recently been found to exhibit an exceptional kinetic selectivity for long polymeric adenine-thymine (AT) DNA. A series of oligonucleotide hairpin duplexes containing a central tract of 6-44 alternating AT base pairs have here been used to investigate the nature of the recognition mechanism. We find that, above a threshold AT tract length corresponding to one helix turn of B-DNA, a dramatic increase in threading intercalation rate occurs. In contrast, such length dependence is not observed for rates of unthreading. Intercalation by any mechanism that depends on the open end of the hairpin was found not to be important in the series of oligonucleotides used, as verified by including in the study a hairpin duplex cyclized by a copper-catalyzed "click" reaction. Our observations are interpreted in terms of a conformational pre-equilibrium, determined by the length of the AT tract. We finally find that mismatches or loops in the oligonucleotide facilitate the threading process, of interest for the development of mismatch-recognizing probes.

Dynamic Quantum Isotope Effects on Multiple Proton-Transfer Reactions

Abstract In order to investigate static quantum isotope effects on the stability of proton-transferred structures, we defined an effective quantal potential energy hypersurface (EQPES), which includes mass-dependent quantum effects. We demonstrated the difference between the ordinary potential energy surface and EQPES of the double well potential as a simple example. The minimum energy path on EQPES describes the zero-point energy-corrected structures and tunneling motion, which is characterized as a classically forbidden motion. We also performed the EQPES analysis of model proton-transfer reactions in DNA base pairs. It was found that the double proton-transferred structure of an adenine–thymine (AT) pair is quantum mechanically unstable and that of a guanine–cytosine (GC) pair is stable within a least uncertainty regime. In order to investigate dynamic quantum isotope effects on the stability of the proton-transferred structures, we performed quantal cumulant dynamics (QCD) simulations of the GC pair. Results show that the proton-transferred structure of the protonated isotopomer is dynamically unstable though the EQPES analysis predicts its stability. It is relevant to include dynamic effects in the investigation of the quantum isotope effects on geometric stability of systems with a small energy gap between global and metastable structures.

Ultrafast dynamics of N–H and O–H stretching excitations in hydrated DNA oligomers

DNA oligomers containing 23 alternating adenine–thymine base pairs are studied at different hydration levels by ultrafast two-color pump–probe spectroscopy. N–H stretching excitations of the base pairs and O–H stretching excitations of water are discerned in DNA–surfactant complex films. In a 0% relative humidity (r.h.) atmosphere, lifetimes of approximately 0.5 ps are found for N–H and O–H stretching modes. The transient pump–probe anisotropies demonstrate the coupling of different N–H stretching modes. DNA films at 92% r.h. show similar N–H stretching bands as at 0% r.h. and two types of O–H stretching responses. An O–H stretching band with maximum at 3500 cm −1, limited spectral diffusion and population kinetics similar to 0% r.h. is attributed to water molecules directly interacting with the DNA oligomers. O–H stretching excitations with a ∼200 fs lifetime, broad absorption and a hot ground state formed by vibrational relaxation are assigned to water molecules weakly interacting with DNA.

Revealing Anharmonic Couplings and Energy Relaxation in DNA Oligomers by Ultrafast Infrared Spectroscopy

The identification and characterization of NH 2 hydrogen-bonded stretching vibrations [nu(NH 2)] in DNA oligomers is usually hampered by the all-dominating absorption of the water stretching band in the spectral range of 3050-3600 cm(-1). Here, we use the two-color IR pump-probe technique to overcome the limitations of linear absorption spectroscopy by exciting adenine-thymine (A-T) oligomer vibrations in the fingerprint region and analyzing induced transient spectral changes in the nu(NH2) spectral region. These transient changes are related to anharmonic couplings to the modes excited in the fingerprint region and to modes populated by intra- and intermolecular energy redistribution and relaxation. The combination of calculated anharmonic coupling parameters and experimental transient IR data allows the assignment of a transition at 3215 cm(-1) to the nu(NH2) vibration of adenine in dA(20)-dT(20) DNA oligomers.

QUANTUM MECHANICAL DESCRIPTION OF THE INTERACTIONS BETWEEN DNA AND 9,10-ANTHRAQUINONE

Molecular geometries of the 9,10-anthraquinone (AQ) and DNA bases (Adenine, Guanine, Cytosine, and Thymine) were optimized using B3LYP/6-31G** method. Properties of isolated intercalator (9,10-anthraquinone) and their stacking interactions with adenine ⋯ thymine (AT) and guanine ⋯ cytosine (GC) nucleic acid base pairs were investigated by means of DFTB method. DFTB method, an approximate version of the DFT method, was extended to cover London dispersion energy. AQ exhibits a large charge delocalization and it has no site with dominant charge. This intercalator has a large polarizability and is a good electron acceptor, while base pairs are good electron donors. B3LYP/6-31G** stabilization energies of intercalator ⋯ base pair complexes are large (-18.83 kcal/mol for AT ⋯ AQ and -15.69 kcal/mol for GC ⋯ AQ). It is concluded that, the dispersion energy predominantly contributes to the stability of intercalator ⋯ DNA base pair complexes. Any procedure which does not cover dispersion energy is thus not suitable for studying the process of intercalation. The results showed that AQ changes the structure of DNA on bond length, bond angle, torsion angle, and charges.