DNA Nucleobases Research Articles

Nucleobase Specific Understanding about the Interaction of Antimalarial Drug Chloroquine with Duplex DNA.

Antimalarial action of a drug is closely associated with the interaction with the parasite's DNA. Hence, in this study, the interaction of an important antimalarial drug, chloroquine (CLQ), has been investigated with six different sequences of DNA having pure adenine (A)-thymine (T) and pure cytosine (C)-guanine (G) as well as mixed nucleobases to achieve the nucleobase level of information in the binding of antimalarial drug with DNA along with binding induced stabilization/destabilization of DNA using different spectroscopic methods and molecular dynamics simulation technique. Further, the experiments have been also performed with 4-amino-7-chloroquinoline (7CLQ), an analogue of CLQ, to understand the role of the quinoline ring and side chain of CLQ in the binding with different sequences of DNA. The binding efficiency of CLQ with any sequence of DNA is higher than 7CLQ suggesting that the presence of charge on CLQ plays a prominent role in DNA binding. The data suggest that the binding of drug as well as induced stabilization of DNA depends significantly on the nature as well as the arrangement of the nucleobases. In general, the binding of CLQ with pure CG DNA is higher than with pure AT DNA; moreover, it prefers an alternate order of CG/AT than continual nucleobases in duplex DNA. CLQ predominately accommodates in the minor groove of AT DNA and prefers to form hydrogen bond mostly with the adenine nucleobase. In contrast to AT DNA, CLQ intrudes into the both major and minor grooves, but it is primarily accommodated into the major groove of CG DNA. CLQ forms a hydrogen bond mainly with guanine in the major groove and cytosine in the minor groove of CG DNA which enhances the binding of CLQ compared to AT DNA as well as induces higher stabilization in CG DNA. The molecular level information obtained about the functional group responsible for the interaction of CLQ as well as the role of chemical nature of nucleobases along with its ordering on the binding of CLQ with DNA may be useful in comprehensive understanding of its action mechanism.

The Design and Application of DNA-Editing Enzymes as Base Editors.

DNA-editing enzymes perform chemical reactions on DNA nucleobases. These reactions can change the genetic identity of the modified base or modulate gene expression. Interest in DNA-editing enzymes has burgeoned in recent years due to the advent of clustered regularly interspaced short palindromic repeat-associated (CRISPR-Cas) systems, which can be used to direct their DNA-editing activity to specific genomic loci of interest. In this review, we showcase DNA-editing enzymes that have been repurposed or redesigned and developed into programmable base editors. These include deaminases, glycosylases, methyltransferases, and demethylases. We highlight the astounding degree to which these enzymes have been redesigned, evolved, and refined and present these collective engineering efforts as a paragon for future efforts to repurpose and engineer other families of enzymes. Collectively, base editors derived from these DNA-editing enzymes facilitate programmable point mutation introduction and gene expression modulation by targeted chemical modification of nucleobases.

Iron(III) Complexes with Non-Steroidal Anti-Inflammatory Drugs: Structure, Antioxidant and Anticholinergic Activity, and Interaction with Biomolecules

One the main research goals of bioinorganic chemists is the synthesis of novel coordination compounds possessing biological potency. Within this context, three novel iron(III) complexes with the non-steroidal anti-inflammatory drugs diflunisal and diclofenac in the presence or absence of the nitrogen donors 1,10-phenanthroline or pyridine were isolated and characterized by diverse techniques. The complexes were evaluated for their ability to scavenge in vitro free radicals such as hydroxyl, 1,1-diphenyl-2-picrylhydrazyl and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) radicals, revealing their selective potency towards hydroxyl radicals. The in vitro inhibitory activity of the complexes towards the enzymes acetylcholinesterase and butyrylcholinesterase was evaluated, and their potential to achieve neuroprotection appeared promising. The interaction of the complexes with calf-thymus DNA was examined in vitro, revealing their ability to intercalate in-between DNA nucleobases. The affinity of the complexes for serum albumins was evaluated in vitro and revealed their tight and reversible binding.

Epigenetic modification of gene expression in cancer cells by terahertz demethylation

Terahertz (THz) radiation can affect the degree of DNA methylation, the spectral characteristics of which exist in the terahertz region. DNA methylation is an epigenetic modification in which a methyl (CH3) group is attached to cytosine, a nucleobase in human DNA. Appropriately controlled DNA methylation leads to proper regulation of gene expression. However, abnormal gene expression that departs from controlled genetic transcription through aberrant DNA methylation may occur in cancer or other diseases. In this study, we demonstrate the modification of gene expression in cells by THz demethylation using resonant THz radiation. Using an enzyme-linked immunosorbent assay, we observed changes in the degree of global DNA methylation in the SK-MEL-3 melanoma cell line under irradiation with 1.6-THz radiation with limited spectral bandwidth. Resonant THz radiation demethylated living melanoma cells by 19%, with no significant occurrence of apurinic/apyrimidinic sites, and the demethylation ratio was linearly proportional to the power of THz radiation. THz demethylation downregulates FOS, JUN, and CXCL8 genes, which are involved in cancer and apoptosis pathways. Our results show that THz demethylation has the potential to be a gene expression modifier with promising applications in cancer treatment.

Electron Attachment to DNA: The Protective Role of Amino Acids.

We have studied the effect of amino acids on the electron attachment properties of a DNA nucleobase, with cytosine as a model system. The equation of motion coupled cluster theory with an extended basis set has been used to simulate the electron-attached state of the DNA model system. Arginine, alanine, lysine, and glycine are the four amino acids considered to investigate their role in electron attachment to a DNA nucleobase. The electron attachment to cytosine in all the four cytosine-amino acid gas-phase dimer complexes follows a doorway mechanism, where the electron gets transferred from the initial dipole-bound doorway state to the final nucleobase-bound state through the mixing of electronic and nuclear degrees of freedom. When cytosine is bulk-solvated with glycine, the glycine-bound state acts as the doorway state, where the initial electron density is localized on the bulk amino acid and away from the nucleobase, thus leading to the physical shielding of the nucleobase from the incoming electron. At the same time, the presence of amino acids can increase the stability of the nucleobase-bound anionic state, which can suppress the sugar-phosphate bond rupture caused by dissociative electron attachment to DNA.

Cu(II) complex of S-benzyl-β-N-(2-methoxybenzylmethylene)dithiocarbazate: Synthesis, DFT calculations, cell cytotoxicity assay and DNA binding studies

A copper(II) complex (CuL2) containing bidentate N,S-donor Schiff base ligands (S-benzyl-β-N-(2-methoxybenzylmethylene) dithiocarbazate, HL) was synthesised and characterised using physicochemical and spectroscopic methods. This work comprehensively includes the single crystal X-ray diffraction analysis of HL, revealing that the centroid of the phenyl ring was engaged in the intermolecular CH interactions that stabilised the three-dimensional (3D) molecular structure. The Hirshfeld surface analysis was used to measure the intermolecular interactions of HL. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations of HL and CuL2 were carried out using B3LYP with the LanL2DZ pseudopotential and 6–311G(d, p) basis set for all the other atoms. The selected calculated frequencies (v(C = N), v(NN), v(C = S)) correlated well with the experimental data obtained, except v(NH). Due to the intra- and intermolecular hydrogen bondings between molecules in solid, some deviation of this band was observed in the calculated gas phase system. The calculated structures and UV–vis results also concur with the experimental findings. It was discovered through cytotoxicity studies that CuL2 had promised good activity against extremely aggressive breast cancer cells (MDA-MB-231). In order to investigate the interactions between cytoactive CuL2 and calf thymus-DNA (DNA), electronic absorption titrations were performed, which revealed moderate binding through groove binding mode with a binding constant (Kb) of 1.75 × 105 M−1. Additionally, the binding capacity of CuL2 with DNA was investigated using molecular docking simulations. The results are comparable with the experimental data, in which CuL2 is bound to the DNA groove via hydrogen bonds and hydrophobic interactions. DNA binding studies have shown that sulfur, nitrogen, and aromatic rings is very important, in terms of the interactions between the lone pairs and π-aromatic ring with nucleobases of DNA.

An Efficient Multilayer Approach to Model DNA-Based Nanobiosensors.

In this work, we present a full computational protocol to successfully obtain the one-electron reduction potential of nanobiosensors based on a self-assembled monolayer of DNA nucleobases linked to a gold substrate. The model is able to account for conformational sampling and environmental effects at a quantum mechanical (QM) level efficiently, by combining molecular mechanics (MM) molecular dynamics and multilayer QM/MM/continuum calculations within the framework of Marcus theory. The theoretical model shows that a guanine-based biosensor is more prone to be oxidized than the isolated nucleobase in water due to the electrostatic interactions between the assembled guanine molecules. In addition, the redox properties of the biosensor can be tuned by modifying the nature of the linker that anchor the nucleobases to the metal support.

Transverse electronic transport properties of single DNA nucleobase pairs between different electrode materials

Detection of gene mutation through electronic transport properties measurements is an attractive research topic. For this purpose, we computed the current–voltage characteristics of adenine-thymine and guanine-cytosine nucleobase pairs, using a combination method of density-functional theory with non-equilibrium Green’s function. Gene mutation was also simulated by structural change in nucleobase pairs by a double proton transfer mechanism. Four different metal electrodes were tested. Comparing the results, nucleobase pairs between platinum surfaces showed distinct electronic transport properties. Such as reverse rectifying direction and negative differential resistance behaviors. The discrepancy can be explained from series of electronic and structural analyses. All these results made identification of structural changes in individual DNA nucleobase pairs possible.

Hyperpolarizing DNA Nucleobases via NMR Signal Amplification by Reversible Exchange.

The present work investigates the potential for enhancing the NMR signals of DNA nucleobases by parahydrogen-based hyperpolarization. Signal amplification by reversible exchange (SABRE) and SABRE in Shield Enables Alignment Transfer to Heteronuclei (SABRE-SHEATH) of selected DNA nucleobases is demonstrated with the enhancement (ε) of 1H, 15N, and/or 13C spins in 3-methyladenine, cytosine, and 6-O-guanine. Solutions of the standard SABRE homogenous catalyst Ir(1,5-cyclooctadeine)(1,3-bis(2,4,6-trimethylphenyl)imidazolium)Cl ("IrIMes") and a given nucleobase in deuterated ethanol/water solutions yielded low 1H ε values (≤10), likely reflecting weak catalyst binding. However, we achieved natural-abundance enhancement of 15N signals for 3-methyladenine of ~3300 and ~1900 for the imidazole ring nitrogen atoms. 1H and 15N 3-methyladenine studies revealed that methylation of adenine affords preferential binding of the imidazole ring over the pyrimidine ring. Interestingly, signal enhancements (ε~240) of both 15N atoms for doubly labelled cytosine reveal the preferential binding of specific tautomer(s), thus giving insight into the matching of polarization-transfer and tautomerization time scales. 13C enhancements of up to nearly 50-fold were also obtained for this cytosine isotopomer. These efforts may enable the future investigation of processes underlying cellular function and/or dysfunction, including how DNA nucleobase tautomerization influences mismatching in base-pairing.

Some Pt(II)-complexes with dpb, Fdpb and F2dpb ligands as potent anticancer agents and their mode of interaction with AT/GC base pairs: A DFT study

In recent years, various Pt(II) metal complexes with N-based intercalating tridentate ligands, such as dpb, Fdpb, and F2dpb, have been developed which exhibit strong anticancer properties because they effectively bind with DNA nucleobase pairs. Past literature has also revealed that the anticancer activity of such square planer Pt(II)-complexes is fully controlled by the presence of halide groups (viz., –F, -Cl and –I) which are directly attached to the Pt(II) ion or tridentate ligands. The proper active sites within Pt(II)-complexes and the role of Pt-X bond may also theoretically be determined by using a molecular electrostatic potential (MEP) map diagram. Moreover, the quantum mechanical TD-DFT (Time-dependent density-functional theory) method is quite useful for predicting the theoretical UV–Vis spectra for such Pt(II)-complexes, during interaction with AT/GC base pairs. The density-functional theory (DFT) is one of the low-cost theoretical methods which is also a useful tool for investigating the various binding modes for anticancer agents with DNA nucleobases. In this current study, we aim to analyze the proper interaction between some dpb-based Pt(II)-complexes as potent anticancer agents with AT/GC base pairs.

Phase-Separation Propensity of Non-ionic Amino Acids in Peptide-Based Complex Coacervation Systems.

Uncovering the sequence-encoded molecular grammar that governs the liquid-liquid phase separation (LLPS) of proteins is a crucial issue to understand dynamic compartmentalization in living cells and the emergence of protocells. Here, we present a model LLPS system that is induced by electrostatic interactions between anionic nucleic acids and cationic oligolysine peptides modified with 12 different non-ionic amino acids, with the aim of creating an index of "phase-separation propensity" that represents the contribution of non-ionic amino acids to LLPS. Based on turbidimetric titrations and microscopic observations, the lower critical peptide concentrations where LLPS occurs (Ccrit) were determined for each peptide. A correlation analysis between these values and known amino acid indices unexpectedly showed that eight non-ionic amino acids inhibit the generation of LLPS, whereby the extent of inhibition increases with increasing hydrophobicity of the amino acids. However, three aromatic amino acids deviate from this trend and rather markedly promote LLPS despite their high hydrophobicity. A comparison with double-stranded DNA and polyacrylic acid revealed that this is primarily due to interactions with DNA nucleobases. Our approach to quantify the contribution of non-ionic amino acids can be expected to help to provide a more accurate description and prediction of the LLPS propensity of peptides/proteins.

Will the Interactions of Some Platinum (II)-Based Drugs with B-Vitamins Reduce Their Therapeutic Effect in Cancer Patients? Comparison of Chemotherapeutic Agents such as Cisplatin, Carboplatin and Oxaliplatin-A Review.

Pt (II) derivatives show anti-cancer activity by interacting with nucleobases of DNA, thus causing some spontaneous and non-spontaneous reactions. As a result, mono- and diaqua products are formed which further undergo complexation with guanine or adenine. Consequently, many processes are triggered, which lead to the death of the cancer cell. The theoretical and experimental studies confirm that such types of interactions can also occur with other chemical compounds. The vitamins from B group have a similar structure to the nucleobases of DNA and have aromatic rings with single-pair orbitals. Theoretical and experimental studies were performed to describe the interactions of B vitamins with Pt (II) derivatives such as cisplatin, oxaliplatin and carboplatin. The obtained results were compared with the values for guanine. Two levels of simulations were implemented at the theoretical level, namely, B3LYP/6-31G(d,p) with LANL2DZ bases set for platinum atoms and MN15/def2-TZVP. The polarizable continuum model (IEF-PCM preparation) and water as a solvent were used. UV-Vis spectroscopy was used to describe the drug-nucleobase and drug-B vitamin interactions. Values of the free energy (ΔGr) show spontaneous reactions with mono- and diaqua derivatives of cisplatin and oxaliplatin; however, interactions with diaqua derivatives are more preferable. The strength of these interactions was also compared. Carboplatin products have the weakest interaction with the studied structures. The presence of non-covalent interactions was demonstrated in the tested complexes. A good agreement between theory and experiment was also demonstrated.

Collision-induced state-changing rate coefficients for cyanogen backbones NCN 3Σ- and CNN 3Σ- in astrophysical environments.

We report quantum calculations involving the dynamics of rotational energy-transfer processes, by collision with He atoms in interstellar environments, of the title molecular species which share the presence of the CN backbone and are considered of importance in those environments. The latter structural feature is taken to be especially relevant for prebiotic chemistry and for its possible role in the processing of the heterocyclic rings of RNA and DNA nucleobases in the interstellar space. We carry out ab initio calculations of their interaction potentials with He atoms and further obtain the state-to-state rotationally inelastic cross sections and rate coefficients over the relevant range of temperatures. The similarities and differences between such species and other similar partners which have been already detected are analyzed and discussed for their significance on internal state populations in interstellar space for the two title molecular radicals.

Meteorites and the RNA World: Synthesis of Nucleobases in Carbonaceous Planetesimals and the Role of Initial Volatile Content

Prebiotic molecules, fundamental building blocks for the origin of life, have been found in carbonaceous chondrites. The exogenous delivery of these organic molecules onto the Hadean Earth could have sparked the polymerization of the first RNA molecules in Darwinian ponds during wet-dry cycles. Here, we investigate the formation of the RNA and DNA nucleobases adenine, uracil, cytosine, guanine, and thymine inside parent body planetesimals of carbonaceous chondrites. An up-to-date thermochemical equilibrium model coupled with a 1D thermodynamic planetesimal model is used to calculate the nucleobase concentrations. Different from previous studies, we assume the initial volatile concentrations more appropriate for the formation zone of carbonaceous chondrite parent bodies. This represents more accurately cosmochemical findings that these bodies have formed inside the inner, ∼2–5 au, warm region of the solar system. Due to these improvements, our model represents the concentrations of adenine and guanine measured in carbonaceous chondrites. Our model did not reproduce per se the measurements of uracil, cytosine, and thymine in these meteorites. This can be explained by transformation reactions between nucleobases and the potential decomposition of thymine. The synthesis of prebiotic organic matter in carbonaceous asteroids could be well explained by a combination of (i) radiogenic heating, (ii) aqueous chemistry involving a few key processes at a specific range of radii inside planetesimals where water can exist in the liquid phase, and (iii) a reduced initial volatile content (H2, CO, , and CH2O) of the protoplanetary disk material in the parent body region compared to the outer region of comets.

Caging of a Strongly Pairing Fluorescent Thymidine Analog with Soft Nucleophiles.

Controlling the pairing strength of nucleobases in DNA through reactions with compounds found inside the cell is a formidable challenge. Here we report how a thiazolyl substituent turns a strongly pairing ethynylpyridone C-nucleoside into a reactive residue in oligonucleotides. The thiazolyl-bearing pyridone reacts with soft nucleophiles, such as glutathione, but not with hard nucleophiles like hydroxide or carbonate. The addition products pair much more weakly with adenine in a complementary strand than the starting material, and also change their fluorescence. This makes oligonucleotides containing the new deoxynucleoside interesting for controlled release. Due to its reactivity toward N, P, S, and Se-nucleophiles, and the visual signal accompanying chemical conversion, the fluorescent nucleotide reported here may also have applications in chemical biology, sensing and diagnostics.

Toward Detecting Biosignatures of DNA, Lipids, and Metabolic Intermediates from Bacteria in Ice Grains Emitted by Enceladus and Europa.

The reliable identification of biosignatures is key to the search for life elsewhere. On ocean worlds like Enceladus or Europa, this can be achieved by impact ionization mass spectrometers, such as the SUrface Dust Analyzer (SUDA) on board NASA's upcoming Europa Clipper mission. During spacecraft flybys, these instruments can sample ice grains formed from subsurface water and emitted by these moons. Previous laboratory analog experiments have demonstrated that SUDA-type instruments could identify amino acids, fatty acids, and peptides in ice grains and discriminate between their abiotic and biotic origins. Here, we report experiments simulating impact ionization mass spectra of ice grains containing DNA, lipids, and metabolic intermediates extracted from two bacterial cultures: Escherichia coli and Sphingopyxis alaskensis. Salty Enceladan or Europan ocean waters were simulated using matrices with different NaCl concentrations. Characteristic mass spectral signals, such as DNA nucleobases, are clearly identifiable at part-per-million-level concentrations. Mass spectra of all substances exhibit unambiguous biogenic patterns, which in some cases show significant differences between the two bacterial species. Sensitivity to the biosignatures decreases with increasing matrix salinity. The experimental parameters indicate that future impact ionization mass spectrometers will be most sensitive to the investigated biosignatures for ice grain encounter speeds of 4-6 km/s.

Ethanolamine Derivatives Prompt Oxidation-Mediated Cleavage of Phosphorothioated DNA via Redox Control and Competition with Desulphurization

Abstract In the early 2000s, an epoch-making discovery of phosphorothioated DNA (PS-DNA, also as medicines) was made to show that sulfur atoms are present on the DNA backbone in microorganisms. However, its reaction activity and mechanism have not been well clarified. We show that PS-DNA is cleaved efficiently via oxidation, but not previously believed alkylation; this sulfur modification can be repaired by desulphurization once the sulfhydryl is further oxidized. When Tris or other ethanolamine derivatives are present, the cleavage becomes extremely efficient. Analyzed by enzymatic digestion, ligation, and mass spectroscopy, a mechanism is proposed to explain effects of ethanolamine derivatives and the competition between repair and breakage. Tris favors cleavage by keeping and utilizing the oxidation at –S(O)OH (sulfinic group) stage. The hydroxyl group on ethanolamine derivatives attacks the activated phosphor atom for cleavage with an intramolecular-like mode to form simultaneously a phosphoester bond. Desulphurization is dominant once the PS-DNA is oxidized to –S(O2)OH (sulfonic group). We believe that the biological significance of PS-DNA is protection of DNA nucleobases from weak oxidants by direct repairing or cleavage-repairing approach, which is affected by amines. Besides understanding the biological significance of PS-DNA, our findings will contribute greatly to developing new bio-techniques and nucleic acid medicines.

Nucleobase-Bonded Graphene Nanoribbon Junctions: Electron Transport from First Principles.

Carbon and hydrogen bonding constitute the backbone of life; in the form of graphene, possibly functionalized by DNA nucleobases, these hold promise for the programmable assembly of graphene-based nanoelectronic devices. It is still unknown how hydrogen-bonded junctions inherent in such devices will perform as electron transport media. Here, we design nucleobase-bonded graphene nanoribbons and quantify their quantum transport characteristics using first-principles calculations. Pronounced rectifying behavior and negative differential resistance are found, as well as high conductance of certain structures, with the guanine-cytosine junction in general being superior to the adenine-thymine junction. The identified sensitivity of the conductance to atomic details of the interfaces offers initial hints and guidance for experimental realization. The dependence of current on electrostatic gate doping, with an on/off ratio of ∼102, shows the potential of the junction as a field effect transistor.

Structural Analysis of the Poly(thymidine)-Melamine Assembly.

Hydrogen bonding between the DNA nucleobases and small organic molecules, such as melamine, is a new strategy for the design of novel DNA materials. Poly(thymidine) DNA and melamine self-assemble into a duplex structure containing two antiparallel DNA strands hydrogen bonded to central melamine units. In this Article, molecular dynamics simulations rationalize the observed antiparallel duplex structure. Alternative duplex and triplex structures with parallel and antiparallel strand orientations are shown to be unstable because of the increase in unfavorable interactions between the DNA backbones.

A quantum mechanical prediction of C24 fullerene as a DNA nucleobase biosensor

We aim to study the interaction of different nucleobases (adenine (A), thymine (T), guanine (G), cytosine (C) and uracil (U)) with the C24 fullerene (D6d symmetry) and to get the binding sequence of these nucleobases using dispersion (D3) corrected density functional theory (DFT). To evaluate the interaction between the nucleobases with the C24 fullerene, we have performed adsorption energy calculation, NBO analysis, Mulliken charge analysis, density of state calculation, sensing response analysis and recovery time calculation. We observed that adsorption sequence of nucleobase follows the trend as A > C > G > T > U. Due to interaction between the nucleobases and C24 fullerene charge redistribution takes place between them and induces the dipole moment. Adenine can be enisled from the other DNA nucleobase molecules, while cytosine and guanine can be sensed with the recovery time of 10−14 s in gas phase. The interaction energy increases for adenine and cytosine with solvent effect confirms their application as carrier.