Nucleic Acid Bases Research Articles

Unraveling DNA Triplex Assembly: Mass Spectrometric Investigation of Modified Triplex Forming Oligonucleotides for Enhanced Gene Targeting.

Deoxyribonucleic acid triplexes have potential roles in a range of biological processes involving gene and transcriptional regulation. A major challenge in exploiting the formation of these higher-order structures to target genes in vivo is their low stability, which is dependent on many factors including the length and composition of bases in the sequence. Here, different DNA base modifications have been explored, primarily using native mass spectrometry, in efforts to enable stronger binding between the triplex forming oligonucleotide (TFO) and duplex target sites. These modifications can also be used to overcome pyrimidine interruptions in the duplex sequence in promoter regions of genomes, to expand triplex target sequences for antigene therapies. Using model sequences with a single pyrimidine interruption, triplex forming oligonucleotides containing locked nucleic acid base modifications were shown to have a higher triplex binding propensity than DNA-only and dSpacer-containing TFOs. However, the triplex forming ability of these systems was limited by the competitive formation of multiple higher order assemblies. Triplex forming sequences that correspond to specific gene targets from the Pseudomonas aeruginosa genome were also investigated, with LNA-containing TFOs the only variant able to form triplex using these sequences. This work indicates the advantages of utilizing synthetically modified TFOs to form triplex assemblies in vivo for potential therapeutic applications and highlights the advantages of native mass spectrometry for the study of their formation.

Novel diaryl dihydropyrimidines as promising anticancer agents: In silico, in vitro investigation

Due to the structural resemblance with the nucleic acid bases, Dihydropyrimidines (DHPs) gained a special attention for exploring for chemotherapeutic agents. Diaryl dihydropyrimidines (DADPs) were reported to have anticancer properties and antiviral and antibacterial activities. In an attempt to design new DADP compounds, we have come up with some novel compounds (3a–3o, 4a–4o, 5a–5o) by incorporating the piperonal to check its significance on biological activity. Initially, computational screening has been performed to shortlist the top molecules which are showing better binding interactions with the selected targets of cancer treatment such as VEGFR2, JAK1 kinase, and JAK3 kinase. Later the selected compounds were synthesized (15 compounds) and characterized by spectral analysis. In the in vitro anti-proliferative activity in the three cell lines, it was observed that the compounds have exhibited potential biological activity (IC50 values 3d – 42.67 ± 2.28 μM against MCF-7; 3n – 59.68 ± 2.81 μM against Hep G-7; 3d – 70.64 ± 3.12 μM against A-549). It was observed that the piperonal, substituted phenyl ring, secondary amine in mannich base has resulted with improved biological activity, the same has been observed in molecular docking studies.

Computational insights into intrinsically disordered regions in protein-nucleic acid complexes

We study transitions in intrinsically disordered regions (IDRs) upon complex formation, utilizing X-ray-solved structural dataset of protein-DNA and protein-RNA complexes, along with their available unbound protein forms. The identified IDRs are categorized into three classes: Disordered-to-Ordered (D-O), Disordered-to-Partial Ordered (D-PO) and Disordered-to-Disordered (D-D) after comparing them in unbound and complex forms. In the D-O class, IDRs form secondary structures like coils, helices, and strands upon binding to nucleic acids. Though a majority of these IDRs are present at the surface of the complexes, a significant number of IDRs are also observed at the interfaces and are involved in polar interactions. The hydrogen bonds made by the interface IDRs (B_IDRs) with phosphates and bases of nucleic acids are comparatively more than those formed with sugars. B_IDRs form more H-bonds with the ribose in protein-RNA than with the deoxyribose in protein-DNA. Among the B_IDRs, Arg and Lys prefer to interact with the major and minor grooves of DNA and RNA, respectively. Ser, however, prefers the minor groove in both the nucleic acids. Interestingly, we report 61 and 48 IDRs in 31 protein-DNA and 22 protein-RNA complexes, respectively, suggesting nucleic acid binding to proteins may also result in ordered-to-disordered transitions.

Exploring the electronic structure and interaction mechanism of nucleic acid bases on pristine graphene and beryllium-oxide-graphene layers

The interaction between nucleic acid bases and graphene, along with its derivatives, is crucial for various applications like biosensors, drug delivery, and bio-nanotechnology. The present study focuses on optimizing nucleic acid bases, and the graphene layer using the B3LYP/6-31G** method and the beryllium-oxide-graphene layer using the PBE/6-31G** method. The optimized coordinates are then used to investigate the interaction of nucleic acid bases with pristine graphene and beryllium-oxide-graphene in parallel stacking mode. Various functionals including hybrid B3LYP, PBEPBE, and range-separated ωB97XD along with 6-31G(d,p) basis sets, are employed for this analysis. Based on the obtained interaction energy values, it is concluded that the wB97XD/6-31G(d,p) method provides superior results for the interaction study. Additionally, it is noted that the interaction with pristine graphene primarily involves aromatic π-π interactions and hydrogen bonds, while beryllium oxide graphene seems to form coordination bonds with electron-rich sites. Also, the beryllium-oxide-graphene layer exhibited reduced rigidity compared to pristine carbon graphene layer.

Nanopores map the acid-base properties of a single site in a single DNA molecule.

Nanopores are increasingly powerful tools for single molecule sensing, in particular, for sequencing DNA, RNA and peptides. This success has spurred efforts to sequence non-canonical nucleic acid bases and amino acids. While canonical DNA and RNA bases have pKas far from neutral, certain non-canonical bases, natural RNA modifications, and amino acids are known to have pKas near neutral pHs at which nanopore sequencing is typically performed. Previous reports have suggested that the nanopore signal may be sensitive to the protonation state of an individual moiety. We sequenced ion currents with the MspA nanopore using a single stranded DNA containing a single non-canonical DNA base (Z) at various pH conditions. The Z-base has a near-neutral pKa ∼ 7.8. We find that the measured ion current is remarkably sensitive to the protonation state of the Z-base. We demonstrate how nanopores can be used to localize and determine the pKa of individual moieties along a polymer. More broadly, these experiments provide a path to mapping different protonation sites along polymers and give insight in how to optimize sequencing of polymers that contain moieties with near-neutral pKas.

ABSORPTION AND LUMINESCENCE PROPERTIES OF ACID AND SALT FORMS OF MONONUCLEOTIDES, THEIR COMPONENTS AND COMPLEXES WITH D-MANNITOL AT ROOM TEMPERATURE

Aim. The aim of this work was to analyze and compare spectral properties of aqueous nucleotide solutions in conditions close to biological systems. We studied the absorption and luminescence (Ex and Em fluorescence and Em phosphorescence) of monoribonucleotides, their disodium salts, bases and nucleosides, and mixes with D-mannitol dissolved in water at room temperature. Methods. There were measured absorbance spectra using a Specord 210plus instrument and fluorescence excitation and emission and phosphorescence spectra using Horiba Fluoro Max 4+ instruments. Results. There were obtained the absorption, excitation, and luminescence spectra of aqueous solutions 1 mg/ml of nucleotides, their components, and mixtures with mannitol (in ratio 1:4). We observed a change in the ratio between the peaks of the spectra of acidic and salt forms of nucleotides. Conclusions. The observations confirmed that nucleotides, nucleosides, and nucleic acid bases exhibit luminescence at room temperature, which might be useful information for further research in this area. In addition, a comparative analysis of the spectra showed possible interactions between nucleotide molecules and mannitol.

Year-Long Stability of Nucleic Acid Bases in Concentrated Sulfuric Acid: Implications for the Persistence of Organic Chemistry in Venus' Clouds.

We show that the nucleic acid bases adenine, cytosine, guanine, thymine, and uracil, as well as 2,6-diaminopurine, and the "core" nucleic acid bases purine and pyrimidine, are stable for more than one year in concentrated sulfuric acid at room temperature and at acid concentrations relevant for Venus clouds (81% w/w to 98% w/w acid, the rest water). This work builds on our initial stability studies and is the first ever to test the reactivity and structural integrity of organic molecules subjected to extended incubation in concentrated sulfuric acid. The one-year-long stability of nucleic acid bases supports the notion that the Venus cloud environment-composed of concentrated sulfuric acid-may be able to support complex organic chemicals for extended periods of time.

Enhancement of intrinsic guanine fluorescence by protonation in DNA of various structures

Understanding the diversity of DNA structure and functions in biology requires tools to study this biomolecule selectively and thoroughly. Fluorescence methods are powerful technique for non-invasive research. Due to the low quantum yield, the intrinsic fluorescence of nucleotides has not been considered for use in the detection and differentiation of nucleic acid bases. Here, we have studied the influence of protonation of nucleotides on their fluorescence properties. We show that protonation of ATP and GTP leads to enhanced intrinsic fluorescence. Fluorescence enhancement at acidic pH has been observed for double-stranded DNA and single-stranded oligonucleotides. The formation of G4 secondary structures apparently protected certain nucleotides from protonation, resulting in less pronounced fluorescence enhancement. Furthermore, acid-induced depurination under protonation was less noticeable in G4 structures than in double-stranded and single-stranded DNA. We show that changes in the intrinsic fluorescence of guanine can be used as a sensitive sensor for changes in the structure of the DNA and for the protonation of specific nucleotides.

IR and Raman markers of the interactions between MoS2 and pyrimidine bases

Changes in vibrational spectra are among the most important manifestations of the interaction between transition metal dichalcogenides and nucleic acid bases (NAB). Infrared and Raman spectra were calculated using the DFT/M06-2X method for the most stable stacked and covalently bonded complexes of pyrimidine bases with MoS2. Obtained spectra were analyzed to determine the spectral markers of the interactions between the pyrimidine bases and MoS2. We found that interaction with MoS2 leads to significant changes in both frequencies and intensities of NAB vibrations. The correlation between the changes and interaction energies of the NAB molecules with MoS2 was demonstrated. In general, changes in the vibrational frequencies in complexes with covalent bonds are significantly greater than ones in stacked ones. For the bonded complexes, the most significant changes are observed for those fragments of the NAB molecules that are directly involved in the formation of the covalent bonds. Calculations predict the decrease of the IR intensity and Raman activities of the NAB molecules in the spectra of stacked complexes and their increase in the spectra of covalently bonded complexes.

Determining local nucleic acid base conformations by two-photon excitation 2D fluorescence spectroscopy of 6-methyl isoxanthopterin-substituted DNA constructs

Determining local nucleic acid base conformations by two-photon excitation 2D fluorescence spectroscopy of 6-methyl isoxanthopterin-substituted DNA constructs

FBPP: software to design PCR primers and probes for nucleic acid base detection of foodborne pathogens

Foodborne pathogens can be found in various foods, and it is important to detect foodborne pathogens to provide a safe food supply and to prevent foodborne diseases. The nucleic acid base detection method is one of the most rapid and widely used methods in the detection of foodborne pathogens; it depends on hybridizing the target nucleic acid sequence to a synthetic oligonucleotide (probes or primers) that is complementary to the target sequence. Designing primers and probes for this method is a preliminary and critical step. However, new bioinformatics tools are needed to automate, specific and improve the design sets to be used in the nucleic acid‒base method. Thus, we developed foodborne pathogen primer probe design (FBPP), an open-source, user-friendly graphical interface Python-based application supported by the SQL database for foodborne pathogen virulence factors, for (i) designing primers/probes for detection purposes, (ii) PCR and gel electrophoresis photo simulation, and (iii) checking the specificity of primers/probes.

On Some Origins of Tautomeric Preferences in Neutral Creatinine in Vacuo: Search for Analogies and Differences in Cyclic Azoles and Azines

In order to look for the origins of tautomeric preferences in neutral creatinine in vacuo, we examined prototropic conversions for model azoles, namely mono-hydroxy and mono-amino imidazoles, and also for their selected 1-methyl derivatives. All possible isomeric forms of creatinine and model compounds, resulting from intramolecular proton transfer (prototropy), conformational isomerism about –OH, and configurational isomerism about =NH, were studied in the gas phase (model of non-polar environment) by means of quantum-chemical methods. Because the bond-length alternation is a consequence of the resonance phenomenon, it was measured for all DFT-optimized structures by means of the harmonic oscillator model of electron delocalization (HOMED) index. Important HOMED analogies were discussed for investigated azoles and compared with those for previously studied cyclic azines, including pyrimidine nucleic acid bases. The internal effects were taken into account, and the stabilities of the investigated tautomers-rotamers were analyzed. Significant conclusions on the favored factors that can dictate the tautomeric preferences in creatinine were derived.

Computationally assisted vibrational spectroscopy of nucleic acid bases. 2. Thymine

As in the case of cytosine [Phys. Chem. Chem. Phys. 2023, 25, 24121–24128], Raman and infrared (IR) spectra of aqueous thymine and its N-deuterated derivative, thymine-d2 have been computationally reproduced and interpreted with the use of the recently developed efficient protocol to explicit quantum mechanical modeling of structure and IR spectra of liquids and solutions [J. Phys. Chem. B, 2020, 124, 6664–6670]. A cluster model of a solute surrounded by 30 water molecules is shown to be sufficient to reproduce experimental vibrational frequencies and relative Raman intensities with the use of B3LYP-D3/def2-TZVP or B3LYP-D3/aug-cc-pVDZ simulations. Analogous PBE-D3 computations provided a less good, but still reasonably accurate, modeling of Raman spectra. It is shown that strong changes of frequencies and relative intensities of the Raman bands of thymine, caused by its hydration, can be interpreted mainly as a result of hydrogen bonding with 6 nearest water molecules. Non-negligible improvement of the quality of simulations for larger clusters comprising water molecules that do not have direct contacts with the solute, suggests that spectroscopic effects of hydration should be ascribed to the joined action of solute–solvent and solvent–solvent interactions. Nevertheless, the moderate number of water molecules required for successful simulations of the Raman spectra of aqueous thymine, suggests that the vibrational modes and derivatives of the polarizability of the solute are mainly locally influenced, while the effect of bulk water is rather modest.

Hybrid PNA-peptide hydrogels as injectable CEST-MRI agents.

The self-assembly of peptides and peptide analogues may be exploited to develop platforms for different biomedical applications, among which CEST-MRI (chemical exchange saturation transfer magnetic resonance imaging) represents one of the most attractive techniques to be explored as a novel metal-free contrast approach in imaging acquisitions. A lysine-containing peptide sequence (LIVAGK-NH2, named K2) was thus modified by insertion, at the N-terminus, of a peptide nucleic acid (PNA) base, leading to a primary amine suitable for the signal generation. a-K2, c-K2, g-K2 and t-K2 peptides were synthesized and characterized. The c-K2 sequence displayed gelling properties and the Watson and Crick pairing, arising from its combination with g-K2, allowed a significant increase in the mechanical responsivity of the hydrogel. These matrices were able to generate a CEST signal around 2.5 ppm from water and, after assessing their cytocompatibility on GL261 (murine glioma), TS/a (murine breast carcinoma), and 3T3-NIH (murine fibroblasts) cell lines, their capability to work as implants for in vivo detection, was proved by intratumor injection in Balb/c mice inoculated with TS/a murine breast cancer cells.

Anomalous Dissociative Capture Cross Section at the Interaction of Singly Charged Ions with Molecules of Nucleic Acid Bases

Anomalous Dissociative Capture Cross Section at the Interaction of Singly Charged Ions with Molecules of Nucleic Acid Bases

On Prototropy and Bond Length Alternation in Neutral and Ionized Pyrimidine Bases and Their Model Azines in Vacuo

In this review, the complete tautomeric equilibria are derived for disubstituted pyrimidine nucleic acid bases starting from phenol, aniline, and their model compounds—monosubstituted aromatic azines. The differences in tautomeric preferences for isolated (gaseous) neutral pyrimidine bases and their model compounds are discussed in light of different functional groups, their positions within the six-membered ring, electronic effects, and intramolecular interactions. For the discussion of tautomeric preferences and for the analysis of internal effects, recent quantum-chemical results are taken into account and compared to some experimental ones. For each possible tautomer-rotamer of the title compounds, the bond length alternation, measured by means of the harmonic oscillator model of electron delocalization (HOMED) index, is examined. Significant HOMED similarities exist for mono- and disubstituted derivatives. The lack of parallelism between the geometric (HOMED) and energetic (ΔG) parameters for all possible isomers clearly shows that aromaticity is not the main factor that dictates tautomeric preferences for pyrimidine bases, particularly for uracil and thymine. The effects of one-electron loss (positive ionization) and one-electron gain (negative ionization) on prototropy and bond length alternation are also reviewed for pyrimidine bases and their models.

Modified styrene-maleic anhydride copolymer-based chromatographic stationary phase for phospholipid separation and analysis

Phospholipids are important signaling molecules, and their metabolism is closely related to various diseases, such as neurodegenerative diseases and cancers. Phospholipids are typically characterized with extreme complexity and structural diversity. For example, phospholipids present in many different forms, such as sn position isomers, double-bond position isomers, double-bond stereochemical isomers, and enantiomers. Therefore, further research on novel separation and analytical techniques for phospholipids is of great importance. As an amphiphilic alternating copolymer, styrene-maleic anhydride copolymer (SMA) can be inserted into the phospholipid bilayer of biofilms to form lipid nanodisks with membrane proteins as the centers, thereby solubilizing membrane proteins and phospholipids. Thus, the introduction of SMA into a chromatographic stationary phase can potentially improve the separation and analysis of phospholipids. In this paper, SMA was successfully grafted onto the surface of silica gel via the "click" reaction and free radical polymerization. After further ring-opening modification of SMA with methyl methionine hydrochloride (MME·HCl), a novel SMA-modified stationary phase material (Sil-SMA-MME) was fabricated. The Sil-SMA-MME stationary phase was characterized using thermogravimetric analysis and Fourier transform infrared spectroscopy (FT-IR), and the results indicated the successful fabrication of the target material. The retention mechanism of the packed Sil-SMA-MME chromatographic column was investigated using hydrophilic nucleosides and nucleic acid bases via high performance liquid chromatography (HPLC) and UV detection. According to the retention characteristics of the nucleosides and nucleic acid bases in different mobile phases, the Sil-SMA-MME chromatographic column exhibited a typical hydrophilic-interaction-based retention mechanism, similar to that of a commercially available amino (SiO2-NH2) column. The separation performance of the Sil-SMA-MME column was evaluated using three types of small-molecule substances, including amides, nucleoside/nucleic acid bases, and phenols. Cyanoacetamide, 2-iodoacetamide, benzamide, p-aminobenzamide, and nicotinamide were used to evaluate the chromatographic performance of the developed Sil-SMA-MME column. When acetonitrile-H2O (96∶4, v/v) was used as the mobile phase, the five compounds exhibited good peak shapes and could be baseline-separated within 8 min. The highest column efficiency achieved was 90900 N/m. By contrast, under the same chromatographic conditions, the test substances were not separated effectively on the SiO2-NH2 column. Regardless of the mobile phase ratio, the peaks of benzamide and 2-iodoacetamide overlapped. These results demonstrate that the developed Sil-SMA-MME column has good separation selectivity. The separation performance of the Sil-SMA-MME column for phospholipid samples was also investigated by HPLC and evaporative light scattering detection (ELSD) to explore its feasibility for phospholipid separation and analysis. Different phospholipid standards were used to evaluate the separation performance of the column. Under certain mobile phase conditions, baseline separation could be achieved for dipalmityl phosphatidyl serine sodium (DPPS), diolyl phosphatidyl choline (DOPC), and dipalmityl phosphatidyl ethanolamine (DPPE), as well as four phosphatidyl choline (PC) standards, namely, lysophosphatidylcholine (LysoPC), dimyristoyl phosphatidyl choline (DMPC), distearyl phosphatidyl choline (DSPC), and dipalmitoyl phosphatidyl choline (DPPC). The separation potential of the developed Sil-SMA-MME column was further evaluated by separating and analyzing phospholipid extracts from Antarctic krill oil and human serum. The results showed that the developed Sil-SMA-MME column has good potential for phospholipid separation and analysis.

Accurate Prediction of Adiabatic Ionization Energies for PAHs and Substituted Analogues.

The accurate calculation of adiabatic ionization energies (AIEs) for polycyclic aromatic hydrocarbons (PAHs) and their substituted analogues is essential for understanding their electronic properties, reactivity, stability, and environmental/health implications. This study demonstrates that the M06-2X density functional theory method excels in predicting the AIEs of polycyclic aromatic hydrocarbons and related molecules, rivaling the (R)CCSD(T)-F12 method in terms of accuracy. These findings suggest that M06-2X, coupled with an appropriate basis set, represents a reliable and efficient method for studying polycyclic aromatic hydrocarbons and related molecules, aligning well with the experimental techniques. The set of molecules examined in this work encompasses numerous polycyclic aromatic hydrocarbons from m/z 67 up to m/z 1,176, containing heteroatoms that may be found in biofuels or nucleic acid bases, making the results highly relevant for photoionization experiments and mass spectrometry. For coronene-derivative molecular species with the C6n2H6n chemical formula, we give an expression to predict their AIEs (AIE (n) = 4.359 + 4.8743n-0.72057, in eV) upon extending the π-aromatic cloud until reaching graphene. In the long term, the application of this method is anticipated to contribute to a deeper understanding of the relationships between PAHs and graphene, guiding research in materials science and electronic applications and serving as a valuable tool for validating theoretical calculation methods.

Screening for Novel Fluorescent Nucleobase Analogues Using Computational and Experimental Methods: 2-Amino-6-chloro-8-vinylpurine (2A6Cl8VP) as a Case Study.

Novel fluorescent nucleic acid base analogues (FBAs) with improved optical properties are needed in a variety of biological applications. 2-Amino-6-chloro-8-vinylpurine (2A6Cl8VP) is structural analogue of two existing highly fluorescent FBAs, 2-aminopurine (2AP) and 8-vinyladenine (8VA), and can therefore be expected to have similar base pairing as well as better optical properties compared to its counterparts. In order to determine the absorption and fluorescence properties of 2A6Cl8VP, as a first step, we used TD-DFT calculations and the polarizable continuum model for simulating the solvents and computationally predicted absorption and fluorescence maxima. To test the computational predictions, we also synthesized 2A6Cl8VP and measured its UV/vis absorbance, fluorescence emission, and fluorescence lifetime. The computationally predicted absorbance and fluorescence maxima of 2A6Cl8VP are in reasonable agreement to the experimental values and are significantly redshifted compared to 2AP and 8VA, allowing for its specific excitation. The fluorescence quantum yield of 2A6Cl8VP, however, is significantly lower than those of 2AP and 8VA. Overall, 2A6Cl8VP is a novel fluorescent nucleobase analogue, which can be useful in studying structural, biophysical, and biochemical applications.

Theoretical Assessment of the Ligand/Metal/Quadruplex Recognition in the Non-Canonical Nucleic Acids Structures.

Quadruplexes (GQs), peculiar DNA/RNA motifs concentrated in specific genomic regions, play a vital role in biological processes including telomere stability and, hence, represent promising targets for anticancer therapy. GQs are formed by folding guanine-rich sequences into square planar G-tetrads which stack onto one another. Metal cations, most often potassium, further stabilize the architecture by coordinating the lone electron pairs of the O atoms. The presence of additional nucleic acid bases, however, has been recently observed experimentally and contributes substantially to the structural heterogeneity of quadruplexes. Therefore, it is of paramount significance to understand the factors governing the underlying complex processes in these structures. The current study employs DFT calculations to model the interactions between metal cations (K+, Na+, Sr2+) and diverse tetrads composed of a guanine layer in combination with a guanine (G)-, adenine (A)-, cytosine (C)-, thymine (T)-, or uracil (U)-based tetrad layer. Moreover, the addition of 4-(3,4-dihydroisoquinolin-2-yl)-2-(quinolin-2-yl)quinazoline to the modeled quadruplexes as a possible mechanism of its well-exerted antitumor effect is assessed. The calculations imply that the metal cation competition and ligand complexation are influenced by the balance between electronic and implicit/explicit solvation effects, the composition of the tetrad layers, as well as by the solvent exposure to the surrounding environment expressed in terms of different dielectric constant values. The provided results significantly enhance our understanding of quadruplex diversity, ligand recognition, and the underlying mechanisms of stabilization at an atomic level.