Base Analogues Research Articles

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.

K-theory of cuspidal curves over a perfectoid base and formal analogues

In this paper we continue the work of using the recent advances in algebraic K-theory to extend computations done in characteristic p to the mixed characteristic setting using perfectoid rings. We extend the work of Hesselholt-Nikolaus in [18] on the algebraic K-Theory of cuspidal curves. We consider both cuspidal curves and the p-completion of cuspidal curves. Along the way we also study the K-theory of the p-completed affine line over a perfectoid ring.

5-Bromo-2'-deoxyuridine labeling: historical perspectives, factors influencing the detection, toxicity, and its implications in the neurogenesis.

The halopyrimidine 5-bromo-2'-deoxyuridine (BrdU) is an exogenous marker of DNA synthesis. Since the introduction of monoclonal antibodies against BrdU, an increasing number of methodologies have been used for the immunodetection of this synthesized bromine-tagged base analogue into replicating DNA. BrdU labeling is widely used for identifying neuron precursors and following their fate during the embryonic, perinatal, and adult neurogenesis in a variety of vertebrate species including birds, reptiles, and mammals. Due to BrdU toxicity, its incorporation into replicating DNA presents adverse consequences on the generation, survival, and settled patterns of cells. This may lead to false results and misinterpretation in the identification of proliferative neuroblasts. In this review, I will indicate the detrimental effects of this nucleoside during the development of the central nervous system, as well as the reliability of BrdU labeling to detect proliferating neuroblasts. Moreover, it will show factors influencing BrdU immunodetection and the contribution of this nucleoside to the study of prenatal, perinatal, and adult neurogenesis. Human adult neurogenesis will also be discussed. It is my hope that this review serves as a reference for those researchers who focused on detecting cells that are in the synthetic phase of the cell cycle.

Synthesis and in Vitro Biological Activity Study of Novel Phenol Mannich Base Analogs Containing Spiroheterocycle as Core Compound

The condensation reactions between Gabapentin lactam and phenols have been carried out in the presence of formaldehyde for the synthesis of various mannich base series. To confirm the formation of these series of newly prepared mannich bases thus synthesized, various characterization techniques have been used, such as, GC-MS, 1H-NMR, 13C-NMR and FT-IR. Further their antibacterial and antifungal activities against pathogenic bacteria have been evaluated. These compounds show promising activities against the pathogenic bacteria, hence are useful as antibacterial and antifungal active compounds.

In-Silico Prediction of Novel Fused Quinazoline Based Topoisomerase Inhibitors as Anticancer Agents.

The prospective uses of tryptanthrin and its analogues in cancer chemotherapy are well known, and they are also predicated on their capacity to reverse drug resistance in cancer therapy. The current project entails developing a novel hybrid analogue that includes modifying the tryptanthrin molecule at the C-6 carbonyl position and is expected to exhibit substantial anticancer action. In the ATPase domain of human topoisomerase II, a series of 162 substituted Schiff base analogues of tryptanthrin were developed, and molecular docking experiments were done using Gold 5.1 software interfaced with Hermes 1.6.2. (PDB ID: 1ZXM). Most of the compounds were found to have Goldscore above 100 and formed interactions with the residues like ASN91, ALA92, ASN95, ARG98, ASN120, ILE125, ILE141, PHE142, SER149, THR215, and ILE217. Compound RK-149 had highest Goldscore of 132.59, forming an interaction with ASN91 but had a lesser Goldscore as compared to the standard drug etoposide and had a better score than tryptanthrin. The nitrogen in the imine bond of the proposed compounds is responsible for significant interactions, demonstrating their anticancer potential.

A Bright and Ionizable Cytosine Mimic for i-Motif Structures.

A new fluorescent cytosine analog "tsC" containing a trans-stilbene moiety was synthesized and incorporated into hemiprotonated base pairs that comprise i-motif structures. Unlike previously reported fluorescent base analogs, tsC mimics the acid-base properties of cytosine (pKa ≈ 4.3) while exhibiting bright (ε × Φ ≈ 1000 cm-1 M-1) and red-shifted fluorescence (λem = 440 → 490 nm) upon its protonation in the water-excluded interface of tsC+:C base pairs. Ratiometric analyses of tsC emission wavelengths facilitate real-time tracking of reversible conversions between single-stranded, double-stranded, and i-motif structures derived from the human telomeric repeat sequence. Comparisons between local changes in tsC protonation with global structure changes according to circular dichroism suggest partial formation of hemiprotonated base pairs in the absence of global i-motif structures at pH = 6.0. In addition to providing a highly fluorescent and ionizable cytosine analog, these results suggest that hemiprotonated C+:C base pairs can form in partially folded single-stranded DNA in the absence of global i-motif structures.

Promising Schiff bases in antiviral drug design and discovery.

Emerging and re-emerging illnesses will probably present a new hazard of infectious diseases and have fostered the urge to research new antiviral agents. Most of the antiviral agents are analogs of nucleosides and only a few are non-nucleoside antiviral agents. There is quite a less percentage of marketed/clinically approved non-nucleoside antiviral medications. Schiff bases are organic compounds that possess a well-demonstrated profile against cancer, viruses, fungus, and bacteria, as well as in the management of diabetes, chemotherapy-resistant cases, and malarial infections. Schiff bases resemble aldehydes or ketones with an imine/azomethine group instead of a carbonyl ring. Schiff bases have a broad application profile not only in therapeutics/medicine but also in industrial applications. Researchers have synthesized and screened various Schiff base analogs for their antiviral potential. Some of the important heterocyclic compounds like istatin, thiosemicarbazide, quinazoline, quinoyl acetohydrazide, etc. have been used to derive novel Schiff base analogs. Keeping in view the outbreak of viral pandemics and epidemics, this manuscript compiles a review of Schiff base analogs concerning their antiviral properties and structural-activity relationship analysis.

Exploring thiazole-based Schiff base analogs as potent α-glucosidase and α-amylase inhibitor: their synthesis and in-silico study

In search of potent antidiabetic agents here in this study a new series of thiazole-based Schiff base analogs (1–20) have been synthesized, characterized by 1HNMR, 13CNMR, HREI-MS and evaluated as dual inhibitor for α-glucosidase and α-amylase. All analogs of the series found active and exhibited variable degree of inhibitory potential ranging from 1.10 ± 0.10–17.20 ± 0.30 µM as compared to reference drug acarbose IC50 = for 9.80 ± 0.20 µM α-glucosidase and from 0.90 ± 0.01 to 16.20 ± 0.30 µM as compared to reference drug acarbose IC50 = 10 0.30 ± 0.20 µM for α-amylase. Compounds 3, 5, 6, 7, 14, 15, 16, 18 and 19 exhibited outstanding α-glucosidase as well as α-amylase inhibitory potential as compared to reference drug acarbose. Structure activity relationships SAR) have established for all the synthesized analogs. A molecular docking study has been conducted to develop an idea about binding interaction of compounds and enzymes. All synthesized compounds were tested for cytotoxicity and found nontoxic.

Constructing Artificial Nucleobase Compilation to Enable Precise Molecular Medicine†

Comprehensive SummaryNucleic acids are the hereditary information storage medium of life. Due to its high programmability and good biocompatibility, the applications of nucleic acids are not limited to their natural function. However, the efficiency of nucleic acids is often hampered by inherent limitations in numerous practical applications, including limited access to complex functional patterns due to only four building blocks, facile degradation by nucleases, rapid renal clearance, poor pharmacokinetic properties, and so on. To end this, the researchers developed unnatural base pairs (UBPs) and numerous artificial analogues of nucleosides and oligonucleotides in recent decades. The developed UBPs and nucleoside base analogues together constitute artificial nucleobase compilation, which promotes the development of biomedical sciences. Here, we describe the development of artificial nucleobase compilation and summarized its applications in precise molecular medicine, including PCR‐based diagnostics, aptamer‐based diagnostics, nucleobase analogue drugs construction, ASO modification, aptamer‐based therapeutics and biomaterials construction. This review provides an overview of current opportunities and challenges of artificial nucleobase‐related precise molecular medicine.

Promoting spontaneous analogical transfer by idealizing target representations.

Recent results demonstrate that inducing an abstract representation of target analogs at retrieval time aids access to analogous situations with mismatching surface features (i.e., the late abstraction principle). A limitation of current implementations of this principle is that they either require the external provision of target-specific information or demand very high intellectual effort. Experiment 1 demonstrated that constructing an idealized situation model of a target problem increases the rate of correct solutions compared with constructing either concrete simulations or no simulations. Experiment 2 confirmed that these results were based on an advantage for accessing the base analog, and not merely an advantage of idealized simulations for understanding the target problem in its own terms. This target idealization strategy has broader applicability than prior interventions based on the late abstraction principle because it can be achieved by a greater proportion of participants and without the need to receive target-specific information. We present a computational model, SampComp, that predicts successful retrieval of a stored situation to understand a target based on the overlap of a random, but potentially biased, sample of features from each. SampComp is able to account for the relative benefits of base and target idealization, and their interaction.

A genome-wide map of DNA replication at single-molecule resolution in the malaria parasite Plasmodium falciparum.

The malaria parasite Plasmodium falciparum replicates via schizogony: an unusual type of cell cycle involving asynchronous replication of multiple nuclei within the same cytoplasm. Here, we present the first comprehensive study of DNA replication origin specification and activation during Plasmodium schizogony. Potential replication origins were abundant, with ORC1-binding sites detected every ∼800 bp. In this extremely A/T-biased genome, the sites were biased towards areas of higher G/C content, and contained no specific sequence motif. Origin activation was then measured at single-molecule resolution using newly developed DNAscent technology: a powerful method of detecting replication fork movement via base analogues in DNA sequenced on the Oxford Nanopore platform. Unusually, origins were preferentially activated in areas of low transcriptional activity, and replication forks also moved fastest through lowly transcribed genes. This contrasts with the way that origin activation is organised in other systems, such as human cells, and suggests that P. falciparum has evolved its S-phase specifically to minimise conflicts between transcription and origin firing. This may be particularly important to maximise the efficiency and accuracy of schizogony, with its multiple rounds of DNA replication and its absence of canonical cell-cycle checkpoints.

High-Throughput Exonuclease Assay Based on the Fluorescent Base Analogue 2-Aminopurine.

Exonucleases are essential enzymes that remove nucleotides from free DNA ends during DNA replication, DNA repair, and telomere maintenance. Due to their essential role, they are potential targets for novel anticancer and antimicrobial drugs but have so far been little exploited. Here, we present a simple and versatile real-time exonuclease assay based on 2-aminopurine, an intrinsically fluorescent nucleotide that is quenched by neighboring bases when embedded in DNA. We show that our assay is applicable to different eukaryotic and bacterial exonucleases acting on both 3' and 5' DNA ends over a wide range of protein activities and suitable for a high-throughput inhibitor screening campaign. Using our assay, we discover a novel inhibitor of the Mycobacterium tuberculosis PHP-exonuclease that is part of the replicative DNA polymerase DnaE1. Hence, our novel assay will be a useful tool for high-throughput screening for novel exonuclease inhibitors that may interfere with DNA replication or DNA maintenance.

Synthesis, spectral characterization of pyrazole derived Schiff base analogs: molecular dynamic simulation, antibacterial and DNA binding studies

We have synthesized the pyrazole-bearing Schiff base derivatives (5a–5e) and (6a–6h) then the structural confirmation was supported by various spectral analyses. The antibacterial activity of all analogs was screened against bacterial strains Staphylococcus aureus, Bacillus subtilis, Enterococcus faecalis, Escherichia coli, Klebsiella pneumonieae and Pseudomonas aeruginosa. In comparison to the reference drug ciprofloxacin, the lead analogs 5c and 6c showed potent activity, with MIC values of 64 µg/mL against E. coli and B. subtilis. Compound 5c showed a moderate effect with a MIC value of 128 µg/mL against B. subtilis, P. aeruginosa and K. pneumonieae, while compound 6c was against E. coli and P. aeruginosa. Furthermore, the compounds 5c and 6c displayed groove binding mode towards CT-DNA by absorption, emission, competitive fluorescence studies using EtBr, CD and time-resolved fluorescence studies. Thermodynamic parameters of analogs 5c and 6c with CT-DNA were also calculated at 298, 303 and 308K temperatures by UV–visible spectroscopy. The molecular docking studies give the docking score for all compounds with PDB codes: 1BNA and 2XCT. The MD simulation study of analogs 5c and 6c was also carried out. The pharmacokinetic and ADME properties were calculated for all of the synthesized analogs (5a–5e) and (6a–6h).Communicated by Ramaswamy H. Sarma

Determining RNA Natural Modifications and Nucleoside Analog-Labeled Sites by a Chemical/Enzyme-Induced Base Mutation Principle.

The natural chemical modifications of messenger RNA (mRNA) in living organisms have shown essential roles in both physiology and pathology. The mapping of mRNA modifications is critical for interpreting their biological functions. In another dimension, the synthesized nucleoside analogs can enable chemical labeling of cellular mRNA through a metabolic pathway, which facilitates the study of RNA dynamics in a pulse-chase manner. In this regard, the sequencing tools for mapping both natural modifications and nucleoside tags on mRNA at single base resolution are highly necessary. In this work, we review the progress of chemical sequencing technology for determining both a variety of naturally occurring base modifications mainly on mRNA and a few on transfer RNA and metabolically incorporated artificial base analogs on mRNA, and further discuss the problems and prospects in the field.

Recognition of recombination intermediates by the mismatch repair protein Msh2-Msh6.

The mismatch repair (MMR) protein MutSα (Msh2-Msh6), known for improving the fidelity of DNA replication, also improves the fidelity of homologous recombination. Msh2-Msh6 and its associated proteins are responsible for suppressing homologous recombination when excessive base mispairing is present between the participating chromosomes. In MMR, Msh2-Msh6 recognizes small insertion/deletion loops and single base pair mismatches while scanning DNA post replication. Interestingly, Sc Msh2-Msh6 binds to Holliday Junctions (HJs) with an affinity comparable to that of mismatched duplex DNA (Kd =15 nM). We study the Msh2-Msh6-HJ binding interaction to gain insight into the mechanistic role of Msh2-Msh6 during the process of homologous recombination. In our previous study we examined the dynamics of single base mismatches and the changes associated with Msh2-Msh6 binding using the fluorescent DNA base analog 6-MI and time-resolved fluorescence methods. Here, we employ a similar strategy to study the dynamics of single bases within HJs alone and upon interaction with Msh2-Msh6. 6-MI probes incorporated into the center and arms of the junction only exhibit perturbed dynamics in the center location upon Msh2-Msh6 binding, suggesting protein binding takes place at the junction center. Successful UV-photo crosslinking of Msh2-Msh6 to HJs containing 5-bromouracil at the junction center further supports this finding. Base dynamics at the center of the junction resemble those of the mismatch, which possibly drives Msh2-Msh6 recognition. Interestingly, introduction of a mismatch in the arms of the HJ shifts the Msh2-Msh6 binding from the center of HJ to the mismatch location despite the similar binding affinities. Additionally, a molecular model of the Msh2-Msh6-HJ interaction has been created and subjected to molecular dynamics simulations to gain further structural insights with particular focus on how the DNA binding domain interacts with HJs compared to mismatched duplex DNA.

MoaE Is Involved in Response to Oxidative Stress in Deinococcus radiodurans.

Molybdenum ions are covalently bound to molybdenum pterin (MPT) to produce molybdenum cofactor (Moco), a compound essential for the catalytic activity of molybdenum enzymes, which is involved in a variety of biological functions. MoaE is the large subunit of MPT synthase and plays a key role in Moco synthesis. Here, we investigated the function of MoaE in Deinococcus radiodurans (DrMoaE) in vitro and in vivo, demonstrating that the protein contributed to the extreme resistance of D. radiodurans. The crystal structure of DrMoaE was determined by 1.9 Å resolution. DrMoaE was shown to be a dimer and the dimerization disappeared after Arg110 had been mutated. The deletion of drmoaE resulted in sensitivity to DNA damage stress and a slower growth rate in D. radiodurans. The increase in drmoaE transcript levels the and accumulation of intracellular reactive oxygen species levels under oxidative stress suggested that it was involved in the antioxidant process in D. radiodurans. In addition, treatment with the base analog 6-hydroxyaminopurine decreased survival and increased intracellular mutation rates in drmoaE deletion mutant strains. Our results reveal that MoaE plays a role in response to external stress mainly through oxidative stress resistance mechanisms in D. radiodurans.

Catalytic Asymmetric Synthesis of Tröger's Base Analogues with Nitrogen Stereocenter.

Nitrogen stereocenters are common chiral units in natural products, pharmaceuticals, and chiral catalysts. However, their research has lagged largely behind, compared with carbon stereocenters and other heteroatom stereocenters. Herein, we report an efficient method for the catalytic asymmetric synthesis of Tröger's base analogues with nitrogen stereocenters via palladium catalysis and home-developed GF-Phos. It allows rapid construction of a new rigid cleft-like structure with both a C- and a N-stereogenic center in high efficiency and selectivity. A variety of applications as a chiral organocatalyst and metallic catalyst precursors were demonstrated. Furthermore, DFT calculations suggest that the NH···O hydrogen bonding and weak interaction between the substrate and ligand are crucial for the excellent enantioselectivity control.

Synthesis, Spectroscopic Analysis, Biological Evaluation, and In Silico Studies of Novel Benzenesulfonate-Derived Schiff-Mannich Bases

In the current study, 3-formyl phenyl benzenesulfonate is created by reacting 3-hydroxybenzaldehyde with benzene sulfonyl chloride, which is aided by triethylamine. Nine unique (Z)-3-[(3-substituted-5-oxo-1,5-dihydro-4H-1,2,4-triazol-4-yl)-iminomethyl] compounds were formed through the reaction of a manufactured 3-formyl phenyl benzenesulfonate chemical with nine 3-alkyl(aryl)-4-amino-4,5-dihydro-1H-1,2,4-triazol-5-one, as detailed in the existing literature. Phenyl benzene sulfonate (S) compounds were purchased. Through the reaction of the Schiff bases that were made a secondary amine, such as morpholine with formaldehyde, heterocyclic Mannich bases of a unique kind were created. Five recently found (Z)-3-[(3-substituted-5-oxo-1,5-dihydro-4H-1,2,4-triazol-4-yl)-iminomethyl] compounds are presented in this work. By reacting phenyl benzene sulfonate (S) with morpholine in the presence of formaldehyde, five new (Z)-3-[(3-substituted-1-(morpholinomethyl)-5-oxo-1,5-dihydro-4H-1,2,4-triazol-4-yl)-iminomethyl] compounds were created. Chemical compounds fall under the category of phenylbenzene sulfonates (M). Utilizing IR, 1H NMR, and 13C NMR spectroscopy, fourteen recently novel compoundsand#39; chemical structures were examined. The ability of the freshly synthesized Schiff and morpholine-derived Mannich bases to obstruct the acetylcholinesterase enzymeand#39;s (AChE) activity was also assessed. The 1,2,4-triazole functional group was modified by adding various groups at the 1 and 3 positions, resulting in a collection of compounds (S1–9 and M1, 2, 4, 5, 7). It was determined whether these synthetic compounds could prevent the human recombinant AR enzyme from working in vitro, and the findings were validated using molecular docking, molecular mechanics, and ADME analyses. To better understand this mechanism, synthetic Schiff and Mannich base derivatives as well as the positive control substance quercetin were tested using molecular docking against the human recombinant AR enzyme in vitro. To assess the drug-like properties of Schiff and Mannich base analogs, a series of absorption, distribution, metabolism, and excretion (ADME) properties were analyzed theoretically.

ОТДЕЛЬНОСТОЯЩИЙ ФУНДАМЕНТ СО СТУПЕНЧАТОЙ ПОДОШВОЙ: РЕЗУЛЬТАТЫ НАТУРНОГО ЭКСПЕРИМЕНТА

Despite the large number of existing solutions, the issue of optimizing the structure of freestanding shallow foundations is still relevant because of poorly studying. The object of the study is foundations with stepped base. To confirm the efficiency of these foundations, we conducted three different experiments: digital modelling, laboratory tests and full-scale experiment. First, the foundations were compared in terms of absolute settlement. In each of the experiments, the foundation with a stepped base was more efficient than its flat-base analogue (by about 30 %). During the full-scale experiment, at a final pressure under the foundation base of 18 t/m2, the foundation with flat base settled by 70.67 mm, while the foundation with stepped base settled by 49.32 mm. The experiment confirmed the results of the previous experiments: the foundation with a stepped base showed a substantially smaller settlement than the flat base analogue. In future studies, we plan to investigate the operation of strip foundations with stepped base in more detail, to determine the internal forces appearing in the body of the foundations, and to define the need of reinforcement for foundations with stepped base.

Direct observation of backtracking by influenza A and B polymerases upon consecutive incorporation of the nucleoside analog T1106

The antiviral pseudo-base T705 and its de-fluoro analog T1106 mimic adenine or guanine and can be competitively incorporated into nascent RNA by viral RNA-dependent RNA polymerases. Although dispersed, single pseudo-base incorporation is mutagenic, consecutive incorporation causes polymerase stalling and chain termination. Using a template encoding single and then consecutive T1106 incorporation four nucleotides later, we obtained a cryogenic electron microscopy structure of stalled influenza A/H7N9 polymerase. This shows that the entire product-template duplex backtracks by 5 nt, bringing the singly incorporated T1106 to the+1 position, where it forms an unexpected T1106:U wobble base pair. Similar structures show that influenza B polymerase also backtracks after consecutive T1106 incorporation, regardless of whether prior single incorporation has occurred. These results give insight into the unusual mechanism of chain termination by pyrazinecarboxamide base analogs. Consecutive incorporation destabilizes the proximal end of the product-template duplex, promoting irreversible backtracking to a more energetically favorable overall configuration.