Nucleic Acids Research Research Articles

The influence of thioether-substituted ligands in dicopper(II) complexes: Enhancing oxidation and biological activities

This paper describes the synthesis, structural analysis, as well as the magnetic and spectroscopic characterizations of three new dicopper(II) complexes with dinucleating phenol-based ligands containing different thioether donor substituents: aromatic (1), aliphatic (2) or thiophene (3). Temperature-dependent magnetometry reveals the presence of antiferromagnetic coupling for 1 and 3 (J = −2.27 cm−1 and -5.01 cm−1, respectively, H = -2JS1S2) and ferromagnetic coupling for 2 (J = 5.72 cm−1). Broken symmetry DFT calculations attribute this behavior to a major contribution from the dz2 orbitals for 1 and 3, and from the dx2-y2 orbitals for 2, along with the p orbitals of the oxygens. The bioinspired catalytic activities of these complexes related to catechol oxidase were studied using 3,5-di-tert-butylcatechol as substrate. The order of catalytic rates for the substrate oxidation follows the trend 1 > 2 > 3 with kcat of (90.79 ± 2.90) × 10−3 for 1, (64.21 ± 0.99) × 10−3 for 2 and (14.20 ± 0.32) × 10−3 s−1 for 3. The complexes also cleave DNA through an oxidative mechanism with minor-groove preference, as indicated by experimental and molecular docking assays. Antimicrobial potential of these highly active complexes has shown that 3 inhibits both Staphylococcus aureus bacterium and Epidermophyton floccosum fungus. Notably, the complexes were found to be nontoxic to normal cells but exhibited cytotoxicity against epidermoid carcinoma cells, surpassing the activity of the metallodrug cisplatin. This research shows the multifaceted properties of these complexes, making them promising candidates for various applications in catalysis, nucleic acids research, and antimicrobial activities.

AMPLON: Amplifying DNA with Multiarm Priming and Looping Optimization of Nucleic Acid.

Nucleic acid amplification, the bedrock of biotechnology and molecular diagnostics, surges in applications-especially isothermal approaches-heightening the demand for advanced and precisely engineered methods. Here, a novel approach for amplifying DNA with multiarm priming and looping optimization of nucleic acid (AMPLON) is presented. AMPLON relies on a novel polymeric material with unique set of multiarm polyethylene glycol-DNA primers for efficient DNA amplification under isothermal conditions. Each arm carries single-stranded DNA complementing the sense or antisense sequence of the target DNA. The amplification reaction begins with antisense arms binding to the target DNA, forming a template for sense-carrying arms to direct multiarm large DNA amplicon synthesis through successive DNA looping and unlooping steps. Using human immunodeficiency virus type 1 (HIV-1) as a model clinical target, AMPLON exhibits high sensitivity, detecting target concentrations as low as 100 copies mL-1. Compared to a quantitative real-time polymerase chain reaction assay using sensitive primers, AMPLON reliably identifies HIV-1 RNA in plasma samples (n = 20) with a significant agreement rate of 95%. With its ability to achieve highly specific and sensitive target amplification within 30 min, AMPLON holds immense potential to transform the field of nucleic acid research and unleashing new possibilities in medicine and biotechnology.

CRISPR in Nucleic Acids Research: the sequel.

CRISPR in Nucleic Acids Research: the sequel.

When Paul Berg meets Donald Crothers: an achiral connection through protein biosynthesis.

Outliers in scientific observations are often ignored and mostly remain unreported. However, presenting them is always beneficial since they could reflect the actual anomalies that might open new avenues. Here, we describe two examples of the above that came out of the laboratories of two of the pioneers of nucleic acid research in the area of protein biosynthesis, Paul Berg and Donald Crothers. Their work on the identification of D-aminoacyl-tRNA deacylase (DTD) and 'Discriminator hypothesis', respectively, were hugely ahead of their time and were partly against the general paradigm at that time. In both of the above works, the smallest and the only achiral amino acid turned out to be an outlier as DTD can act weakly on glycine charged tRNAs with a unique discriminator base of 'Uracil'. This peculiar nature of glycine remained an enigma for nearly half a century. With a load of available information on the subject by the turn of the century, our work on 'chiral proofreading' mechanisms during protein biosynthesis serendipitously led us to revisit these findings. Here, we describe how we uncovered an unexpected connection between them that has implications for evolution of different eukaryotic life forms.

Quenching of 2-aminopurine by phosphates: Implications for nucleic acid research

Quenching of 2-aminopurine by phosphates: Implications for nucleic acid research

PhyloString: A web server designed to identify, visualize, and evaluate functional relationships between orthologous protein groups across different phylogenetic lineages.

Proteins are biological units whose essence is defined by their functional relationships with other proteins or biomolecules such as RNA, DNA, lipids, or carbohydrates. These functions encompass enzymatic, structural, regulatory, or physical interaction roles. The STRING database (Nucleic Acids Research, 8 Jan 2021;49(D1): D605-12) provides an index that defines the functional interaction networks between proteins in model organisms. To facilitate the identification, visualization, and evaluation of potential functional networks across organisms from different phylogenetic lineages, we have developed PhyloString (https://biocomputo.ibt.unam.mx/phylostring/), a web server that utilizes the indices of the STRING database. PhyloString decomposes these functional networks into modules, representing cohesive units of proteins grouped based on their similarity of STRING values and the phylogenetic origins of their respective organisms. This study presents and thoroughly discusses examples of such functional networks and their modules identified using PhyloString.

Fifty years of Nucleic Acids Research.

Fifty years of Nucleic Acids Research.

Multifaceted nucleic acid probing with a rationally upgraded molecular rotor.

Probing the sequence alterations, structures, interactions, and other important aspects of nucleic acids serves as the cornerstone of understanding nucleic acid-mediated biology and etiology, as well as the development of nucleic acid-based therapeutics. New strategies capable of accommodating these imperatives without necessitating specialized instrument or skills and potentially complementing existing methods are highly desired. Herein, we describe a rationally designed molecular rotor CCVJ-H ((9-(2-carboxy-2-cyanovinyl)julolidine-hydrazide)) and its superior performances compared to the universal base excision reporter probe CCVJ-1 in applications such as nucleic acid detection and DNA glycosylase assays. Furthermore, we showcase that the CCVJ-H probe accurately profiles the interactions between nucleic acids and small molecules, providing binding affinity and binding site information in a single reaction. We subsequently demonstrate the feasibility of applying the CCVJ-H system in high-throughput screening to identify nucleic acid-binding small molecules such as DNA CTG repeat expansion binders, potentially providing therapeutic interventions for myotonic dystrophy type 1. Finally, we profile the recognition difference between DNA/DNA and DNA/RNA against a library of small molecules, uncovering two drug-like molecules that preferentially bind DNA/RNA. We anticipate the versatile CCVJ-H probe will be a useful tool for both fundamental and translational nucleic acid research and application.

Advances in Nucleic Acid Research: Exploring the Potential of Oligonucleotides for Therapeutic Applications and Biological Studies.

In recent years, nucleic acids have emerged as powerful biomaterials, revolutionizing the field of biomedicine. This review explores the multifaceted applications of nucleic acids, focusing on their pivotal role in various biomedical applications. Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), possess unique properties such as molecular recognition ability, programmability, and ease of synthesis, making them versatile tools in biosensing and for gene regulation, drug delivery, and targeted therapy. Their compatibility with chemical modifications enhances their binding affinity and resistance to degradation, elevating their effectiveness in targeted applications. Additionally, nucleic acids have found utility as self-assembling building blocks, leading to the creation of nanostructures whose high order underpins their enhanced biological stability and affects the cellular uptake efficiency. Furthermore, this review delves into the significant role of oligonucleotides (ODNs) as indispensable tools for biological studies and biomarker discovery. ODNs, short sequences of nucleic acids, have been instrumental in unraveling complex biological mechanisms. They serve as probes for studying gene expression, protein interactions, and cellular pathways, providing invaluable insights into fundamental biological processes. By examining the synergistic interplay between nucleic acids as powerful biomaterials and ODNs as indispensable tools for biological studies and biomarkers, this review highlights the transformative impact of these molecules on biomedical research. Their versatile applications not only deepen our understanding of biological systems but also are the driving force for innovation in diagnostics and therapeutics, ultimately advancing the field of biomedicine.

The 2024 Nucleic Acids Research database issue and the online molecular biology database collection.

The 2024 Nucleic Acids Research database issue contains 180 papers from across biology and neighbouring disciplines. There are 90 papers reporting on new databases and 83 updates from resources previously published in the Issue. Updates from databases most recently published elsewhere account for a further seven. Nucleic acid databases include the new NAKB for structural information and updates from Genbank, ENA, GEO, Tarbase and JASPAR. The Issue's Breakthrough Article concerns NMPFamsDB for novel prokaryotic protein families and the AlphaFold Protein Structure Database has an important update. Metabolism is covered by updates from Reactome, Wikipathways and Metabolights. Microbes are covered by RefSeq, UNITE, SPIRE and P10K; viruses by ViralZone and PhageScope. Medically-oriented databases include the familiar COSMIC, Drugbank and TTD. Genomics-related resources include Ensembl, UCSC Genome Browser and Monarch. New arrivals cover plant imaging (OPIA and PlantPAD) and crop plants (SoyMD, TCOD and CropGS-Hub). The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). Over the last year the NAR online Molecular Biology Database Collection has been updated, reviewing 1060 entries, adding 97 new resources and eliminating 388 discontinued URLs bringing the current total to 1959 databases. It is available at http://www.oxfordjournals.org/nar/database/c/.

Editorial: Nucleic Acids Research virtual issue dedicated to nucleic acid therapeutics, 2018-2023.

Editorial: Nucleic Acids Research virtual issue dedicated to nucleic acid therapeutics, 2018-2023.

Post-Transcriptional Features of CAR-T Cell Excessively Activated By Tonic Signaling

Introduction：Strong tonic signaling caused by spontaneous CAR aggregation is an important mechanism of CAR-T cell exhaustion which can impair the anti-tumor function. Many studies have illustrated the features of CAR-T cell activated excessively by tonic signaling at transcriptional, protein and epigenetic levels. Regulation of tonic signaling and downstream responses could enhance the anti-tumor effect. However, post-transcriptional features is little known while a lot of studies have demonstrated that post-transcripitonal processes such as exon skipping (ES), intron removal and alternative polyadenylation (APA) play critical roles in T cell activation and homeostasis. Methods and results：To investigate post-transcriptional features of CAR-T cell excessively activated by tonic signaling, we performed RNA sequencing on CAR-T cells and untransduced T cells at day6 or day12 after anti-CD3/CD28 beads stimulation. These samples were sequenced with high read depth (>80 M reads) to enable accurate quantification of alternative splicing in downstream analysis. Exon skipping events were identified by rMATS (≥10 splice junction reads per event, |dPSI|>0.1 and p value <0.05), then we predicted whether these events affect protein domains and protein-protein interactions. We performed enrichment analysis based on these affected interaction edges. From early to late stage after stimulation, CAR-T cells underwent exon skipping events which were significantly enriched in pathways such as cytokine signaling, calcium mobilization and adaptive immune system. Conversely, untransduced T cells from early to late stage also underwent amounts of ES events while the affected interactions were rarely enriched in meaningful pathways. Previous study has discovered that T cell activation could induce global reduction of intron retention (IR) level and intron-retained transcripts are less stable than fully spliced transcripts (Ni Ting et al. Nucleic acids research 2016). We found that IR level was in line with the activation level of the these groups. As CAR-T cells were continuously activated from day6 to day12, the global IR level didn't changed significantly while untransduced T cells has significantly elevated the global IR level (Fig.1). We also investigated the features of alternative polyadenylation which occurred in over 70% of mammalian mRNA genes, turning out expression of alternative polyadenylation isoforms with different 3′UTR lengths. A total of 448 genes showed a significant difference (P-value <0.05, a relative abundance change >5%）in the proximal-to-distal poly(A) site use between day6 and day12 CAR-T cells. Compared to day6, 229 genes increased use of the proximal poly(A) site and 219 genes increased use of the distal poly(A) site in day12 CAR-T cells. In untransduced T cells, we found that the number of genes showing lengthening 3′UTRs was 4.1-fold greater than the number of genes showing the opposite trend (589 vs. 143), indicating the general 3′UTR lengthening in the cell. Previous studies have described that T cell activation can cause global 3′UTR shortening and suggested that longer 3′UTR may expose more miRNA binding sites which impaired the stability of RNA (Sandberg R et. al. Science 2009). As all above post-transcriptional features we found seemed to contribute to activation signal and RNA stability, we asked whether we could prevent excessive activation and exhaustion by regulating post-transcriptional process. We treated CAR-T cells with madrasin for 72 hours which is a splicing inhibitor interfering with the early stages of spliceosome assembly. We found that madrasin at a low concentration can significantly inhibit the CAR-T cells' activation, exhaustion, terminal differentiation without affecting the apoptosis rate. Significance: We have discovered the importance of efficient post-transcriptional machinery during the process of CAR-T cell being excessively activated by tonic signaling.

The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods.

ChEMBL (https://www.ebi.ac.uk/chembl/) is a manually curated, high-quality, large-scale, open, FAIRand Global Core Biodata Resource of bioactive molecules with drug-like properties, previously described in the 2012, 2014, 2017 and 2019 Nucleic Acids Research Database Issues. Since its introduction in 2009, ChEMBL's content has changed dramatically in size and diversity of data types. Through incorporation of multiple new datasets from depositors since the 2019 update, ChEMBL now contains slightly more bioactivity data from deposited data vs data extracted from literature. In collaboration with the EUbOPEN consortium, chemical probe data is now regularly deposited into ChEMBL. Release 27 made curated data available for compounds screened for potential anti-SARS-CoV-2 activity from several large-scale drug repurposing screens. In addition, new patent bioactivity data have been added to the latest ChEMBL releases, and various new features have been incorporated, including a Natural Product likeness score, updated flags for Natural Products, a new flag for Chemical Probes, and the initial annotation of the action type for ∼270000 bioactivity measurements.

A web-based platform for the annotation and analysis of NAR-published databases.

Biological databases are essential resources for life science research, but finding and selecting the most relevant and up-to-date databases can be challenging due to the large number and diversity of available databases. The Nucleic Acids Research (NAR) journal publishes annual database issues that provide a comprehensive list of databases in the molecular biology domain. However, the information provided by NAR is limited and sometimes does not reflect the current status and quality of the databases. In this article, we present a web-based platform for the annotation and analysis of NAR-published databases. The platform allows users to manually curate and enrich the NAR entries with additional information such as availability, downloadability, source code links, cross-references, and duplicates. Statistics and visualizations on various aspects of the database landscape, such as recency, status, category, and curation history are also provided. Currently, it contains a total of 2,246 database entries of which 2,025 are unique with the majority updated within the last five years. Around 75% of all databases are still available and more than half provide a download option. Cross references to Database Commons are available for 1,889 entries. The platform is freely available online at https://nardbstatus.kalis-amts.de and aims to help researchers in database selection and decision-making. It also provides insights into the current state and challenges of a subset of all databases in the life sciences.

A CRISPR-based system to investigate HBV cccDNA biology.

Hepatitis B virus cccDNA is the key target for the necessary development of antiviral therapies aimed at curing chronic hepatitis B. The CRISPR-based system to produce covalently closed circular (cccDNA)-like extrachromosomal DNAs described in this report enables large-scale screens of chemical libraries to identify drug candidates with the potential to permanently inactivate cccDNA. Moreover, this approach permits investigations on unresolved problems as described in this report concerning cccDNA biology including mechanisms of SMC5/6-dependent transcriptional silencing and the contributions of the SMC5/6 complex to cccDNA stability in resting and dividing hepatocytes.

The Evolution of Molecular Genotyping in Plant Breeding

The era of plant genotyping began in the early 1980s with the progress in molecular biology and nucleic acid research and the advent of molecular marker technology [...]

Can artificial intelligence-strengthened ChatGPT or other large language models transform nucleic acid research?

Can artificial intelligence-strengthened ChatGPT or other large language models transform nucleic acid research?

MicroRNA Pools Synthesized Using Tandem Solid-Phase Oligonucleotide Synthesis.

Herein, we describe a new approach to make pools of microRNA targeting breast cancer cells. The microRNA pools were synthesized at once on the same solid support using the "Tandem Oligonucleotide Synthesis" strategy. We make up to four consecutive microRNAs (miR129-1-5p, miR31, miR206, and miR27b-3p) using 2'/3'OAc nucleotide phosphoramidites, with the total length of the pool reaching 88 nucleotides. The developed phosphoramidites, when combined, give a cleavable moiety that separates the microRNAs and is cleaved using standard post-RNA synthesis cleavage conditions. Furthermore, we investigate making branched pools (microRNA dendrimers) versus linear pools as a strategy to further improve the product yields. Our approach provides with microRNA pools in high yields, which is of relevance to the growing demand on synthetic RNA oligomers for nucleic acid research and technology.

SEMI-QUANTITATIVE ANALYSISOF NUCLEIC ACIDS ON AGAROSE GELS WITH CHOICE OF BEVERAGES AS ELECTROPHORETIC BUFFER

The pH of beverages is known to be low, and has therefore been involved in the increasing acidity incidence. In this study,to report on a rapid and cost-effective approach for nucleic acid characterization using different running buffers for agarose gel electrophoresis.Commercial DNA is used in electrophoretic analysis using a variety of beverages by optimizing its pH value.The results suggest that Royal Stag has little effect on nucleic acid research, while Peter Scot shows high concentration and sensitivity in nucleic acid characterization.Royal Stag drink has revealed that concentration, time, and voltage have little effect on nucleic acid research, although Peter Scot has reported high concentration and sensitivity in nucleic acid characterization. We conclude that this approach is simple, easy, and cost-effective compared to using TAE or TBE as running buffers in electrophoresis of the agarose gel.

RNAcanvas: interactive drawing and exploration of nucleic acid structures.

Two-dimensional drawing of nucleic acid structures, particularly RNA structures, is fundamental to the communication of nucleic acids research. However, manually drawing structures is laborious and infeasible for structures thousands of nucleotides long. RNAcanvas automatically arranges residues into strictly shaped stems and loops while providing robust interactive editing features, including click-and-drag layout adjustment. Drawn elements are highly customizable in a point-and-click manner, including colours, fonts, size and shading, flexible numbering, and outlining of bases. Tertiary interactions can be drawn as draggable, curved lines. Leontis-Westhof notation for depicting non-canonical base-pairs is fully supported, as well as text labels for structural features (e.g. hairpins). RNAcanvas also has many unique features and performance optimizations for large structures that cannot be correctly predicted and require manual refinement based on the researcher's own analyses and expertise. To this end, RNAcanvas has point-and-click structure editing with real-time highlighting of complementary sequences and motif search functionality, novel features that greatly aid in the identification of putative long-range tertiary interactions, de novo analysis of local structures, and phylogenetic comparisons. For ease in producing publication quality figures, drawings can be exported in both SVG and PowerPoint formats. URL: https://rnacanvas.app.