Search Results (1,048)

Protein and nucleic acid play central roles in biology and pharmaceuticals. Both share a similar architecture made of a backbone and side chains. Protein has a peptide backbone and various side chains, whereas nucleic acid has a phosphate backbone and aromatic side chains. However, they are significantly different in the chemical properties of the backbone and side chains. The protein backbone is uncharged, while nucleic acid backbone is negatively charged. The protein side chains comprise widely different chemical properties. On the other hand, the nucleic acid side chains comprise a uniform chemical property of aromatic bases. Such differences lead to fundamentally different folding, molecular interactions and co-solvent interactions, which are the focus of this review. In regular protein secondary structures, the peptide groups form polar hydrogen bonds, making the interior hydrophilic. The side chains of different chemical properties are exposed on the outside of the protein secondary structures and participate in molecular and co-solvent interactions. On the other hand, hydrophobic/aromatic nucleobase side chains are located inside the typical double helix or quadruplex structures. The charged phosphate groups of the nucleic acid backbone are located outside, participating in electrostatic interactions. The nucleobases are also involved in molecular interactions, when exposed in breaks, hairpins, kinks and loops. These structural differences between protein and nucleic acid confer different interactions with commonly used co-solvents, such as denaturants, organic solvents and polymers. Full article

A new series of styryl hemicyanine dyes featuring substituted N-phenylpiperazine end groups was synthesized using an environmentally friendly procedure. The photophysical properties of the dyes were systematically investigated in organic solvents of varying polarity and when bound to DNA, using a combination of spectroscopic techniques. The dyes show strong negative solvatochromism and exhibit fluorescence quenching upon DNA binding. The dyes are definitely halochromic, exhibiting pronounced fluorescent acidochromism, accompanied by a photoinduced electron transfer (PET) effect. Titration with acid of the dye–DNA complexes restores fluorescence, indicating suppression of the PET and, at the same time, rigidizing of the chemical structure. UV/VIS and fluorescence titration, circular dichroism spectroscopy, and molecular docking methods were used to investigate the interaction mode between the dyes and DNA. Density functional theory (DFT) and time-dependent density functional theory (TDDFT) quantum chemical calculations were employed in deciphering the observed spectroscopic behavior and PET-related effects. The obtained results suggest the dyes’ potential as pH-responsive fluorescent probes for nucleic acid environments. Full article

Small interfering RNAs (siRNAs) provide strong therapeutic potential due to their efficient gene-silencing properties; however, their instability limits clinical application. Nanoparticle carriers may overcome this problem; in particular, magnetic nanoparticles show great promise as they can be directed to the target sites by external magnetic fields, thus improving delivery efficiency and reducing off-target effects. In addition, magnetic nanoparticles offer a novel nanoplatform for theranostic applications, integrating siRNA delivery with magnetic resonance imaging and magnetic hyperthermia for synergistic diagnostic and therapeutic advantages. The present work reports the development of a novel platform based on biomimetic magnetic nanoparticles made of Fe(II)/Fe(III)-doped apatite (FeHA) nucleated and grown in the presence of cherry and pomegranate leaf extracts to enhance the colloidal stability and make it suitable for nucleic acid delivery under the guidance of magnetic fields. This approach allowed the obtention of FeHA suspension with increased negative zeta potential leading to very good stability. In addition, the functionalization with natural extracts conferred antioxidant properties also favoring the maintenance of the Fe(III)/Fe(II) ratio in the apatitic structure, inducing the superparamagnetic properties. To evaluate the delivery capability of the system, a model GAPDH-targeting siRNA molecule was employed. Its interaction with the nanoplatform was characterized by assessing loading capacity and release kinetics, which were further interpreted using mathematical modeling to elucidate the underlying release mechanisms. Full article

The study of gene expression regulation systems, transcriptional, post-transcriptional, and translational processes require in-depth knowledge of the structure and dynamics of protein–DNA and protein–RNA complexes. Furthermore, the discovery of the multiple roles played by different types of RNA, including within extracellular vesicles, has raised new questions about the systems responsible for stabilizing and transporting these RNAs. Over the years, numerous experimental approaches have been developed for the study of complexes between proteins and nucleic acids, both in terms of the type and degree of accuracy of the information they are able to provide. Furthermore, some techniques have proven suitable for monitoring dynamic processes, while others provide very high-resolution data. Finally, the different methods also differ in their applicability directly to the study of complexes within their biological environment, while others can only be used on purified samples. The purpose of this review is to provide an overview of many of these approaches, accompanied by some examples of recent applications, to highlight their strengths and limitations. Full article

To identify novel peptides with potential antiviral activities, a database search was performed based on the primary sequence of the peptide I24 (CLAFYACFC), the effective part of the antiviral peptide TAT-I24 consisting of peptide I24 and the cell penetrating TAT-peptide (amino-acids 48–60; GRKKRRQRRRPPQ). A Protein BLAST search identified several sequences with high similarity to I24 in diverse proteins, some of which are known to be involved in the interaction with nucleic acids. Selected sequences and newly designed variants of I24 were synthesized as TAT fusion peptides and tested for antiviral activity in two well-established models: baculovirus transduction of HEK293 cells and mouse cytomegalovirus (MCMV) infection of NIH/3T3 cells. Several of the TAT-fusion peptides exhibited antiviral activities with a potency comparable to TAT-I24. The ability of these peptides to bind double-stranded DNA suggested the same mode of action. Several peptides caused swelling of red blood cells (RBC) but with only one peptide clearly inducing haemolysis. With two exceptions, RBC swelling was observed with antivirally active peptides but not with less active peptides, indicating that antiviral activities are linked to an effect on membrane integrity of target cells. Structural prediction of the TAT-fusion peptides indicated formation of two α-helical elements, with several of these peptides showing remarkable similarity when subjected to structural alignment. Full article

G-quadruplexes (G4s) are non-canonical nucleic acid structures that function as key regulatory elements in crucial cellular processes. Their biological functions are intrinsically linked to thermostability, which is governed by specific sequence features. This review systematically synthesizes evidence from high-precision biophysical studies and high-throughput genomic assays to delineate the sequence determinants of G4 thermostability. Analyses align the trends derived from both methodological paradigms and establish that stability emerges from a complex interplay among three structural elements: the G-tract core, whose length and integrity generally govern stability despite notable exceptions such as the anomalous stability of short G-tracts with 1-nt loops and the stabilization induced by large, structured bulges; the loops, which exhibit a consistent inverse relationship between length and stability across methods, though with context-dependent compositional effects and methodological disparities; and the flanking sequences, whose composition modulates stability and can bias topological outcomes. By integrating findings across scales, this work provides a unified conceptual framework connecting biophysical measurements with genomic observations—a critical step toward computationally predicting G4 stability, topology, and function directly from sequence, thereby advancing the understanding of their roles in health and disease. Full article

R-loops are three-stranded nucleic acid structures implicated in genome regulation and stability. In Arabidopsis thaliana, the chloroplast-localized RNase H1 enzyme (AtRNH1C) is important for chloroplast development and genome integrity; however, its molecular activity has not been experimentally verified. In the present study, we characterized the enzymatic activity of recombinant AtRNH1C toward model R-loops of various structures. Using a set of synthetic R-loop substrates, we demonstrate that AtRNH1C cleaves the RNA within DNA/RNA hybrids with a strong preference for purine-rich sequences, most notably at G↓X dinucleotides. Kinetic assays showed that the enzyme’s efficiency is highly dependent on the length of the hybrid duplex but is not affected by a G-quadruplex structure in the single-stranded DNA flap of the R-loop. The most rapid degradation was observed for an R-loop with an 11 nt DNA/RNA hybrid region. This study provides a comparative analysis of chloroplast-localized RNase H1 activity and elucidates its substrate preferences, suggesting that an R-loop with a heteroduplex length closest to the native size found in transcription elongation complexes is the most efficient substrate. These findings suggest that the enzymatic activity of AtRNH1C is sufficient to perform its function in maintaining chloroplast genome stability by the degradation of R-loops in DNA. Full article

The Receptor for Advanced Glycation End-Products (RAGE) is a cell surface receptor of the immunoglobulin-like receptor superfamily. RAGE is a pattern-recognition, multi-ligand receptor that binds glycated proteins, specific non-glycated proteins, and nucleic acids. RAGE ligands are typically part of the group of damage-associated molecular patterns (DAMPs) or alarmins. As such, RAGE is a receptor for molecular products of cellular stress, abnormal metabolism, and inflammation. Activation of RAGE by its ligands leads to pro-inflammatory signaling, often resulting in persistent RAGE activation in various disease states. Consequently, RAGE has been investigated as a potential drug target in the treatment of diabetic complications, vascular disease, Alzheimer’s disease, and multiple types of cancer. An underexplored aspect of RAGE is its role in cell adhesion. Structural comparison of the extracellular domain of RAGE has revealed structural similarity to the activated leukocyte cell adhesion molecule (ALCAM). The present study reveals the role and mechanism of RAGE in regulating cell adhesion. We investigated the role of individual RAGE domains in cell adhesion to extracellular matrix proteins and the changes in protein expression resulting from RAGE upregulation. Key findings include that RAGE displays substrate-specific adhesion to extracellular matrix proteins, that the intracellular domain of RAGE is required for modulating cell spreading, and that regulation of ITGA8 depends on the cytoplasmic domain of RAGE. Full article

Background/Objectives: Natural metabolites, due to their abundance, structural diversity, and availability in enantiomerically pure form, are broadly utilized in the synthesis of reagents, catalysts, building blocks, and potential therapeutics. To date, various organoselenium compounds, including selenides, diselenides, selenols, selenonium salts, and ylides, have been created based on the scaffold of primary and secondary metabolites like amino acids, sugars, nucleic bases, terpenes, and steroids. Their synthesis and application routes as reagents and catalysts in organic synthesis and biological systems are summarized in the presented review. Methods: The gathered material has been divided into two sections—naturally derived organoselenium compounds, such as antioxidants and GPx-mimetics, and reagents utilized in modern organic transformations. Results: The review summarizes the utility of natural scaffolds in the construction of organoselenium compounds with promising applications as antioxidant-type catalysts in biological systems (GPx-mimetics) and potent reagents for organic transformations, including asymmetric reactions. Conclusions: This review provides a comprehensive overview of known organoselenium reagents derived from natural compounds, discusses the advantages of their use in medicinal chemistry and modern organic synthesis, and outlines prospective directions for future development in this area. Full article

Translation of mRNAs is a tightly regulated process in gene expression. In mRNA, the 5′ untranslated region (5′ UTR) controls ribosome recruitment and frequently contains structured elements that modulate translation efficacy. This study investigates stable structural motifs within the 5′ UTR of DDX23 mRNA, encoding a protein relevant for anticancer therapy, as potential regulators and targets for antisense oligonucleotides (ASOs). Despite bioinformatic predictions and transcriptomic validations suggesting RNA G-quadruplex (rG4) formation, comprehensive structural analysis using a light-up assay and CD, UV, and NMR spectroscopy revealed that most putative rG4-forming sequences do not fold into stable rG4 structures, although one of them exists in an equilibrium between rG4 and an alternative, likely hairpin, conformation. Reporter assays using a robust G4 stabilizer also argue against the significant regulatory role of rG4s in DDX23 mRNA translation. Instead, we identified and characterized a stable hairpin structure with potential regulatory function. Based on these findings, we designed fully locked nucleic acid (LNA)-modified ASOs to target this hairpin and regions flanking the upstream open reading frame (uORF) and start codon of the coding sequence. A reporter assay demonstrated that cap-proximal targeting achieved robust translation inhibition up to 80%. In contrast, targeting the efficiently translated uORF was ineffective, presumably due to steric hindrances from the ribosomal complex. The study yields crucial design principles for translation-regulating ASOs: avoid targeting regions shielded by efficient uORF translation and carefully tune ASO-RNA duplex stability to surpass endogenous structures without disrupting regulatory mechanisms. These findings provide insights into the regulation of DDX23 expression and establish a framework for developing ASO-based therapeutics with broad implications for mRNA targeting in anticancer applications. Full article

In this study, a sliding microfluidic biosensor integrating RPA-SDA cascaded amplification was developed for the rapid, visual detection of Shigella. A novel RPA primer targeting the specific ipaH gene was designed to include a 5′-end G-quadruplex (G4) sequence and the complementary sequence of an Nt.BstNBI endonuclease recognition site. The RPA product templates a subsequent SDA reaction, generating abundant G4 structures that form peroxidase-mimicking DNAzymes with hemin, catalyzing a TMB reaction that produces a distinct blue color for visual readout (on-chip detection at OD₃₇₀, distinct from conventional tube assays at OD₄₅₀). The core on-chip detection process was completed within 13 min (10 min for SDA and 3 min for color development), achieving a limit of detection of 3.5 × 10⁻⁴ ng/μL for Shigella genomic DNA. This timing explicitly excludes the preceding, off-chip steps of nucleic acid extraction and RPA amplification. Validation using spiked lettuce samples confirmed the platform’s high specificity and sensitivity. This work establishes a proof-of-concept for a portable screening tool, highlighting its potential for on-site food safety applications. However, further validation in diverse food matrices and under real-world field conditions is required to fully establish its practical utility. Full article

The human papillomavirus (HPV) is a small, non-enveloped virus with a circular double-stranded DNA genome. The HPV genome encodes the E2 activator protein, which is required for viral transcription. R-loops are triple-stranded nucleic acid structures that occur when newly synthesized single-stranded RNA anneals to duplex DNA. These structures form during papillomavirus transcription. We and others have demonstrated that resolution of viral R loops is crucial for HPV episomal maintenance. ZPR1 is a zinc finger protein that can recruit SETX to mammalian R-loops to mediate resolution. E2 binds to and recruits SETX, an R-loop helicase, to the viral promoter. We observed E2 in complex with SETX and ZPR1. However, we found that ZPR1 depletion decreased viral R-loops while enhancing cellular R-loops. ZPR1 depletion also increased SETX binding to the viral promoter. These data suggest that ZPR1 is not required for HPV R-loop resolution, in contrast to what has been observed in mammalian cells. We detected the E2 protein associated with R-loops and found that E2 overexpression increases cell-derived R-loop formation. Analysis of TCGA datasets revealed that ZPR1, but not SETX, mRNA expression is significantly reduced in HPV-positive cervical and head and neck cancers. Together, these findings indicate that while E2 mediates HPV R-loop resolution, it also promotes R-loop accumulation in the host genome, likely through SETX sequestration. Full article

Nucleic acid aptamers leverage defined tertiary structures for precise molecular recognition, positioning them as transformative biomedical tools. We engineered AP1-F, a G-quadruplex (G4)-structured aptamer that selectively binds membrane-anchored nucleolin (NCL) non-permeabilizing, overcoming a key limitation of conventional probes. Microscale thermophoresis confirmed nanomolar affinity to NCL. By means of rigorous optimization, AP1-F attained a greater than ten-fold fluorescence signal ratio between malignant and normal cells in co-cultures, exceeding the extensively researched AS1411. Dual-channel flow cytometry demonstrated over 98.78% specificity at single-cell resolution within heterogeneous cell populations, owing to AP1-F’s unique membrane localization—unlike AS1411’s intracellular uptake, which elicited erroneous signals from cytoplasmic NCL. Competitive binding experiments and Laser Confocal Imaging confirmed that AP1-F specifically identifies cancer cells by binding to the NCL recognition site on the membrane. In pathological sections, AP1-F exhibited a 40.5-fold fluorescence intensity ratio between tumor and normal tissue, facilitating accurate tissue-level differentiation. Significantly, it delineated molecular subtypes by associating membrane NCL patterns with morphometric analysis: luminal-like MCF-7 displayed consistent staining in cohesive clusters, whereas basal-like MDA-MB-468 revealed sporadic NCL with irregular outlines—characteristics imperceptible to intracellular-targeted antibodies, thus offering subtype-specific diagnostic insights. This combination biochemical–morphological approach accomplished subtype differentiation with a single-step, non-permeabilized process that maintained lower cytotoxicity and tissue integrity. AP1-F enhances diagnostic accuracy by utilizing spatial confinement to eradicate intracellular interference, connecting molecular specificity to intraoperative margin evaluation or biopsy categorization. Full article

Flow cytometry typically reveals two heterotrophic prokaryote (HP) subpopulations when stained with SYBR Green: high nucleic acid (HNA) and low nucleic acid (LNA) cells. Evidence suggests these populations have distinct physiological and ecological roles with implications for mortality. We assessed HP abundance, production, the relative proportion of HNA and LNA, virus-mediated mortality, and the distribution of lytic versus lysogenic strategies within HP host communities across a latitudinal gradient in the North Atlantic during spring. The study area, characterized by dynamic physicochemical conditions consistent with the onset of seasonal stratification, was divided into three regions based on bio-physicochemical properties: Pre-bloom, Bloom, and Oligotrophic. Multivariant analysis showed these regions significantly structured HPs, as well as influenced the relative abundance and production of virus subpopulations (i.e., V1 and V2). Specifically, V1 viruses increased with the potential of encountering HNA hosts, which were elevated in the surface waters of stratified Oligotrophic and Bloom regions. In contrast, V2 abundance and production correlated with LNA cells, more prominent in DEEP samples and in surface waters of the deeper mixed Pre-bloom region. Lysogeny occurred across all regions, with the percentage of lysogens within the HP community, increasing (largely V1-driven) with HP-specific growth rate until reaching a threshold of 0.1 d⁻¹, after which it declined. We discuss the potential ecological underpinnings driving these patterns and implications for carbon flux. Full article

Sirtuins are NAD⁺-dependent enzymes widely implicated in organismal ageing. In particular, nuclear-located sirtuins are histone deacetylases and/or monoADPrybosiltransferases that exert key roles in maintaining genomic stability. Although sirtuins have been reported to play an inhibitory role in cellular senescence, their specific targets and underlying mechanisms remain poorly understood. In this study, we use single-cell Synchrotron radiation-based Fourier-transform infrared spectroscopy (FTIR) to identify changes in biomolecular composition associated with cellular senescence induced by oxidative stress and replicative passaging in human primary fibroblasts. We also use the sirtuin activator resveratrol to determine which of these changes may be related to sirtuin activity. Resveratrol induced changes related to nuclear architecture, such as DNA conformation and nucleic acid–protein abundance ratios. Individual targeting of nuclear sirtuins was used to validate impaired DNA/protein ratios experimentally and provided a specific structural footprint associated with sirtuins in the context of cellular senescence. Altogether, this study reveals for the first time a sirtuin-dependent structural and biomolecular signature of senescence through single-cell FTIR, offering new insights into the cellular events underlying cellular senescence. Full article