Hybrid RNA/DNA Concatemers and Self-Limited Complexes: Structure and Prospects for Therapeutic Applications.

The development of new convenient tools for the design of multicomponent nucleic acid (NA) complexes is one of the challenges in biomedicine and NA nanotechnology. In this paper, we analyzed the formation of hybrid RNA/DNA concatemers and self-limited complexes by a pair of oligonucleotides using UV melting, circular dichroism spectroscopy, and a gel shift assay. Effects of the size of the linker between duplex-forming segments of the oligonucleotides on complexes' shape and number of subunits were compared and systematized for RNA/DNA, DNA/DNA, and RNA/RNA assemblies.

Expanding Horizons of CRISPR/Cas Technology: Clinical Advancements, Therapeutic Applications, and Challenges in Gene Therapy.

CRISPR-Cas technology has transformed the field of gene editing, opening new possibilities for treatment of various genetic disorders. Recent years have seen a surge in clinical trials using CRISPR-Cas-based therapies. This review examines the current landscape of CRISPR-Cas implementation in clinical trials, with data from key registries, including the Australian New Zealand Clinical Trials Registry, the Chinese Clinical Trial Register, and ClinicalTrials.

An Approach to Identifying Single-Nucleotide Mutations Using Noncovalent Associates of Gold Nanoparticles with Fluorescently Labeled Oligonucleotides.

Globally, widespread tuberculosis is one of the acute problems of healthcare. Drug-resistant forms of tuberculosis require a personalized approach to treatment. Currently, rapid methods for detecting drug resistance of (MTB) to some antituberculosis drugs are often used and involve optical, electrochemical, or PCR-based assays.

Characterization and PCR Application of Family B DNA Polymerases from .

DNA polymerases from the hyperthermophilic Archaea have attracted considerable attention as PCR enzymes due to their high thermal stability and proofreading 3' → 5' exonuclease activity. This study is the first to report data concerning the purification and biochemical characteristics of the Tst DNA polymerase from . Both the wild type Tst(wt) DNA polymerase and its chimeric form containing the P36H substitution-which reduces the enzyme's affinity for the U-containing template and dUTP-and the DNA-binding domain Sso7d from were obtained and analyzed.

Proteins Associated with Neurodegenerative Diseases: Link to DNA Repair.

The nervous system is susceptible to DNA damage and DNA repair defects, and if DNA damage is not repaired, neuronal cells can die, causing neurodegenerative diseases in humans. The overall picture of what is known about DNA repair mechanisms in the nervous system is still unclear. The current challenge is to use the accumulated knowledge of basic science on DNA repair to improve the treatment of neurodegenerative disorders.

Fast and Simple Protocol for N-Glycome Analysis of Human Blood Plasma Proteome.

N-glycome analysis of individual proteins and tissues is crucial for fundamental and applied biomedical research and medical diagnosis and plays an important role in the evaluation of the quality of biopharmaceutical and biotechnological products. The interest in this research area continues to grow annually, thereby increasing the demand for the high-throughput profiling of human blood plasma N-glycome. In response to this need, we have developed an optimized, simple, and rapid protocol for the N-glycome profiling of human plasma proteins.

DNA Damage Response Network and Intracellular Redox Status in the Clinical Outcome of Patients with Lung Cancer.

: DNA damage response (DDR) is a network of molecular pathways associated with the pathogenesis and progression of several diseases, as well as the outcome of chemotherapy. Moreover, the intracellular redox status is essential for maintaining cell viability and controlling cellular signaling. Herein, we analyzed DDR signals and redox status in peripheral blood mononuclear cells (PBMCs) from patients with lung cancer with different response rates to platinum-based chemotherapy.

RosettaHDX: Predicting antibody-antigen interaction from hydrogen-deuterium exchange mass spectrometry data.

High-throughput characterization of antibody-antigen complexes at the atomic level is critical for understanding antibody function and enabling therapeutic development. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) enables rapid epitope mapping, but its data are too sparse for independent structure determination. In this study, we introduce RosettaHDX, a hybrid method that combines computational docking with differential HDX-MS data to enhance the accuracy of antibody-antigen complex models beyond what either method can achieve individually.

Attempts to preserve and visualize protein corona on the surface of biological nanoparticles in blood serum using photomodification.

A protein corona is present on any nanoparticle (NP) entering biological fluids; however, the existence of a natural protein corona on natural NPs has not been experimentally confirmed. We used our previously developed photomodification method to fix the natural corona on "biological nanoparticles" (bio-NPs) in fetal bovine serum and newborn bovine serum; native sera served as a control. To isolate photomodified bio-NPs, we used ultracentrifugation (UC), sucrose gradient (12%, 30%, and 50%), and sucrose cushion (30%) methods.

Polyamine Adducts with AP Sites: Interaction with DNA Polymerases and AP Endonucleases.

Biological polyamines, such as spermine, spermidine, and putrescine, are abundant intracellular compounds mostly bound to nucleic acids. Due to their nucleophilic nature, polyamines easily react with apurinic/apyrimidinic (AP) sites, DNA lesions that are constantly formed in DNA by spontaneous base loss and as intermediates of base excision repair. A covalent intermediate is formed, promoting DNA strand cleavage at the AP site, and is later hydrolyzed regenerating the polyamine.

Development of Receptor Desolvation Scoring and Covalent Sampling in DOCK 6: Methods Evaluated on a RAS Test Set.

Molecular docking methods are widely used in drug discovery efforts. RAS proteins are important cancer drug targets, and are useful systems for evaluating docking methods, including accounting for solvation effects and covalent small molecule binding. Water often plays a key role in small molecule binding to RAS proteins, and many inhibitors─including FDA-approved drugs─covalently bind to oncogenic RAS proteins.

Elucidating Binding Selectivity in Cyclin-Dependent Kinases 4, 6, and 9: Development of Highly Potent and Selective CDK4/9 Inhibitors.

CDK4/6 inhibitors are effective in treating HR/HER2 breast cancer but face limitations due to therapeutic resistance and hematological toxicity, particularly from strong CDK6 inhibition. To address these challenges, designing selective inhibitors targeting specific cyclin-dependent kinases (CDK) members could offer clinical advantages and broaden CDK inhibitor indications. However, the highly conserved binding pockets of CDKs complicate selective targeting.

Refining breast cancer genetic risk and biology through multi-ancestry fine-mapping analyses of 192 risk regions.

Genome-wide association studies have identified approximately 200 genetic risk loci for breast cancer, but the causal variants and target genes are mostly unknown. We sought to fine-map all known breast cancer risk loci using genome-wide association study data from 172,737 female breast cancer cases and 242,009 controls of African, Asian and European ancestry. We identified 332 independent association signals for breast cancer risk, including 131 signals not reported previously, and for 50 of them, we narrowed the credible causal variants down to a single variant.

Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets.

Molecular subtypes, such as defined by The Cancer Genome Atlas (TCGA), delineate a cancer's underlying biology, bringing hope to inform a patient's prognosis and treatment plan. However, most approaches used in the discovery of subtypes are not suitable for assigning subtype labels to new cancer specimens from other studies or clinical trials. Here, we address this barrier by applying five different machine learning approaches to multi-omic data from 8,791 TCGA tumor samples comprising 106 subtypes from 26 different cancer cohorts to build models based upon small numbers of features that can classify new samples into previously defined TCGA molecular subtypes-a step toward molecular subtype application in the clinic.

Pleiotropic Function of Cellular Prion Protein: Encompassing Endoplasmic-Reticulum Stress, Cell Proliferation in Vascular Smooth Muscle Cells.

Cellular prion protein (PRNP) has been implicated in various physiological processes in different cell types, for decades. Little has been known how PRNP functions in multiple, yet related processes within a particular system. In our current study, with the aid of high-throughput RNA-sequencing technique, we have presented an overall transcriptome profile of rat vascular smooth muscle cells (VSMCs) with Prnp knockdown.

Corrigendum: Interplay of various evolutionary modes in genome diversification and adaptive evolution of the family .

[This corrects the article DOI: 10.3389/fmicb.2021.

Structural insights into the biochemical mechanism of the E2/E3 hybrid enzyme UBE2O.

The E2/E3 hybrid enzyme UBE2O plays important roles in key biological events, but its autoubiquitination mechanism remains largely unclear. In this study, we determined the crystal structures of full-length (FL) UBE2O from Trametes pubescens (tp) and its ubiquitin-conjugating (UBC) domain. The dimeric FL-tpUBE2O structure revealed interdomain interactions between the conserved regions (CR1-CR2) and UBC.

Trojan horse peptide conjugates remodel the activity spectrum of clinical antibiotics.

Infections caused by gram-negative pathogens continue to be a major risk to human health because of the innate antibiotic resistance endowed by their unique cell membrane architecture. Nature has developed an elegant solution to target gram-negative strains, namely by conjugating toxic antibiotic warheads to a suitable carrier to facilitate the active import of the drug to a specific target organism. Microcin C7 (McC) is a Trojan horse peptide-conjugated antibiotic that specifically targets enterobacteria by exploiting active import through oligopeptide transport systems.

CryoSeek II: Cryo-EM analysis of glycofibrils from freshwater reveals well-structured glycans coating linear tetrapeptide repeats.

Despite the recent breakthrough in structure determination and prediction of proteins, the structural investigation of carbohydrates remains a challenge. Here, we report the cryo-EM analysis of a glycofibril found in the freshwater in the Tsinghua Lotus Pond. The fibril, which we name TLP-4, is made of a linear chain of tetrapeptide repeats coated with >4 nm thick glycans.

Revealing and mitigating the inhibitory effect of serotonin on HRP-mediated protein labelling.

Proximity-dependent biotinylation coupled with mass spectrometry enables the characterization of subcellular proteomes. This technique has significantly advanced neuroscience by revealing sub-synaptic protein networks, such as the synaptic cleft and post-synaptic density. Profiling proteins at this detailed level is essential for understanding the molecular mechanisms of neuronal connectivity and transmission.

Microenvironmental modulation breaks intrinsic pH limitations of nanozymes to boost their activities.

Functional nanomaterials with enzyme-mimicking activities, termed as nanozymes, have found wide applications in various fields. However, the deviation between the working and optimal pHs of nanozymes has been limiting their practical applications. Here we develop a strategy to modulate the microenvironmental pHs of metal-organic framework (MOF) nanozymes by confining polyacids or polybases (serving as Brønsted acids or bases).

Nutraceuticals silybin B, resveratrol, and epigallocatechin-3 gallate-bind to cardiac muscle troponin to restore the loss of lusitropy caused by cardiomyopathy mutations , , and .

Introduction: Adrenergic activation of protein kinase A (PKA) in cardiac muscle targets the sarcolemma, sarcoplasmic reticulum, and contractile apparatus to increase contractile force and heart rate. In the thin filaments of the contractile apparatus, cardiac troponin I (cTnI) Ser22 and Ser23 in the cardiac-specific N-terminal peptide (NcTnI: residues 1 to 32) are the targets for PKA phosphorylation. Phosphorylation causes a 2-3 fold decrease of affinity of cTn for Ca associated with a higher rate of Ca dissociation from cTnC leading to a faster relaxation rate of the cardiac muscle (lusitropy).

Efficient and Visual Detention of Ammonia and TNP Vapors by a Sustainable Highly Luminescent 1D Zn(II) Coordination Polymer.

To realize the aim of easy and accurate detection of ammonia and picric acid (PA) in both aqueous and vapor phases based on function-oriented investigation principles, in the present study, we include a luminescent performance with recognition performance, taking into account the application conditions. Zn(II) ions with luminescence qualities and an amine-substituted imidazole moiety with selective recognition properties towards picric acid and ammonia are coupled to generate a novel 1D luminous Zn(II) coordination polymer, Zn-CP [{Zn(II)( 2-ABZ)2(2-BDC)}].MeOH]∞, where 2-ABZ and 2-BDC stand for terephthalic acid and protonated 2 aminobenzimidazole, respectively.

Genomic scarring score predicts the response to PARP inhibitors in non-small cell lung cancer.

PARP inhibitors (PARPi) have shown efficacy in tumours harbouring mutations in homologous recombination repair (HRR) genes. Somatic HRR mutations have been described in patients with Non-Small Cell Lung Cancer (NSCLC), but PARP inhibitors (PARPi) are not yet a therapeutic option. Here we assessed the homologous recombination status of early-stage NSCLC and explored the therapeutic benefit of PARPi in preclinical models.

Homologous recombination deficiency (HRD) diagnostics: underlying mechanisms and new perspectives.

Homologous recombination deficiency (HRD) is considered a universal and effective sign of a tumor's sensitivity to poly(ADP-ribose) polymerase (PARP) inhibitors. HRD diagnostics have undergone several stages of transformations: from detection of point mutations in HR-related genes and large regions with loss of heterozygosity detected using single-nucleotide polymorphism arrays to whole-genome signatures of single-nucleotide variants, large genomic rearrangements (LGRs), and copy number alterations. All these methods have their own advantages and limitations.