Structural Insights into an Antiparallel Chair-Type G-Quadruplex From the Intron of NOP56 Oncogene.

G-quadruplex (G4) structures play important roles in various biological processes, especially the gene regulation. Nucleolar protein 56 (NOP56) is an essential component in ribosome biogenesis while its overexpression associates with various types of cancers, rendering it a significant therapeutic target. Here for the first time, an antiparallel chair-type G4 structure formed by a 21-nt DNA sequence from the intron 1 of NOP56 is reported, and its high-resolution structure is determined using solution nuclear magnetic resonance spectroscopy.

Development of a nano-targeting chimera for the degradation of membrane and cytoplasmic proteins.

Various targeted protein degradation (TPD) approaches have been developed to overcome the limitations of traditional drug in eliminating pathogenic proteins by exploiting either the proteasomal or lysosomal pathway. However, there is still a lack of design strategies for TPD that utilize two distinct pathways to achieve the degradation of membrane and cytoplasmic proteins. Here, we develop a Nano-Targeting Chimera (Nano-APTAC), which is engineered by covalently attaching the protein-targeting aptamer to graphene oxide (GO) via the amide linkage, to hijack the autophagy-lysosome and ubiquitin-proteasome systems for targeted degradation of membrane and cytoplasmic proteins respectively.

A Multi-Input Molecular Classifier Based on Digital DNA Strand Displacement for Disease Diagnostics.

DNA-based molecular computing systems for biomarkers have emerged as powerful tools for intelligent diagnostics. However, with the variety of feature biomarkers expanding, current molecular computing systems suffer from the use of a large number of oligonucleotides and limited encoding capability. Here, the study develops an alternative molecular computing approach termed Digital DNA Strand Displacement (DDSD) which recognizes targets and operates target valence through DNA polymerase-based extension and strand release.

Dynamic Genomic Imaging and Tracking in Living Cells by a DNA Origami-Based CRISPR‒dCas9 System.

The clustered regularly interspaced short palindromic repeat (CRISPR)-associated system has displayed promise in visualizing the dynamics of target loci in living cells, which is important for studying genome regulation. However, developing a cell-friendly and rapid transfection method for achieving dynamic and long-term genomic imaging in living cells with high specificity and accuracy is still challenging. Herein, a robust and versatile method is presented that employs a barrel-shaped DNA nanostructure (TUBE) modified with aptamers for loading, protecting, and delivering CRISPR-Cas9 to visualize specific genomic loci in living cells.

Small CAG Repeat RNA Forms a Duplex Structure with Sticky Ends That Promote RNA Condensation.

Biomolecular condensation lays the foundation of forming biologically important membraneless organelles, but abnormal condensation processes are often associated with human diseases. Ribonucleic acid (RNA) plays a critical role in the formation of biomolecular condensates by mediating the phase transition through its interactions with proteins and other RNAs. However, the physicochemical principles governing RNA phase transitions, especially for short RNAs, remain inadequately understood.

Artificial Intelligence-Based Classification and Segmentation of Bladder Cancer in Cystoscope Images.

Background/objectives: Cystoscopy is necessary for diagnosing bladder cancer, but it has limitations in identifying ambiguous lesions, such as carcinoma in situ (CIS), which leads to a high recurrence rate of bladder cancer. With the significant advancements in deep learning in the medical field, several studies have explored its application in cystoscopy. This study aimed to utilize the VGG19 and Deeplab v3+ deep learning models to classify and segment cystoscope images, respectively.

Artificial dynamic structure ensemble-guided rational design of a universal RNA aptamer-based sensing tag.

Artificially functional RNAs, such as fluorogenic RNA aptamer (FRApt)-based biosensing tag, represent significant advancements in various biological applications but are limited by the lack of insight into dynamic structure ensembles and universal design concepts. Through the development of an artificial RNA structure ensemble, we rationally established an RNA reconstitution model, "SSPepper-Apt," to generate a universal fluorogenic RNA biosensing tag. By utilizing various target-recognizing RNA motifs, SSPepper-Apt enables the modular generation of sensing tags for low-background, highly selective imaging of metabolites, peptides, and proteins in living cells.

Aptamer-Based Activatable Tyramide Signal Amplification for Low-Background Detection of SARS-CoV-2 Nucleocapsid Protein.

As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection posed a significant threat to public health and the global economy, in vitro diagnosis of the SARS-CoV-2 nucleocapsid protein proved to be an effective way for SARS-CoV-2 infection control in the past years. Tyramide signal amplification (TSA) has been extensively utilized in tissue imaging and pathological diagnosis owing to the powerful signal enhancement. However, the elevated "ALWAYS ON" fluorescence background limited the accuracy and sensitivity of the conventional TSA assay.

siRNADiscovery: a graph neural network for siRNA efficacy prediction via deep RNA sequence analysis.

The clinical adoption of small interfering RNAs (siRNAs) has prompted the development of various computational strategies for siRNA design, from traditional data analysis to advanced machine learning techniques. However, previous studies have inadequately considered the full complexity of the siRNA silencing mechanism, neglecting critical elements such as siRNA positioning on mRNA, RNA base-pairing probabilities, and RNA-AGO2 interactions, thereby limiting the insight and accuracy of existing models. Here, we introduce siRNADiscovery, a Graph Neural Network (GNN) framework that leverages both non-empirical and empirical rule-based features of siRNA and mRNA to effectively capture the complex dynamics of gene silencing.

Enhanced Sensitivity of Cell Identification in Complex Environments Using Chirally Inverted L-DNA-Based Logic Devices.

Accurate identification and isolation of target cells are crucial for precision diagnosis and treatment. DNA aptamer-based logic devices provide a distinct advantage in this context, as they can logically analyze multiple cell surface markers with high efficiency. However, the susceptibility of natural DNA (D-DNA) to degradation can compromise the sensitivity and specificity of these devices, potentially leading to false-positive and false-negative results, particularly in complex biological environments.

Correction: Dong et al. Smurf1 Suppression Enhances Temozolomide Chemosensitivity in Glioblastoma by Facilitating PTEN Nuclear Translocation. 2022, , 3302.

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Serum Circulating mRNA Panel for the Early Detection of Gastric Cancer: A Potential Biomarker Test.

Circulating free messenger RNAs (cfmRNAs) in serum have emerged as potential noninvasive biomarkers for cancer diagnosis, including gastric cancer (GC). This study utilized RNA-sequencing data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases to identify a training set of 100 differentially expressed genes (DEGs) specific to GC patients. Employing a support vector machine (SVM) classification, we narrowed down the candidate gene set to 23, which was further refined to 4 genes-DMBX1, EVX1, MAL, and PIWIL1-after validation through reverse transcription quantitative polymerase chain reaction (RT-qPCR).

Structure-based investigation of a DNA aptamer targeting PTK7 reveals an intricate 3D fold guiding functional optimization.

DNA aptamers have emerged as novel molecular tools in disease theranostics owing to their high binding affinity and specificity for protein targets, which rely on their ability to fold into distinctive three-dimensional (3D) structures. However, delicate atomic interactions that shape the 3D structures are often ignored when designing and modeling aptamers, leading to inefficient functional optimization. Challenges persist in determining high-resolution aptamer-protein complex structures.

Leveraging DNA-Encoded Cell-Mimics for Environment-Adaptive Transmembrane Channel Release-Induced Cell Death.

The advancement of cell-mimic materials, which can forge sophisticated physicochemical dialogues with living cells, has unlocked a realm of intriguing prospects within the fields of synthetic biology and biomedical engineering. Inspired by the evolutionarily acquired ability of T lymphocytes to release perforin and generate transmembrane channels on targeted cells for killing, herein we present a pioneering DNA-encoded artificial T cell mimic model (ARTC) that accurately mimics T-cell-like behavior. ARTC responds to acidic conditions similar to those found in the tumor microenvironment and then selectively releases a G-rich DNA strand (LG4) embedded with C12 lipid and cholesterol molecules.

A DNA circuit that records molecular events.

Characterizing the relative onset time, strength, and duration of molecular signals is critical for understanding the operation of signal transduction and genetic regulatory networks. However, detecting multiple such molecules as they are produced and then quickly consumed is challenging. A MER can encode information about transient molecular events as stable DNA sequences and are amenable to downstream sequencing or other analysis.

The Impact of Oxygen Concentration on the Postcuring of 3D-Printed Dental Resin.

Purpose: This study investigated the impact of reducing the oxygen concentration via nitrogen injection during the postcuring process of 3D-printed dental materials.

Materials And Methods: Resin specimens for dental crown and bridge (15-mm diameter, both 1-mm and 2-mm heights) were 3D-printed and rinsed. Subsequently, the postcuring process was conducted on nine groups categorized according to atmospheric conditions within the curing device (20% [control], 10%, and 5% oxygen) and curing times (10, 15, and 20 minutes).

Monodispersed and Monofunctionalized DNA-Caged Au Nano-Clusters with Enhanced Optical Properties for STED Imaging.

The performance of Stimulated Emission Depletion (STED) microscopy depends critically on the fluorescent probe. Ultrasmall Au nanoclusters (Au NCs) exhibit large Stokes shift, and good stimulated emission response, which are potentially useful for STED imaging. However, Au NCs are polydispersed in size, sensitive to the surrounding environment, and difficult to control surface functional group stoichiometry, which results in reduced density and high heterogeneity in the labeling of biological structures.

Structural investigation of pathogenic RFC1 AAGGG pentanucleotide repeats reveals a role of G-quadruplex in dysregulated gene expression in CANVAS.

An expansion of AAGGG pentanucleotide repeats in the replication factor C subunit 1 (RFC1) gene is the genetic cause of cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS), and it also links to several other neurodegenerative diseases including the Parkinson's disease. However, the pathogenic mechanism of RFC1 AAGGG repeat expansion remains enigmatic. Here, we report that the pathogenic RFC1 AAGGG repeats form DNA and RNA parallel G-quadruplex (G4) structures that play a role in impairing biological processes.

Insulin-like Growth Factor 2-Tagged Aptamer Chimeras (ITACs) Modular Assembly for Targeted and Efficient Degradation of Two Membrane Proteins.

Overexpression of pathogenic membrane proteins drives abnormal proliferation and invasion of tumor cells. Various strategies to durably knockdown membrane proteins with heterobifunctional degraders have been successfully developed, including LYTAC, KineTAC, and AbTAC. However, challenges including complicated synthetic procedures and the inability to simultaneously degrade multiple pathogenic proteins still exist.

Covalent LYTAC Enabled by DNA Aptamers for Immune Checkpoint Degradation Therapy.

Immune checkpoint blockade (ICB) therapy, while achieving tremendous clinical successes, still suffers from a low objective response rate in clinical cancer treatment. As a proof-of-concept study, we propose a new immune checkpoint degradation (ICD) therapy relying on lysosome-targeting chimera (LYTAC) to deplete immune checkpoint programmed death ligand-1 (PD-L1) on the tumor cell surface. Our designed chimeric aptamer on one side targets lysosome-trafficking receptor, and on the other side allows biorthogonal covalent-conjugation-reinforced specific binding of PD-L1.

FINDER: A Fluidly Confined CRISPR-Based DNA Reporter on Living Cell Membranes for Rapid and Sensitive Cancer Cell Identification.

The accurate, rapid, and sensitive identification of cancer cells in complex physiological environments is significant in biological studies, personalized medicine, and biomedical engineering. Inspired by the naturally confined enzymes on fluid cell membranes, a fluidly confined CRISPR-based DNA reporter (FINDER) was developed on living cell membranes, which was successfully applied for rapid and sensitive cancer cell identification in clinical blood samples. Benefiting from the spatial confinement effect for improved local concentration, and membrane fluidity for higher collision efficiency, the activity of CRISPR-Cas12a was, for the first time, found to be significantly enhanced on living cell membranes.