DNA and Nucleic Acid Chemistry

Development of a DNA-encoded library screening method DEL Zipper to empower the study of RNA-targeted chemical matter

This study introduces a DNA-encoded library screening method called DEL Zipper to improve RNA-targeted small molecule screening by reducing DNA-RNA interaction signals.

Unveiling the Promise of Peptide Nucleic Acids as Functional Linkers for Riboglow RNA Imaging Platform

This paper introduces PNA-based linkers to enhance RNA imaging probes by improving binding affinity and specificity, demonstrating significant improvements in RNA visualization in live cells.

The Role of BAZ2-dependent Chromatin Remodeling in Suppressing G4 DNA Structures and Associated Genomic Instability

This study identifies BAZ2 chromatin remodelers as suppressors of G4 DNA structures and shows that their depletion increases G4 formation and genomic instability.

Efficient High-Throughput DNA Breathing Features Generation Using Jax-EPBD

The paper introduces JAX-EPBD, a high-throughput framework for simulating DNA breathing dynamics, showing 30x speedup and improved predictions of transcription factor binding using SELEX datasets.

Small-molecule-based regulation of gene expression in human astrocytes upon both positive and negative actuations of G-quadruplex control systems

This study compares the effects of G-quadruplex stabilization and destabilization on gene expression in human astrocytes using PDS and PhpC, revealing distinct transcriptomic and proteomic responses.

Higher frequency of transition mutation over transversion mutation in genomes: evidence from the binding energy calculation of base pairs using DFT

This study uses DFT to calculate binding energies of base pairs, showing transition mutations are more stable than transversion mutations, supporting their higher frequency in genomes.

Multiple factors regulate i-motif and G-quadruplex structures in vitro: analysis of repeated and non-repeated polyG/polyC clusters by circular dichroism

This study uses circular dichroism to analyze how environmental factors and DNA sequences affect G-quadruplex and i-motif formation in vitro.

AGAPE (computAtional G-quadruplex Affinitiy PrEdiction): The first AI In-silico workflow for G-quadruplex binding affinity prediction.

AGAPE predicts G-quadruplex binding affinity using ML, achieving 91% accuracy with molecular descriptors and quantum chemistry data.

Kinetics of i-motif folding within the duplex context

The paper investigates pH-dependent i-motif folding in a duplex context and shows stabilization near the i-motif-duplex junction.

Stick of Sticks: Structural Features of the Amyloidogenic Peptide-DNA Complex

This study investigates how an amyloidogenic peptide binds to DNA, showing its structural interactions and effects on DNA function.

G4-Attention: Deep Learning Model with Attention for predicting DNA G-Quadruplexes

G4-Attention is a deep learning model that improves G4 quadruplex prediction accuracy using CNN, Bi-LSTM, and attention layers, outperforming existing methods.

Understanding Cu binding with DNA: A molecular dynamics study comparing Cu and Mg binding to the Dickerson DNA

This study uses molecular dynamics to compare Cu2+ and Mg2+ binding to Dickerson DNA, revealing similar binding preferences but distinct binding mechanisms for Cu2+.

Targeting the G-quadruplex structure in the hTERT promoter: In silico screening of phytocompounds and replica exchange molecular dynamics simulations.

This study identifies phytocompounds that stabilize G4 structures in the hTERT promoter using in silico screening and molecular dynamics simulations.

The predominant binding mode of Palmatine to DNA

This study identifies intercalation as the dominant binding mode of palmatine to DNA through long-range molecular dynamics simulations and enhanced sampling.

Genome-wide mapping of native co-localized G4s and R-loops in living cells

The paper develops methods to map native co-localized G4s and R-loops in living cells and shows their role in transcriptional regulation.

Torsional Mechanics of Circular DNA

This study investigates the torsional mechanics of circular DNA, showing that underwound DNA has a torque near the melting threshold and equal force/torque distribution, with implications for DNA-protein interactions.

Resolving the Structure of a Guanine Quadruplex in TMPRSS2 Messenger RNA by Circular Dichroism and Molecular Modeling

The paper predicts the atomic structure of a guanine quadruplex in TMPRSS2 mRNA using circular dichroism and molecular modeling.

Structural and dynamic consequences of inosine, 2'-O-methylation, and N6-methyladenosine modifications in RNA G-quadruplex: A molecular dynamics study

This study investigates how RNA modifications affect G-quadruplex structure using molecular dynamics simulations, revealing dynamic and energetic changes in inter-quadruplex interactions.

Properties of DNA in concentrated aqueous solutions of LiCl suggest transition to C-DNA

The paper investigates the B-to-C DNA transition in aqueous LiCl solutions and finds increased helical twist across all tested concentrations, suggesting C-DNA stability above 8 M LiCl.

Human genomic DNA is widely interspersed with i-motif structures

The paper identifies over 650,000 i-motif structures in human genomic DNA using immunoprecipitation and sequencing, showing their widespread distribution and association with highly expressed genes and G0/G1 phase upregulated genes.

G-quadruplexes as pivotal components of cis-regulatory elements in the human genome

This study identifies G-quadruplexes as key regulatory elements in human cis-regulatory elements, showing their association with chromatin states and cancer.

Cyclic Electromagnetic DNA Simulation (CEDS) influences the functions of Long Oligo-dsDNAs and Plasmid DNAs

CEDS enhances DNA function by affecting oligo-dsDNA and plasmid DNA in a sequence-specific manner through conformational changes and promoter activation.

Hydrogen Bonding Magnetic Resonance (HBMR)-based Cyclic Electromagnetic DNA Simulation (CEDS) can affect DNA Hybridization and Conformation

This paper investigates how weak magnetic fields can induce hydrogen bonding magnetic resonance (HBMR) in DNA, affecting hybridization and conformation through cyclic electromagnetic DNA simulation (CEDS).

DNA Base Pair Polarities of Pyrimidine(s)-Purine(s) (Pyu) dsDNA induce stronger Hybridization and unique DNA Conformation compared to Purine(s)-Pyrimidine(s) (Puy) dsDNA

This study compares Pyu and Puy dsDNA hybridization and conformation, finding Pyu dsDNA exhibits stronger hybridization and unique conformation, enhancing RNA transcription.

Recognition of RNA secondary structures with a programmable peptide nucleic acid-based platform

This paper introduces daPNAs, a programmable platform combining dbPNAs and asPNAs to target RNA junctions, demonstrating their use in inhibiting Dicer and regulating ribosomal frameshifting.

Effective lowering of α-synuclein expression by targeting G-quadruplex structures within the SNCA gene

This study identifies G-quadruplex structures in the SNCA gene and demonstrates their modulation using ligands and peptide nucleic acids to lower alpha-synuclein expression.

Enhanced Recognition of a Herbal Compound Epiberberine by a DNA Quadruplex-Duplex Structure

This paper investigates how epiberberine binds to a DNA quadruplex structure and shows how modifying the DNA structure enhances binding affinity, leading to a new method for extracting the compound from plant extracts.

HLTF Prevents G4 Accumulation and Promotes G4-induced Fork Slowing to Maintain Genome Stability

This paper shows that HLTF has two roles in managing G4s: preventing their accumulation and slowing replication forks to maintain genome stability.

Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes

This study benchmarks force-field performance for DNA/RNA hybrid duplexes, finding no force field accurately reproduces all structural features and highlighting parameter conflicts.

Quadrupia: Derivation of G-quadruplexes for organismal genomes across the tree of life

Quadrupia identifies and characterizes G-quadruplex sequences across 108,449 genomes, revealing taxonomic patterns and experimentally validating key structures.