Molecular dynamics simulations for the structure-based drug design: targeting small-GTPases proteins

A Parise, S Cresca, A Magistrato - Expert Opinion on Drug …, 2024 - Taylor & Francis
ABSTRACT Introduction Molecular Dynamics (MD) simulations can support mechanism-
based drug design. Indeed, MD simulations by capturing biomolecule motions at finite …

Structural insights into i-motif DNA structures in sequences from the insulin-linked polymorphic region

D Guneri, E Alexandrou, K El Omari… - Nature …, 2024 - nature.com
The insulin-linked polymorphic region is a variable number of tandem repeats region of DNA
in the promoter of the insulin gene that regulates transcription of insulin. This region is …

DNA Programmable Peroxidase Activity of Oxidized Polypyrrole Quantum Dots

W Yang, T Leng, H Sun, W Miao… - Advanced Functional …, 2023 - Wiley Online Library
Significant progress has recently been made in the application of oxidized graphene (GO)
quantum dots as enzyme mimics in various biomedical fields due to their bio‐compatibility …

[HTML][HTML] Switching off cancer–An overview of G-quadruplex and i-motif functional role in oncogene expression

C Roxo, A Pasternak - Bioorganic & Medicinal Chemistry Letters, 2024 - Elsevier
DNA can self-assemble into G-quadruplexes and i-motifs non-canonical secondary
structures that are formed by guanine-rich sequences and the cytosine-rich sequences …

Native Characterization of Noncanonical Nucleic Acid Thermodynamics via Programmable Dynamic DNA Chemistry

Y Wu, GA Wang, Q Yang, F Li - Journal of the American Chemical …, 2024 - ACS Publications
Folding thermodynamics, quantitatively described using parameters such as Δ G fold°, Δ H
fold°, and Δ S fold°, is essential for characterizing the stability and functionality of …

A Screening Protocol for Exploring Loop Length Requirements for the Formation of a Three Cytosine‐Cytosine+ Base‐Paired i‐Motif

M Ghezzo, M Trajkovski, J Plavec… - Angewandte Chemie, 2023 - Wiley Online Library
DNA sequences containing at least four runs of repetitive cytosines can fold into tetra‐helical
structures called i‐Motifs (iMs). The interest in these DNA secondary structures is increasing …

Nanopore-based single-molecule investigation of the effects of anthracycline anticancer drugs on i-motif

Z Wang, L Liu, Z Li, L Li, X Liu, R Cui, F Yao, L Tian… - Microchemical …, 2024 - Elsevier
Intercalated binding of anthracycline anticancer drugs to DNA is associated with anticancer
mechanisms. The i-motif, a cytosine-rich DNA secondary structure found in the promoter …

On Water Arrangements in Right-and Left-Handed DNA Structures

LA Yatsunyk, S Neidle - Molecules, 2024 - mdpi.com
DNA requires hydration to maintain its structural integrity. Crystallographic analyses have
enabled patterns of water arrangements to be visualized. We survey these water motifs in …

Structural insights into regulation of insulin expression involving i-motif DNA structures in the insulin-linked polymorphic region

D Guneri, E Alexandrou, K El Omari, Z Dvořáková… - BioRxiv, 2023 - biorxiv.org
The insulin linked polymorphic region (ILPR) is a variable number of tandem repeats
(VNTR) region of DNA in the promoter of the insulin gene that regulates transcription of …