Structural and dynamic consequences of inosine, 2'-O-methylation, and N6-methyladenosine modifications in RNA G-quadruplex: A molecular dynamics study
Dutta, N.; Deb, I.; Sarzynska, J.; Lahiri, A.
Show abstract
RNA G-quadruplexes (rG4) are stable non-canonical structures, often found to regulate important biological processes such as transcription, translation, splicing, RNA localization, and other steps in gene expression. rG4 structures can also influence DNA-related processes e.g. DNA replication, telomere elongation and homeostasis, and recombination. Due to the involvement of rG4s in such important processes, these structures are potential therapeutic targets against different diseases e.g., viral infection and cancer. Hence, a better understanding of the structure and stability of rG4s and their role in various therapeutically important cellular processes can help in the design of effective therapeutic strategies for targeting such structures. In the present study, we present our findings on the structural and dynamic effect of RNA modifications (inosine; 2'-O-methylation, and m6A-methylation) on RNA G-quadruplex structure from molecular dynamics simulations. Additionally, we also report the dynamic and energetic aspects of inter-quadruplex interactions and the influence of non-G purine tetrads neighboring the inter-quadruplex junction on the interactions.
Matching journals
The top 9 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Thermodynamic Parameter Estimation for Modified Oligonucleotides Using Molecular Dynamics Simulations 95%
- Complex Conformational Space of RNA Polymerase II C-Terminal Domain upon Phosphorylation 95%
- Photopharmacology in Action: Conformational Landscape of a Photoswitchable Covalent Kinase Inhibitor 95%
Similar papers in this journal
- Molecular dynamics simulations reveal DNA gate opening mechanisms for M. smegmatis topoisomerase 1A 94%
- RNA-binding tunes the conformational plasticity and intradomain stability of TDP-43 tandem RNA recognition motifs 94%
- Free Energy Landscape and Conformational Kinetics of Hoogsteen Base-Pairing in DNA vs RNA 94%
Similar papers in this journal
- The iron maiden. Cytosolic aconitase/IRP1 conformational transition in the regulation of ferritin translation and iron hemostasis 94%
- Allosteric inhibition of adenylyl cyclase type 5 by G-protein: a molecular dynamics study 93%
- Structural and Computational Analysis of Pseudomonas Aeruginosa DNA Gyrase Reveals Molecular Characteristics That May Contribute to Ciprofloxacin Resistance 93%
Similar papers in this journal
- Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study 96%
- Force Field Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA 95%
- AMOEBA Polarizable Molecular Dynamics Simulations of Guanine Quadruplexes: from the c-Kit Proto-oncogene to HIV-1 95%
Similar papers in this journal
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.