Nucleic acids in modern molecular therapies: A realm of opportunities for strategic drug design

V Genna, L Reyes-Fraile, J Iglesias-Fernandez… - Current Opinion in …, 2024 - Elsevier
RNA vaccines have made evident to society what was already known by the scientific
community: nucleic acids will be the “drugs of the future.” By modifying the genome …

Therapeutic phosphorodiamidate morpholino oligonucleotides: Physical properties, solution structures, and folding thermodynamics

F Maksudov, E Kliuchnikov, D Pierson, ML Ujwal… - … Therapy-Nucleic Acids, 2023 - cell.com
Elucidating the structure-function relationships for therapeutic RNA mimicking
phosphorodiamidate morpholino oligonucleotides (PMOs) is challenging due to the lack of …

Calculation of energy for RNA/RNA and DNA/RNA duplex formation by molecular dynamics simulation

VM Golyshev, DV Pyshnyi, AA Lomzov - Molecular Biology, 2021 - Springer
The development of approaches for predictive calculation of hybridization properties of
various nucleic acid (NA) derivatives is the basis for the rational design of the NA-based …

Effects of phosphoryl guanidine modification of phosphate residues on the structure and hybridization of oligodeoxyribonucleotides

VM Golyshev, DV Pyshnyi… - The Journal of Physical …, 2021 - ACS Publications
Phosphoryl guanidine oligonucleotides (PGOs) are promising tools for biological research
and development of biosensors and therapeutics. We performed structural and hybridization …

[HTML][HTML] Diversity of Self-Assembled RNA Complexes: From Nanoarchitecture to Nanomachines

MA Kanarskaya, DV Pyshnyi, AA Lomzov - Molecules, 2023 - mdpi.com
New tool development for various nucleic acid applications is an essential task in RNA
nanotechnology. Here, we determined the ability of self-limited complex formation by a pair …

[HTML][HTML] Improving the potency prediction for chemically modified siRNAs through insights from molecular modeling of individual sequence positions

E Kliuchnikov, F Maksudov, J Zuber, S Hyde… - … Therapy Nucleic Acids, 2025 - cell.com
Chemical modifications are applied to small interfering RNAs (siRNAs) to improve their
metabolic stability, specificity, and duration of pharmacodynamic effects. Despite …

Comparative molecular dynamics calculations of duplexation of chemically modified analogs of DNA used for antisense applications

R Galindo-Murillo, JS Cohen… - NAR Genomics and …, 2024 - academic.oup.com
We have subjected several analogs of DNA that have been widely used as antisense
oligonucleotide (ASO) inhibitors of gene expression to comparative molecular dynamics …

[HTML][HTML] Investigation of the lncRNA THOR in Mice Highlights the Importance of Noncoding RNAs in Mammalian Male Reproduction

L Zhou, J Li, J Liu, A Wang, Y Liu, H Yu, H Ouyang… - Biomedicines, 2021 - mdpi.com
THOR is a highly conserved testis-specific long noncoding RNA (lncRNA). The interaction
between THOR and the development of the male reproductive system remains unclear …

Change of hydration patterns upon RNA melting probed by excitations of phosphate backbone vibrations

A Kundu, J Schauss, BP Fingerhut… - The Journal of Physical …, 2020 - ACS Publications
The water hydration shell has a decisive impact on the structural and functional properties of
RNA. Changes of the RNA structure upon melting and in biochemical processes are …