Development of approaches to targeted increase in mRNA stability and translational efficiency using modified oligonucleotides

A current trend in modern medicine is the development of approaches to the treatment and prevention of diseases accompanied by reduced levels of functional proteins, for example, apolyprotein C3 (coronary heart disease) and frataxin (Friedreich's ataxia). Increases can be achieved through the use of protein-based drugs, as well as manipulation of protein-coding mRNA. In the latter case, ineffective or insufficient production of the target protein is often observed, which can be corrected by increasing mRNA translation efficiency and stability. It has been shown that translation can be specifically enhanced using antisense oligonucleotides (ASOs), which compensate for the function of negative regulatory elements (hairpins) present in the 5'-untranslated region (5'-UTR) of some mRNAs. In turn, increasing the stability of mRNA can be achieved by using ASO, as well as by introducing exonuclease-resistant chemical modifications into the poly(A) tail of the mRNA. This project can be divided into two areas: 1) Specific impact on highly structured elements in the 5'-UTR of mRNA in order to increase translation efficiency ASO can be used not only to specifically reduce gene expression through transcript degradation, but also to specifically increase protein levels by increasing the efficiency of mRNA translation. In this case, the targets of ASOs are hairpins or sORFs (short open reading frames) in the 5'UTR of the mRNA. However, until now, G-quadruplexes, which are also present in the 5'-UTR and can regulate translation, have not been considered as ASO targets. Thus, it is advisable to develop new modifications and design principles for ASOs with improved properties, as well as to search for highly structured elements in the 5'-UTR that can regulate translation efficiency. A search for targets will be carried out and an approach to increasing translation efficiency through targeted action will be tested. The approach is based on the design of constructs containing a low-molecular-weight fragment capable of disrupting classical GC pairs in hairpins and G tetrads in G-quadruplexes, and an oligonucleotide part that provides selectivity due to complementarity to single-stranded fragments flanking the secondary structure. 2) Development of efficient and scalable methods for obtaining functional mRNA conjugates with increased stability Chemical modification of synthetic mRNA, for example with N1-methylpseudouridine, is a promising method to improve the efficiency of mRNA vectors. Alternative strategies provide increased mRNA stability through enzymatic extension of the poly(A) tail with modified nucleotides or enzymatic ligation at the 3' end of modified oligonucleotides (ON). However, extension has variable efficiency and produces poly(A) tails of variable length, and conjugation does not allow obtaining mRNA conjugates in quantities sufficient for therapeutic purposes. For the first time, approaches to increasing mRNA stability through scalable chemical ON conjugation will be tested. For this purpose, corresponding phosphoramidites will be developed, introduced at the 5'-end of the ONs and ensuring effective conjugation. To increase the stability of mRNA conjugates, an approach using modified ONs that “extend” the poly(A) tail, and the original principle of “looping” the mRNA, will be tested. If positive results are obtained, in vivo studies of the effectiveness of the developed approach will be conducted. During the implementation of the project, several approaches to targeted increase in protein amounts will be proposed and tested by increasing the translation efficiency and stability of mRNA using synthetic ONs. The results obtained may find application in biology (study of protein functions) and medicine (specific correction of protein deficiency in pathologies, increasing the effectiveness of mRNA-based therapeutics).

January 6, 2024 — December 31, 2026

Aralov A.V. (PI)

The group of molecular tools for living system studies

Grant, RSF

List of publications

  1. Kamzeeva PN, Alferova VA, Korshun VA, Varizhuk AM, Aralov AV (2025). 5′-UTR G-Quadruplex-Mediated Translation Regulation in Eukaryotes: Current Understanding and Methodological Challenges. Int J Mol Sci 26 (3), 1187
  2. Kamzeeva P, Shepelev N, Zabbarova V, Brylev V, Chistov A, Ryazantsev D, Kot E, Novopashina D, Rubtsova M, Aralov A (2025). Structural Characterization of DDX23 5′ UTR Regulatory Elements and Their Targeting by LNA-Modified Antisense Oligonucleotides. Int J Mol Sci 26 (22), 11047