TY - JOUR

T1 - Synthesis and Properties of Phosphoryl Guanidine Oligonucleotides Containing 2′,4′-Locked Nucleotides

AU - Dyudeeva, E. S.

AU - Lyapin, P. K.

AU - Dmitrienko, E. V.

N1 - The study was supported by the grant from the Russian Science Foundation (no. 24-24-20105, https://rscf.ru/project/24-24-20105/) as part of a project supported by the Government of the Novosibirsk Region (agreement no. p-97).

PY - 2025/4/6

Y1 - 2025/4/6

N2 - Objective: Chimeric oligonucleotides are an important modern tool for various molecular biological problems. The aim of this work is to study a new type of synthetic analogues of oligonucleotides containing two types of modifications – phosphoryl guanidine (PG) internucleotide group and 2′,4′-locked ribose fragments (LNA)—in one nucleotide unit. Methods: All oligonucleotides were synthesized via the solid phase phosphoramidite method. To investigate the physico-chemical properties of PG-LNAs, modified oligonucleotides were analysed by reversed-phase liquid chromatography, denaturing electrophoresis in polyacrylamide gel, and electrospray ionization mass spectrometry. The stability and structure of DNA-duplexes, containing PG-LNA oligonucleotides, were studied using thermal denaturation and circular dichroism spectropolarimetry. Results and Discussion: It has been shown the presence of PG-LNA linkages decreases the electrophoretic mobility of the oligonucleotides, primarily due to the electroneutrality of the PG group. Additionally, the PG-LNA modifications increase the hydrophobicity of the oligonucleotides, resulting in longer retention times during reversed-phase chromatography. The thermal stability of complementary duplexes containing PG-LNA oligonucleotides has been investigated. It was found the melting temperature increases by 1.5–4.0°C per modification, depending on the position of the modified unit and the ionic strength of the solution. Furthermore, circular dichroism spectropolarimetry revealed the secondary structure of the complexes formed by PG-LNA differs from the B-form, which may be attributed to the presence of LNA fragments exhibiting a 3′-endo conformation of the ribose ring. Thus, PG-LNA oligonucleotides can be considered as a new structural analogue of RNA with a partially uncharged backbone. Conclusions: Based on the data obtained, it can be concluded that PG-LNA oligonucleotides can be considered a promising tool for various methods of isolation and analysis of nucleic acids.

AB - Objective: Chimeric oligonucleotides are an important modern tool for various molecular biological problems. The aim of this work is to study a new type of synthetic analogues of oligonucleotides containing two types of modifications – phosphoryl guanidine (PG) internucleotide group and 2′,4′-locked ribose fragments (LNA)—in one nucleotide unit. Methods: All oligonucleotides were synthesized via the solid phase phosphoramidite method. To investigate the physico-chemical properties of PG-LNAs, modified oligonucleotides were analysed by reversed-phase liquid chromatography, denaturing electrophoresis in polyacrylamide gel, and electrospray ionization mass spectrometry. The stability and structure of DNA-duplexes, containing PG-LNA oligonucleotides, were studied using thermal denaturation and circular dichroism spectropolarimetry. Results and Discussion: It has been shown the presence of PG-LNA linkages decreases the electrophoretic mobility of the oligonucleotides, primarily due to the electroneutrality of the PG group. Additionally, the PG-LNA modifications increase the hydrophobicity of the oligonucleotides, resulting in longer retention times during reversed-phase chromatography. The thermal stability of complementary duplexes containing PG-LNA oligonucleotides has been investigated. It was found the melting temperature increases by 1.5–4.0°C per modification, depending on the position of the modified unit and the ionic strength of the solution. Furthermore, circular dichroism spectropolarimetry revealed the secondary structure of the complexes formed by PG-LNA differs from the B-form, which may be attributed to the presence of LNA fragments exhibiting a 3′-endo conformation of the ribose ring. Thus, PG-LNA oligonucleotides can be considered as a new structural analogue of RNA with a partially uncharged backbone. Conclusions: Based on the data obtained, it can be concluded that PG-LNA oligonucleotides can be considered a promising tool for various methods of isolation and analysis of nucleic acids.

KW - locked nucleic acids (LNA)

KW - melting temperature of modified duplexes

KW - modified oligonucleotides

KW - phosphoryl guanidine (PG) oligonucleotides

UR - https://www.mendeley.com/catalogue/3b6b8bcf-d378-38eb-a70d-099b840cbba2/

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-105003019485&origin=inward&txGid=af26693e71edf2d0a2819a20e94b0e29

U2 - 10.1134/S1068162024606384

DO - 10.1134/S1068162024606384

M3 - Article

VL - 51

SP - 850

EP - 859

JO - Russian Journal of Bioorganic Chemistry

JF - Russian Journal of Bioorganic Chemistry

SN - 1068-1620

IS - 2

ER -