TY - JOUR

T1 - Amphiphilic Oligonucleotide Derivatives as a Tool to Study DNA Repair Proteins

AU - Khodyreva, Svetlana N

AU - Yamskikh, Alexandra A

AU - Ilina, Ekaterina S

AU - Kutuzov, Mikhail M

AU - Belousova, Ekaterina A

AU - Kupryushkin, Maxim S

AU - Zharkov, Timofey D

AU - Koval, Olga A

AU - Zvereva, Sofia P.

AU - Lavrik, Olga I

N1 - The work was supported by a grant 075-15-2024-548 from the Ministry of Science and Higher Education of the Russian Federation.

PY - 2025/7/23

Y1 - 2025/7/23

N2 - Modified oligonucleotides (oligos) are widely used as convenient tools in many scientific fields, including biomedical applications and therapies. In particular, oligos with lipophilic groups attached to the backbone ensure penetration of the cell membrane without the need for transfection. This study examines the interaction between amphiphilic DNA duplexes, in which one of the chains contains a lipophilic substituent, and several DNA repair proteins, particularly DNA-damage-dependent PARPs, using various biochemical approaches. DNA with a lipophilic substituent (LS-DNA) demonstrates more efficient binding with DNA damage activated poly(AD-ribose) polymerases 1-3 (PARP1, PARP2, PARP3) and DNA polymerase β. Chemically reactive LS-DNA derivatives containing a photoactivatable nucleotide (photo-LS-DNAs) or a 5' deoxyribose phosphate (dRP) group in the vicinity of double-strand breaks (DSBs) are used for the affinity labelling of PARPs and other proteins in several whole-cell extracts of human cells. In particular, photo-LS-DNAs are used to track the level of Ku antigen in the extracts of neuron-like differentiated SH-SY5Y, undifferentiated SH-SY5Y, and olfactory epithelial cells. In vitro, PARP1-PARP3 are shown to be able to slowly excise the 5' dRP group at DSBs. LS-DNAs can activate PARP1 and PARP2 for autoPARylation, albeit less effectively than regular DNA duplexes.

AB - Modified oligonucleotides (oligos) are widely used as convenient tools in many scientific fields, including biomedical applications and therapies. In particular, oligos with lipophilic groups attached to the backbone ensure penetration of the cell membrane without the need for transfection. This study examines the interaction between amphiphilic DNA duplexes, in which one of the chains contains a lipophilic substituent, and several DNA repair proteins, particularly DNA-damage-dependent PARPs, using various biochemical approaches. DNA with a lipophilic substituent (LS-DNA) demonstrates more efficient binding with DNA damage activated poly(AD-ribose) polymerases 1-3 (PARP1, PARP2, PARP3) and DNA polymerase β. Chemically reactive LS-DNA derivatives containing a photoactivatable nucleotide (photo-LS-DNAs) or a 5' deoxyribose phosphate (dRP) group in the vicinity of double-strand breaks (DSBs) are used for the affinity labelling of PARPs and other proteins in several whole-cell extracts of human cells. In particular, photo-LS-DNAs are used to track the level of Ku antigen in the extracts of neuron-like differentiated SH-SY5Y, undifferentiated SH-SY5Y, and olfactory epithelial cells. In vitro, PARP1-PARP3 are shown to be able to slowly excise the 5' dRP group at DSBs. LS-DNAs can activate PARP1 and PARP2 for autoPARylation, albeit less effectively than regular DNA duplexes.

UR - https://pubmed.ncbi.nlm.nih.gov/40806211/

UR - https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=105013254900&origin=inward

U2 - 10.3390/ijms26157078

DO - 10.3390/ijms26157078

M3 - Article

C2 - 40806211

VL - 26

JO - International Journal of Molecular Sciences

JF - International Journal of Molecular Sciences

SN - 1661-6596

IS - 15

M1 - 7078

ER -