TY - JOUR

T1 - Probing the Conformational Restraints of DNA Damage Recognition with β-L-Nucleotides

AU - Yudkina, Anna V.

AU - Kim, Daria V.

AU - Zharkov, Timofey D.

AU - Zharkov, Dmitry O.

AU - Endutkin, Anton V.

N1 - This research was supported by Russian Science Foundation (grant 21-74-10104 to A.V.E., biochemical experiments). Partial support from the Russian Ministry of Science and Higher Education is acknowledged (075-15-2022-263).

PY - 2024/6

Y1 - 2024/6

N2 - The DNA building blocks 2′-deoxynucleotides are enantiomeric, with their natural β-D-configuration dictated by the sugar moiety. Their synthetic β-L-enantiomers (βLdNs) can be used to obtain L-DNA, which, when fully substituted, is resistant to nucleases and is finding use in many biosensing and nanotechnology applications. However, much less is known about the enzymatic recognition and processing of individual βLdNs embedded in D-DNA. Here, we address the template properties of βLdNs for several DNA polymerases and the ability of base excision repair enzymes to remove these modifications from DNA. The Klenow fragment was fully blocked by βLdNs, whereas DNA polymerase κ bypassed them in an error-free manner. Phage RB69 DNA polymerase and DNA polymerase β treated βLdNs as non-instructive but the latter enzyme shifted towards error-free incorporation on a gapped DNA substrate. DNA glycosylases and AP endonucleases did not process βLdNs. DNA glycosylases sensitive to the base opposite their cognate lesions also did not recognize βLdNs as a correct pairing partner. Nevertheless, when placed in a reporter plasmid, pyrimidine βLdNs were resistant to repair in human cells, whereas purine βLdNs appear to be partly repaired. Overall, βLdNs are unique modifications that are mostly non-instructive but have dual non-instructive/instructive properties in special cases.

AB - The DNA building blocks 2′-deoxynucleotides are enantiomeric, with their natural β-D-configuration dictated by the sugar moiety. Their synthetic β-L-enantiomers (βLdNs) can be used to obtain L-DNA, which, when fully substituted, is resistant to nucleases and is finding use in many biosensing and nanotechnology applications. However, much less is known about the enzymatic recognition and processing of individual βLdNs embedded in D-DNA. Here, we address the template properties of βLdNs for several DNA polymerases and the ability of base excision repair enzymes to remove these modifications from DNA. The Klenow fragment was fully blocked by βLdNs, whereas DNA polymerase κ bypassed them in an error-free manner. Phage RB69 DNA polymerase and DNA polymerase β treated βLdNs as non-instructive but the latter enzyme shifted towards error-free incorporation on a gapped DNA substrate. DNA glycosylases and AP endonucleases did not process βLdNs. DNA glycosylases sensitive to the base opposite their cognate lesions also did not recognize βLdNs as a correct pairing partner. Nevertheless, when placed in a reporter plasmid, pyrimidine βLdNs were resistant to repair in human cells, whereas purine βLdNs appear to be partly repaired. Overall, βLdNs are unique modifications that are mostly non-instructive but have dual non-instructive/instructive properties in special cases.

KW - AP endonucleases

KW - DNA glycosylases

KW - DNA polymerases

KW - DNA repair

KW - translesion synthesis

KW - β-L-nucleotides

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85195872430&origin=inward&txGid=fc46ea90e2aac252122efcec50999978

UR - https://www.mendeley.com/catalogue/6c85e3a0-0348-37fc-bb48-35bbd64fd482/

U2 - 10.3390/ijms25116006

DO - 10.3390/ijms25116006

M3 - Article

C2 - 38892193

VL - 25

JO - International Journal of Molecular Sciences

JF - International Journal of Molecular Sciences

SN - 1661-6596

IS - 11

M1 - 6006

ER -