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Biochemistry (Moscow)

, Volume 81, Issue 3, pp 263–274 | Cite as

DNA with damage in both strands as affinity probes and nucleotide excision repair substrates

  • N. V. Lukyanchikova
  • I. O. Petruseva
  • A. N. Evdokimov
  • V. N. Silnikov
  • O. I. LavrikEmail author
Article

Abstract

Nucleotide excision repair (NER) is a multistep process of recognition and elimination of a wide spectrum of damages that cause significant distortions in DNA structure, such as UV-induced damage and bulky chemical adducts. A series of model DNAs containing new bulky fluoro-azidobenzoyl photoactive lesion dCFAB and well-recognized nonnucleoside lesions nFlu and nAnt have been designed and their interaction with repair proteins investigated. We demonstrate that modified DNA duplexes dCFAB/dG (probe I), dCFAB/nFlu+4 (probe II), and dCFAB/nFlu−3 (probe III) have increased (as compared to unmodified DNA, umDNA) structure-dependent affinity for XPC—HR23B (Kd um > Kd I > Kd II Kd III ) and differentially crosslink to XPC and proteins of NER-competent extracts. The presence of dCFAB results in (i) decreased melting temperature (ΔTm = −3°C) and (ii) 12° DNA bending. The extended dCFAB/dG-DNA (137 bp) was demonstrated to be an effective NER substrate. Lack of correlation between the affinity to XPC—HR23B and substrate properties of the model DNA suggests a high impact of the verification stage on the overall NER process. In addition, DNAs containing closely positioned, well-recognized lesions in the complementary strands represent hardly repairable (dCFAB/nFlu+4, dCFAB/nFlu−3) or irreparable (nFlu/nFlu+4, nFlu/nFlu−3, nAnt/nFlu+4, nAnt/nFlu−3) structures. Our data provide evidence that the NER system of higher eukaryotes recognizes and eliminates damaged DNA fragments on a multi-criterion basis.

Key words

DNA bulky DNA lesions protein factors of NER photoaffinity labeling 

Abbreviations

dCFAB

5-[3-(4-azido-2,3,5,6-tetrafluorobenzamido)propoxyprop-1-inyl]-2′-deoxycytidine

dCFABG

exo-N-[(4-azi-dotetrafluorobenzylidenehydrazinocarbonyl)butylcarbamoyl]-2′-deoxycytidine

dCFAP

exo-N-{2-[N-(4-azido-2,5-difluoro-3-chloropyridin-6-yl)-3-aminopropionyl]amino-ethyl}-2′-deoxycytidine

dsDNA

double-stranded DNA

dUFAP

5-{N-[N-(4-azido-2,5-difluoro-3-chloropyridin-6-yl)-3-aminopropionyl]-trans-3-aminopropenyl-1}-2′-deoxy-uridine

Kd

dissociation constant

n

nucleotide

nAnt

a nonnucleoside insert containing anthracenyl residue (N-[6-(9-anthracenyl-carbamoyl)hexanoyl]-3-amino-1,2-propanediol)

NER

nucleotide excision repair

nFlu

a nonnucleoside insert containing fluorescein residue (N-[6-(dipivaloyl-5(6)-fluoresceinyl-carbamoyl)hexanoyl]-O1-(4,4′-dimethoxytrityl)-O2-[(diisopropylamino)(2-cyanoethoxy)phosphino]-3-amino-1,2-propanediol)

ODN

oligo(deoxy)ribonucleotide

RPA

replication protein A

TFIIH

transcription factor II human

Tm

DNA duplex melting temperature

T4 PNK

T4 polynucleotide kinase

umDNA

unmodified DNA

XPC and XPD

xeroderma pigmentosum group C

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Copyright information

© Pleiades Publishing, Ltd. 2016

Authors and Affiliations

  • N. V. Lukyanchikova
    • 1
    • 2
  • I. O. Petruseva
    • 1
  • A. N. Evdokimov
    • 1
  • V. N. Silnikov
    • 1
  • O. I. Lavrik
    • 1
    • 2
    • 3
    Email author
  1. 1.Institute of Chemical Biology and Fundamental MedicineSiberian Branch of the Russian Academy of SciencesNovosibirskRussia
  2. 2.Novosibirsk State UniversityNovosibirskRussia
  3. 3.Altai State UniversityBarnaulRussia

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