Poly(ADP-ribosyl)ation and DNA repair synthesis in the extracts of naked mole rat, mouse, and human cells

DNA repair capacity in cells of naked mole rat (Hgl), a species known for its longevity and resistance to cancer, is still poorly characterized. Here, using the whole-cell extracts (WCEs) of Hgl, mouse and human cells, we studied the interrelation between DNA synthesis on the substrates of base excision repair and the activity of poly(ADP-ribose) polymerases (PARPs) responsible for the transfer of the ADP-ribose moieties onto different targets. The level of PAR synthesis was more than ten-fold higher in human WCE as compared to rodent WCEs, while the efficiency of DNA synthesis was comparable. Under conditions of PAR synthesis, the efficiency of DNA synthesis was only slightly enhanced in all extracts and in mouse WCEs unusual products of the primer elongation were detected. The results obtained with WCEs, recombinant proteins and recently found ability of PARPs to attach the ADP-ribose moieties to DNA allowed us to attribute these products to primer mono(ADP-ribosyl)ation (MARylation) at the 5ʹ-terminal phosphate by PARP3 during the DNA synthesis. PARP1/PARP2 can then transfer the ADP-ribose moieties onto initial ADP-ribose. Our results suggest that MARylation/PARylation of DNA in the extracts depends on the ratios between PARPs and can be controlled by DNA-binding proteins.

[DNA Bearing Bulky Fluorescent and Photoreactive Damage in Both Strands as Substrates of the Nucleotide Excision Repair System]

Model DNA molecules that contain bulky lesions in both strands have been created, and their properties as substrates of the nucleotide excision repair (NER) system have been analyzed. The modified nucleoside, 5-[3-(4-azido-2,3,5,6-tetrafluorobenzamido)-1-propoxypropyl]-2'-deoxycytidine (dC^(FAB)), or the nonnucleoside fragment, N-[6-(9-anthracenylcarbamoyl)hexanoyl]-3-amino-1,2-propanediol (nAnt), have been inserted as damage in certain positions of the first DNA strand ("0"). The position of N-[6-5(6)-fluoresceinylcarbamoyl]hexanoyl] -3-amino-1,2-propanediol (nFlu) has been varied within the second DNA strand. This residue has been located opposite the removable damaging fragment of the first strand at positions -20, -10, -4, 0, +3, and +8 relative to the first lesion. It has been demonstrated that the presence of nFlu at the -4, 0, or +3 position of the second strand significantly reduces the thermostability of DNA duplexes, especially in the case of nAnt-DNA and completely excludes the possibility of NER-catalyzed excision from dC^(FAB)- and nAnt-containing 137-meric DNA with the second lesion at these positions. The introduction of nFlu at positions -20, -10, or +8 differently affects the excision efficiency of dC^(FAB)- and nAnt-containing fragments from the first strand. The excision efficiency of dC^(FAB)-containing fragments from extended double-damaged DNA is as high as from DNA that contains a single dC^(FAB) damage, while the excision of nAnt-containing fragments occurs with 80-90% lower efficiency from double-damaged DNA occurs from DNA that contains the single nAnt insert. The nFlu insert differently affects the interaction of the sensory XPC-HR23B dimer with dC^(FAB)- and nAnt-containing DNAs, although in all cases, this interaction occurs with increased efficiency compared to that with single-damaged DNAs. No direct correlation between the thermostability of the DNA duplex and XPC-DNA affinity on the one hand, and the excision efficiency of lesions on the other hand has been shown. The absence of the correlation may be caused by both functional features of variable multiprotein complexes involved in the recognition and verification of damage during NER and the sensitivity of the complexes to the structure of the damage and damage-surrounding DNA. The results are important for understanding the NER mechanism of elimination of bulky damage located in both DNA strands.

DNA with Damage in Both Strands as Affinity Probes and Nucleotide Excision Repair Substrates

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 dC(FAB) and well-recognized nonnucleoside lesions nFlu and nAnt have been designed and their interaction with repair proteins investigated. We demonstrate that modified DNA duplexes dC(FAB)/dG (probe I), dC(FAB)/nFlu+4 (probe II), and dC(FAB)/nFlu-3 (probe III) have increased (as compared to unmodified DNA, umDNA) structure-dependent affinity for XPC-HR23B (Kdum > KdI > KdII ≈ KdIII) and differentially crosslink to XPC and proteins of NER-competent extracts. The presence of dC(FAB) results in (i) decreased melting temperature (ΔTm = -3°C) and (ii) 12° DNA bending. The extended dC(FAB)/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 (dC(FAB)/nFlu+4, dC(FAB)/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.

Photoactivated DNA analogs of substrates of the nucleotide excision repair system and their interaction with proteins of NER-competent extract of HeLa cells. Synthesis and application of long model DNA

Long linear DNA analogs of nucleotide excision repair (NER) substrates have been synthesized. They are 137-mer duplexes containing in their internal positions nucleotides with bulky substitutes imitating lesions with fluorochloroazidopyridyl and fluorescein groups introduced using spacer fragments at the 4N and 5C positions of dCMP and dUMP (Fap-dC- and Flu-dU-DNA) and DNA containing a (+)-cis-stereoisomer of benzo[a]pyrene-N2-deoxyguanidine (BP-dG-DNA, 131 bp). The interaction of the modified DNA duplexes with the proteins of NER-competent HeLa extract was investigated. The substrate properties of the model DNA in the reaction of specific excision were shown to vary in the series Fap-dC-DNA << Flu-dU-DNA < BP-dG-DNA. During the experiments on affinity modification of the proteins of NER-competent extract, Fap-dC-DNA (137 bp) containing a (32)P-label in the photoactive nucleotide demonstrated properties of a highly efficient and selective probe. The set of the main targets of labeling included polypeptides of the extract with the same values of apparent molecular weights (35-90 kDa) as when using the shorter (48 bp) Fap-dC-DNA. Besides, some of the extract proteins were shown capable of specific and effective interaction with the long analog of NER substrate. Electrophoretic mobility of these proteins coincided with the mobilities of DNA-binding subunits of XPC-HR23B and PARP1 (~127 and ~115 kDa, respectively). The 115-kDa target protein was identified as PARP1 using NAD+-based functional testing. The results suggest that the linear Fap-dC-DNA is an unrepairable substrate analog that can compete with effective NER substrates in the binding of the proteins responsible for lesion recognition and excision.