NDLI: Use of Modified Flap Structures for Study of Base Excision Repair Proteins

Content Provider	Springer Nature Link
Author	Nazarkina, Zh. K. Pyshnyi, D. V. Pyshnaya, I. A. Lavrik, O. I. Khodyreva, S. N.
Copyright Year	2005
Abstract	To investigate interactions between proteins participating in the long-patch pathway of base excision repair (BER), DNA duplexes with flap strand containing modifications in sugar phosphate backbone within the flap-forming oligonucleotides were designed. When the flap-forming oligonucleotide consisted of two sequences bridged by a decanediol linker located in the flap strand near the branch point, the efficiency and position of cleavage by flap endonuclease 1 (FEN1) differed from those for natural flap. The cleavage rate of chimeric structure by FEN1 was lower than that of a normal substrate. When we introduced the second modification in the flap-forming oligonucleotide, the cleavage rate decreased significantly. To estimate efficiency of recognition and processing of the chimeric structures by BER proteins, we studied the rate of DNA synthesis by DNA polymerase β (Pol β) and the rate of nucleotide excision at the 3′-end of the initiating primer by apurinic/apyrimidinic endonuclease 1 (APE1) compared with those for the natural DNA duplexes. Efficiency of strand-displacement DNA synthesis catalyzed by Pol β was shown to be higher for flap structures containing non-nucleotide linkers. The chimeric structures were processed by the 3′-exonuclease activity of APE1 with efficiency lower than that for a normal flap structure. Thus, DNA duplexes with modifications in sugar phosphate backbone can be used to mimic intermediates of the long-patch pathway of BER in reconstituted systems containing FEN1. Based on chimeric and natural oligonucleotides, photoreactive DNA structures were designed. The photoreactive dCMP moiety was introduced into the 3′-end of DNA primer via the activity of Pol β. The photoreactive DNA duplexes—3′-recessed DNA, nicked DNA, and flap structures containing natural and chimeric oligonucleotides—were used for photoaffinity labeling of BER proteins.
Starting Page	1327
Ending Page	1334
Page Count	8
File Format	PDF
ISSN	00062979
Journal	Biochemistry (Moscow)
Volume Number	70
Issue Number	12
e-ISSN	16083040
Language	English
Publisher	Nauka/Interperiodica
Publisher Date	2005-01-01
Publisher Place	Moscow
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	flap endonuclease 1 base excision repair photoaffinity labeling Biomedicine general Bioorganic Chemistry Microbiology Biochemistry
Content Type	Text
Resource Type	Article
Subject	Biochemistry Biophysics Geriatrics and Gerontology

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