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Nucleic Acids Research, 2001, Vol. 29, No. 2 373-379
© 2001 Oxford University Press

Polarity of human replication protein A binding to DNA

Dmitry M. Kolpashchikov1,2, Svetlana N. Khodyreva1, Denis Yu. Khlimankov1,2, Marc S. Wold3, Alain Favre2 and Olga I. Lavrik1,2,*

1Novosibirsk Institute of Bioorganic Chemistry, Siberian Division of Russian Academy of Sciences, Prospect Lavrentiev 8, 630090, Novosibirsk, Russia, 2Institut Jacques Monod CNRS, Universite Paris 6, Universite Paris 7, 75351 Paris Cedex 05, France and 3Department of Biochemistry, University of Iowa College of Medicine, 51 Newton Road, Iowa City, IA 52242-1109, USA

Replication protein A (RPA), the nuclear single-stranded DNA binding protein is involved in DNA replication, nucleotide excision repair (NER) and homologous recombination. It is a stable heterotrimer consisting of subunits with molecular masses of 70, 32 and 14 kDa (p70, p32 and p14, respectively). Gapped DNA structures are common intermediates during DNA replication and NER. To analyze the interaction of RPA and its subunits with gapped DNA we designed structures containing 9 and 30 nucleotide gaps with a photoreactive arylazido group at the 3'-end of the upstream oligonucleotide or at the 5'-end of the downstream oligonucleotide. UV crosslinking and subsequent analysis showed that the p70 subunit mainly interacts with the 5'-end of DNA irrespective of DNA structure, while the subunit orientation towards the 3'-end of DNA in the gap structures strongly depends on the gap size. The results are compared with the data obtained previously with the primer–template systems containing 5'- or 3'-protruding DNA strands. Our results suggest a model of polar RPA binding to the gapped DNA.

* To whom correspondence should be addressed at: Novosibirsk Institute of Bioorganic Chemistry, Siberian Division of Russian Academy of Sciences, Prospect Lavrentiev 8, 630090, Novosibirsk, Russia. Tel: +7 3832 344296; Fax: +7 3832 333677; Email: lavrik{at}niboch.nsc.ru


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