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REVIEW: Proteins Tightly Bound to DNA: New Data and Old Problems

N. Sjakste1,2*, L. Bagdoniene3, A. Gutcaits2, D. Labeikyte3, K. Bielskiene3,4,5, I. Trapiņa1,6, I. Muižnieks7, Y. Vassetzky4, and T. Sjakste6

1Faculty of Medicine, University of Latvia, Šarlotes 1a, Riga LV1001, Latvia; fax: (371) 782-8114; E-mail: Nikolajs.Sjakste@lu.lv

2Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV 1006, Latvia

3Department of Biochemistry and Biophysics, Vilnius University, M. K. Čiurlionio 21, Vilnius LT-03101, Lithuania

4UMR-8126, Institut Gustave Roussy, 39, rue Camille-Desmoulins, Villejuif 94805, France

5Laboratory of Molecular Oncology, Institute of Oncology, Vilnius University, P. Baublio Str. 36, Vilnius LT-08406, Lithuania

6Genomics and Bioinformatics, Institute of Biology, University of Latvia, Miera 3, Salaspils LV2169, Latvia

7Faculty of Biology, University of Latvia, Kronvalda bulvaris 4, Riga LV1586, Latvia

* To whom correspondence should be addressed.

Received November 6, 2009; Revision received June 15, 2010
Proteins tightly bound to DNA (TBP) comprise a group of proteins that remain bound to DNA after usual deproteinization procedures such as salting out and treatment with phenol or chloroform. TBP bind to DNA by covalent phosphotriester and noncovalent ionic and hydrogen bonds. Some TBP are conservative, and they are usually covalently bound to DNA. However, the TBP composition is very diverse and significantly different in different tissues and in different organisms. TBP include transcription factors, enzymes of the ubiquitin–proteasome system, phosphatases, protein kinases, serpins, and proteins of retrotransposons. Their distribution within the genome is nonrandom. However, the DNA primary structure or DNA curvatures do not define the affinity of TBP to DNA. But there are repetitive DNA sequences with which TBP interact more often. The TBP distribution within genes and chromosomes depends on a cell’s physiological state, differentiation type, and stage of organism development. TBP do not interact with DNA in the sites of its association with nuclear matrix and most likely they are not components of the latter.
KEY WORDS: proteins tightly bound to DNA, nuclear matrix, repetitive DNA sequences, serpins, phosphatases, transcription factors, differentiation

DOI: 10.1134/S0006297910100056