Matthias Bochtler

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Matthias Bochtler
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The basics of protein nucleic acid interactions have been worked out a long time ago (1), but new themes are still emerging. I my talk, I will emphasize the DNA structure and symmetry, degenerate protein-DNA interactions (2,3), and the specific recognition of modified DNA bases (4-6). Using examples from our own work, I will cover indirect sequence readout, sequence readout by intercalation (7), or single and double nucleotide flipping (2,8,9), and the readout of DNA modifications by hydrophobic interactions and modification induced DNA distortions (4,5).

1. Saenger, W. (1984) Principles of nucleic acid structure. Springer-Verlag, New York.

2. Szczepanowski, R.H., Carpenter, M.A., Czapinska, H., Zaremba, M., Tamulaitis, G., Siksnys, V., Bhagwat, A.S. and Bochtler, M. (2008) Central base pair flipping and discrimination by PspGI. Nucleic Acids Res, 36, 6109-6117.

3. Sokolowska, M., Kaus-Drobek, M., Czapinska, H., Tamulaitis, G., Szczepanowski, R.H., Urbanke, C., Siksnys, V. and Bochtler, M. (2007) Monomeric restriction endonuclease BcnI in the apo form and in an asymmetric complex with target DNA. J Mol Biol, 369, 722-734.

4. Mierzejewska, K., Siwek, W., Czapinska, H., Kaus-Drobek, M., Radlinska, M., Skowronek, K., Bujnicki, J.M., Dadlez, M. and Bochtler, M. (2014) Structural basis of the methylation specificity of R.DpnI. Nucleic Acids Res, 42, 8745-8754.

5. Siwek, W., Czapinska, H., Bochtler, M., Bujnicki, J.M. and Skowronek, K. (2012) Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI. Nucleic Acids Res, 40, 7563-7572.

6. Kazrani, A.A., Kowalska, M., Czapinska, H. and Bochtler, M. (2014) Crystal structure of the 5hmC specific endonuclease PvuRts1I. Nucleic Acids Res, 42, 5929-5936.

7. Firczuk, M., Wojciechowski, M., Czapinska, H. and Bochtler, M. (2011) DNA intercalation without flipping in the specific ThaI-DNA complex. Nucleic Acids Res, 39, 744-754.

8. Bochtler, M., Szczepanowski, R.H., Tamulaitis, G., Grazulis, S., Czapinska, H., Manakova, E. and Siksnys, V. (2006) Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease. EMBO J, 25, 2219-2229.

9. Wojciechowski, M., Czapinska, H. and Bochtler, M. (2013) CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI. Proc Natl Acad Sci U S A, 110, 105-110.