Mechanisms of protein-DNA interactions

Course unit title

Scientific direction

Scietific code

Facuty

Department (s)

Mechanisms of protein-DNA interactions

Biochemistry N 004

Life Sciences Center

Institute of Biotechnology

Total number of credits

Mode of studies

Number of credits

Mode of studies

Number of credits

Lectures

0

Consultations

0

Self-studies

8

Seminars

0

Aims of course

Advanced understanding of structures and mechanisms of protein-nucleic acid complexes.

Main topics

Experimental methods for structure determination of proteins and nucleic acids: X-ray diffraction, electron microscopy. Structure data banks. Visualization of structural data: practical skills. Proteins that specifically interact with nucleic acids. Determinants of specific protein - DNA interactions ("direct" or "indirect" recognition). Quantitative description of protein - DNA interactions: binding constants and methods of determination; binding affinity and specificity. Quantitative measure of specificity. Protein engineering methods and redesign of sequence specificity. Biochemical methods for the study of protein - DNA interactions. Proteins that specifically interact with DNA. Enzymes that specifically interact with DNA. Structure, specificity and catalytic mechanisms of phosphodiesterases. Targeted genome modification using proteins that interact with nucleic acids. Genome editing tools. CRISPR-Cas9 genome editing technology.

Main literature

• Protein-Nucleic Acid Interactions: Structural Biology. Editors: Phoebe A Rice, Carl C Correll. RCS Publishing; Cambridge, 2008, ISBN: 978-0-85404-272-2; https://pubs.rsc.org/en/content/ebook/978-0-85404-272-2
• Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS. Origins of specificity in protein-DNA recognition. Annual Rev Biochem 2010; 79:233-69. https://www.annualreviews.org/doi/10.1146/annurev-biochem-060408-091030?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub++0pubmed
• Yang, W. Nucleases: diversity of structure, function and mechanism. Q Rev Biophys.  2011; 44(1):1- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6320257/93.
• Jiang F, Doudna JA. CRISPR-Cas9 Structures and Mechanisms. Annu Rev Biophys. 2017 May 22;46:505-529. doi: 10.1146/annurev-biophys-062215-010822. https://www.annualreviews.org/doi/10.1146/annurev-biophys-062215-010822

Assessment strategy

Assessment criteria

Seminar presentation

Duration of the presentation 45-60 min., number of publications discussed during the seminar >10.

Virginijus Šikšnys

prof.

Approved by the Council of Doctoral School of Life Sciences Center No (4.10)600000-KT-… on the 14th of October 2021

Chairman dr. Daiva Baltriukienė