TRANSCRIPTION FACTOR DISCOVERY

MICHAEL
VAN DYKE

Michael Van Dyke is a Foundation Fellow in Biochemistry and Director of the College of Science and Mathematics Nucleic Acids Core Facility at Kennesaw State University. From cutting-edge research to hands-on learning experiences, you will find your future in the Van Dyke Laboratory.

BIO CHEM

Caltech Ph.D. with Peter Dervan; Rockefeller postdoc with Robert Roeder, Michael Van Dyke has held academic research positions in institutions ranging from MD Anderson to Kennesaw State. A long-time lover of all things ligand-nucleic acid, the Van Dyke laboratory has made advances in several fields, including class II general transcription machinery characterization, G*G multiplex nucleic acids and the proteins that recognize them, and universal combinatorial selection method development.

RESEARCH

PROJECTS & DREAMS

DNA-BINDING PROTEIN DISCOVERY

NIH 1R15GM104833-01

Our goal is to advance our understanding of predicted and/or unexpected DNA-binding proteins by identifying their preferred binding sites by the novel combinatorial approach, Restriction Endonuclease Protection, Selection and Amplification (REPSA). While various genome projects have yielded a wealth of information for both the human genome and other model organisms, much remains to be determined regarding individual genes and the biological roles played by their encoded products.

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REFRACTORY CLEAVAGE SITES

NSF CHE 1709263

This research project is undertaken to mechanistically determine why specific DNA sequences are refractory to the type IIS restriction endonuclease FokI. Cleavage-resistant sequences identified through the combinatorial approach REPSA will be investigated by stopped-flow spectroscopy studies to dissect individual steps affected. Information from this study may provide a better understanding of DNA recognition and cleavage by IIS restriction endonucleases, with potential applicability to other DNA cleavage/modification systems.

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TRANSCRIPTION FACTOR DISCOVERY

NSF MCB 1714778 & 2041202

We seek to better understand transcriptional regulatory networks in the model extremophile T. thermophilus HB8. The binding specificity of putative transcription factors will be determined by the combinatorial approach REPSA, followed by massively parallel semiconductor sequencing and MEME analysis. Potential binding sites will be mapped to the T. thermophilus genome and functionally validated both in vitro and in vivo. Information from this study will provide a better understanding of regulons within a model eubacterial extremophile.

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PUBLISHED WORK

SEQUENCE SPECIFICITY OF TRIPLEX DNA

We have devised a combinatorial method, restriction endonuclease protection selection and amplification (REPSA), to identify consensus ligand binding sequences in DNA. Here we report the use of REPSA to identify the consensus duplex DNA sequence recognized by a G/T-rich oligodeoxyribonucleotide under conditions favoring purine-motif triple-helix formation.

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REPSA AND DRUG-DNA BINDING

Many agents successfully used in cancer chemotherapy either directly or indirectly covalently modify DNA. Using the combinatorial method REPSA, we determined the DNA-binding specificity of the semisynthetic covalent DNA-binding polyamide tallimustine.

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TRANSCRIPTION FACTOR DISCOVERY

Here we describe using REPSA, massively parallel sequencing, and bioinformatics to identify the preferred DNA-binding sites for the Thermus thermophilus HB8 transcriptional regulator SbtR. From the resulting position weight matrix, we can identify multiple operons potentially regulated by SbtR and postulate a biological role for this protein in regulating extracellular transport processes.

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