Craig T. Martin

Professor of Chemistry, University of Massachusetts
C. Martin Chemistry Dept Website
C. Martin Chemistry Group Page

Ph.D.: California Institute of Technology
Postdoctoral Training: Yale University

Transcription; Protein-DNA Interactions

Although much is known about which DNA sequences are involved in cellular regulation, much less is known about how such regulation occurs. Central to genomic expression, an RNA polymerase must initiate RNA synthesis at a unique site in the DNA, release the promoter and transcribe faithfully and stably, and then terminate transcription at specific signals in the DNA. Regulation of gene expression can (and does) occur at each of these steps.

Our group aims to tie an understanding of structure-function relationships to the detailed mechanism of transcription. The family of RNA polymerases encoded by the bacteriophages T7, T3, and SP6 presents an ideal model system in which to study fundamental aspects of transcription. T7 RNA polymerase is the only RNA polymerase for which high resolution crystal structures are available not only for the enzyme in isolation, but also bound to promoter DNA and in the process of initial transcription. Through a variety of approaches merging biophysical and enzymological tools with approaches from molecular biology, we have made substantial advances in our understanding of structure and function in this system.

In particular, we have shown via mutation of both the protein and the DNA that the crystal structures, while extremely valuable in guiding experiment, can be misleading in terms of energetics and mechanism. Fluorescence probes have shed light on both the initial transcription complex and on a complex paused away from the promoter (for which no x-ray data exists). Biochemical assays have allowed us to propose specific mechanisms for various stages in transcription. Major challenges remain, however, including a mechanistic understanding of how the enzyme translocates away from the promoter and converts into a stably elongating complex.

Representative Publications:

"Structure and Function in Promoter Escape by T7 RNA Polymerase ," Craig T. Martin, Edward A. Esposito, Karsten Theis, & Peng Gong, Prog Nucl Acids Res & Mol Biol , Kivie Moldave, Ed., 80 323-347, 2005

" Topological and conformational analysis of the initiation and elongation complex of T7 RNA polymerase suggests a new twist ," Karsten Theis, Peng Gong and Craig T. Martin, Biochemistry , 43 , 12709-12715, 2004

" Initial bubble collapse plays a key role in the transition to elongation in T7 RNA polymerase ," Peng Gong, Edward A. Esposito and Craig T. Martin, J. Biol. Chem. 279 , 44277-44285, 2004 .

" Crosslinking of Promoter DNA to T7 RNA Polymerase Does Not Prevent Formation of a Stable Elongation Complex ," Edward A. Esposito and Craig T. Martin, J. Biol. Chem. 279 , 44270-44276, 2004 .

" Evaluation of fluorescence spectroscopy methods for mapping melted regions of DNA along the transcription pathway ," Craig T. Martin , Andrea Újvári, & Cuihua Liu, Methods Enzymol. 371 , 13-33, 2003 .

" Binding of the Priming Nucleotide in the Initiation of Transcription by T7 RNA Polymerase ," Iaroslav Kuzmine, Philip A. Gottlieb, & Craig T. Martin, J. Biol. Chem. 278 , 2819-2823, 2003 .

" Promoter Clearance by T7 RNA Polymerase: Initial Bubble Collapse and Transcript Dissociation Monitored by Base Analog Fluorescence ," Cuihua Liu & Craig T. Martin, J. Biol. Chem. 277 , 2725-2731, 2002 .
Selected as a " Must Read " by Faculty of 1000 !

" Interrupting the Template Strand of the T7 Promoter Facilitates Translocation of the DNA During Initiation, Reducing Transcript Slippage and the Release of Abortive Products ," Manli Jiang, Minqing Rong, Craig Martin, and William T. McAllister, J. Mol. Biol. 310 , 509-522, 2001 .

" Gold Nanoparticles with Biological Activity: Disruption of Transcription via Electrostatic Attraction ," Catherine M. McIntosh, Edward A. Esposito, III, Andrew K. Boal, Joseph M. Simard, Craig T. Martin, & Vincent M. Rotello, J. Am. Chem. Soc. 123 , 7626-7629, 2001 .

" Structure in Nascent RNA Leads to Termination of Slippage Transcription by T7 RNA Polymerase ," Iaroslav Kuzmine, Philip A. Gottlieb, & Craig T. Martin , Nucl. Acids Res. 29 , 2601-2606, 2001.