Research Interests:                          Biochemistry of Protein-DNA Interactions,

                                                                    Structure-Function Relationships in Transcription

                                                                    Complexes of E. coli RNA Polymerase, Nucleic

                                                                    Acid Structure and Enzymology


Research in Progress:


The expression of genes in living cells is carried out by proteins that can recognize and bind to specific nucleotide sequences in DNA. These proteins then act in various ways to extract genetic information from the DNA in a highly regulated manner. My research focuses in general on understanding the mechanisms by which DNA-binding proteins are able to recognize specific signals in DNA and carry out their specific functions. Recognition may involve chemical as well as structural features of DNA, such as its ability to be deformed into bent or kinked conformations. These features of DNA may also play important roles in the subsequent action of DNA-binding proteins during gene expression. My experimental approach uses chemical techniques to investigate the structures of protein-DNA complexes in order to gain insight into the mechanisms by which they function.


Of particular interest to me (among other DNA-binding proteins) is an enzyme called RNA polymerase, which binds to DNA and moves along it, transcribing the genetic information in the DNA into a corresponding RNA molecule.  Very little is known about the structure of the transcribing enzyme complex or the mechanics of its motion as it progresses along a DNA molecule.  Investigation of this process by the chemical techniques mentioned above is an important step toward the ultimate goal of understanding how this biological "machine" may be regulated in living cells.



Representative Student Independent Research Projects:


Carolyn Pizoli                Generation of Transcription Templates Using Polymerase Chain



Meredith Brown           Characterization of Steady-State Transcription of Bent DNA                                                    Templates by E. coli RNA Polymerase.


Jennifer Galli                  The Effect of DNA Bending on Transcription by Bacteriophage                                                 RNA  Polymerases: Template Construction.


Cynthia Polhamus       Kinetics of Single-Round Transcription of Bent DNA by E. coli                                                   RNA Polymerase:  Analysis by Gel Electrophoresis


JUDITH R. LEVIN   (cont.)



Representative Student Independent Research Projects  (cont.)


Anna Odnopozova      Characterization of Pausing by E. coli RNA Polymerase at

                                         A-tract-Induced Bends in DNA


Carolyn Mochel            The Effect of DNA Bending on Transcription by Bacteriophage       

                                         RNA Polymerases: Template Construction and Preliminary                                                       Analysis


Stephanie Solter          The Effects of Single Template Nucleoside Gaps on

                                         Transcription Initiation by E. coli  RNA Polymerase


Genevieve Monsees   Statistical Analysis of Data on the Kinetics of Transcription                                                       Initiation by E. coli  RNA Polymerase



Representative Publications:


Levin, J.R., Krummel, B. and Chamberlin, M.J. (1987) Isolation and Properties of Transcribing Ternary Complexes of Escherichia coli RNA Polymerase  Positioned at a Single Template Base.  J. Mol. Biol. 196:  85-100.


Levin, J.R., Burkhoff, A.M. and Tullius, T.D. (1991) "Using the Chemistry of the Hydroxyl Radical to Determine Structural Details about DNA and Protein-DNA

Complexes".  In A Laboratory Guide to In Vitro Studies of Protein-DNA Interactions

(J.P. Jost and H.P. Saluz, eds.), Biomethods (Birkhauser Verlag) 5:  133-144.


Dixon, W.J., Hayes, J.J., Levin, J.R., Weidner, M.F., Dombroski, B.A. and Tullius, T.D. (1991)  Hydroxyl Radical Footprinting of Protein-DNA Complexes.   Meth. Enzymol.

208:  380.


Draganescu, A., Levin, J.R. and Tullius, T.D. (1995) Homeodomain Proteins: What Governs Their Ability to Recognize Specific DNA Sequences?  J. Mol. Biol. 250:  595-608.


Levin, J.R., Blake, J.J., Ganunis, R.A. and Tullius, T.D. (2000) The Roles of Specific Template Nucleosides in the Formation of Stable Transcription Complexes by Escherichia coli RNA Polymerase.  J. Biol. Chem. 275: 6885 - 6893.