Research Interest/Area of Expertise
Biochemistry, molecular biology, chemical carcinogenesis, DNA replicaton, enzyme mechanism
Understanding how carcinogenic DNA adducts compromise accurate DNA replication is an important goal in cancer research. These lesions can occur by endogenous agents in the cell or by exposure to exogenous agents such as the toxins found in cigarette smoke. The DNA damage caused by these agents can result in mutations by reducing the accuracy of DNA replication across from or near the damaged site. A central goal of the studies in our lab is to determine the molecular mechanism that allows a DNA polymerase to incorporate a nucleotide across from and past a bulky adduct in a DNA template, which we anticipate will lead to a better understanding of how the damage leads to mutations.
It is well established that during synthesis DNA polymerases incorporate a nucleotide through a multi-step mechanism that involves a conformational change from an open binary to a catalytically active closed ternary complex. We have developed a method to detect the formation of this closed complex which forms only in presence of the next correct nucleotide. Any deviation from correct Watson/Crick (W/C) geometry for the resulting base-pair was shown to have a destabilizing effect on the complex. The presence of a bulky carcinogenic adduct, such as an N-acetyl-2-aminofluorene-dG adduct (dG-AAF), resulted in two interesting effects. First, surprisingly, the polymerase binds much more tightly to the modified primer-template than to an unmodified one. Second, the presence of the adduct completely inhibited the conformational change, explaining why this adduct acts as a strong block to DNA synthesis. We have recently obtained a crystal structure of a polymerase bound to an AAF-modified primer-template (shown in the figure) and find that this structure provides an explanation for the biochemical effects of the adduct. We found that the adduct caused the O helix to tilt forward and block the site were the nucleotide must bind prior to incorporation. We have recently begun to determine how specific amino acid substitutions within the polymerase active site contribute to the properties that affect polymerase mechanism and fidelity. We have shown that the substitution of a serine for a tyrosine at the base of the O helix result in a significant increase in the relative ability to incorporate the correct nucleotide dC opposite the dG-AAF adduct. Moreover, we are able to detect a conformational change for the mutant polymerase when it is bound to an AAF-modified template, suggesting that the increased room provided by removing the bulky tyrosine allows for nucleotide binding in the active site. Finally, our most recent studies involve using FRET at the single molecule level to determine how these types of adducts effect the rate of polymerase binding and synthesis on DNA templates.
Education – Degrees, Licenses, Certifications
- B.A. Chemistry Rutgers College (1972)
- Ph.D. Organic Chemistry (1976), Rutgers University
- NIH Postdoctoral Fellowship, Harvard Medical School (1976-1980)
Liyanage, P. S., Walker, A, Brenlla, A., Cisneros, G. A., *Romano, L. J. and *Rueda, D (2017) "Bulky Lesion Bypass Requires Dpo4 Binding in Distinct Conformations", Nature Scientific Reports, 7, 17383-17397.
Gahlon, H. L., *Romano, L. J. and *Rueda, D. (2017) "Influence of DNA Lesions on Polymerase-Mediated DNA Replication at Single-Molecule Resolution", Chemical Research in Toxicology, 30, 1972-1983
Brenlla, A., *Rueda. D., and *Romano, L. J., (2015) "Mechanism of aromatic amine carcinogen bypass by the Y-family polymerase, Dpo4", Nucleic Acids Res., 42, 9918-9927.
Brenlla, A., Markiewicz, R.P., *Rueda. D., and *Romano, L. J., (2014) "Nucleotide selection by the Y-family DNA polymerase Dpo4 involves template translocation and misalignment", Nucleic Acids Res., 41, 2555-63. PMID: 24270793
Vrtis, K. Markiewicz, R.P., *Romano, L. J., and *Rueda. D. (2013) "Carcinogenic adducts induce distinct DNA polymerase binding orientations", Nucleic Acids Res., 41, 7843-53, PMC3763543
Markiewicz, R.P., Vrtis, K., *Rueda. D., and *Romano, L. J., (2012) "Single-molecule microscopy re-veals new insights into nucleotide selection by DNA polymerase I", Nucleic Acids Res., 40 7975-84 (featured article).
Federley, R. G. and *Romano, L. J. (2010) "DNA Polymerase: Structural Homology, Conformational Dynamics, and the Effects of Carcinogenic DNA Adducts", J. Nucleic Acids, 2010, PMC2933918.
Christian, T. D., *Romano, L. J., and *Rueda. D. (2009) "Single Molecule Measurements of Synthesis by DNA Polymerase with Base-Pair Resolution", Proc. Nat. Acad. Sci. USA, 106, 21109-21114. PMC2795520
Christian, T. D. and *Romano, L. J., (2009) "Monitoring the Conformation of Benzo[a]pyrene Adducts in the Polymerase Active Site using Fluorescence Resonance Energy Transfer", Biochemistry, 49, 5382-5388. PMC2864109