Joseph Falcone

Principles of Chemistry I
Principles of Chemistry I Lab
Fundamental Organic Chemistry I
Fundamental Organic Chemistry I Lab
Fundamental Organic Chemistry II
Fundamental Organic Chemistry II Lab
Medical Ethics
Senior Project

Falcone, J.M., Becker, D., Sevilla, M.D., Swarts, S.G., (2005) “Products of the reactions of the dry and aqueous electron with hydrated DNA: hydrogen and 5,6-dihydropyrimidines”, Radiation Physics and Chemistry, Volume 72, Issues 2-3, Pages 257-264 Christiane Ferradini Memorial Issue

Falcone, J.M., Box, H.C., (1997), “Selective hydrolysis of damaged DNA by nuclease P1 “, Biochemica et Biophysica Acta 1337: 267-275

Razskazovskii,Y., Swarts, S.G., Falcone, J.M., Taylor, C., Sevilla, M.D., (1997), ” Competitive Electron Scavenging by Chemically Modified Pyrimidine Bases in Bromine-Doped DNA: Relative Efficiencies and Relevance to Intrastrand Electron Migration Distances”, Journal of Physical Chemistry B, 101 (8), 1460-1467

Falcone, J.M., Box, H.C., Miller, J.H.,” Catalytic Activity of Nuclease P1: Experiment and Theory” Radiation Damage in DNA:Structure/Function Relationships at Early Times(Eds. A.F. Fuciarelli, J.H.Miller, J.D. Zimbrick) Columbus, OH, Battelle Press, 1994, pp 346-353

Over the years I have worked with numerous undergraduate students on mentored research projects. Many of those have gone on to graduate and professional degrees in science and medicine. I'm always looking for folks willing to learn and explore in the lab.

My Research Interests:

Free Radical Chemistry:

The focus of my research efforts is on elucidating the mechanisms by which DNA is damaged by ionizing radiation and oxidative stress. Radiation induced DNA damage results from either direct ionization of the DNA macromolecule or from free radicals generated within the surrounding environment. Of particular importance in my research is assessing the influence that water content has on the formation of radiation induced DNA damage products.

Eukaryotic cells contain double stranded DNA bearing about 6x10^9 nucleotide base pairs. A polymer of this size if fully extended would be about 60 cm in length. In order to fit inside the cell nucleus, which is about 50mm in diameter, DNA must undergo a 100,000 fold reduction in apparent length. Nature solves this dilemma in eukaryotic cells by wrapping genomic DNA around the histone proteins, forming chromatin. The compaction of DNA into the small volume of the nucleus, as well as association of DNA with histones and other nuclear proteins(enzymes, lamins, microfilaments, etc.) results in the exclusion of bulk water near the DNA. The DNA in chromatin exists as an intermediate between the solution state and the solid state.

Classically it has been thought that irradiation of the bulk water surrounding the DNA produces free radicals( e.g. the hydroxyl radical and the aqueous electron) that can diffuse to and react with DNA. In my work with Dr. Steven Swarts( Bowman Gray School of Medicine, Wake Forest University, Winston-Salem NC) we have been able to establish that the water molecules located closest to the DNA are qualitatively different from bulk water. The irradiation of the water molecules tightly bound to the DNA, within the first hydration layer, will damage DNA through a charge transfer mechanism. By this mechanism, electron deficient "holes" and electrons from the first hydration layer migrate to the DNA. The damage from charge transfer processes is similar to damage expected from direct ionization of the DNA(e.g. base release, dihydrothymine, dihydrocytosine), but different from that expected from bulk water radical attack on DNA(e.g.strand breaks, thymine glycol). This is significant because the tightly bound water molecules, which have largely been overlooked, constitute approximately 50% of the water that surrounds DNA in a cellular environment, with the other half constituting bulk water. Further characterization of the tightly bound water molecules and their role in radiation induced DNA damage is necessary. I plan to extend this work to consider the effects of irradiation of DNA in the presence of free radical scavengers such as thiols, and in the presence of nucleoproteins.

The measurements described above are obtained from reverse phase high performance liquid chromatography(HPLC) and gas chromatography/ mass spectrometry (GC/MS) techniques that have been developed and optimized to quantify irradiated DNA end products. Novel product identification and characterization are done using the GC/MS in total ion mode, or using proton 1D nuclear magnetic resonance (NMR) spectroscopy.


Enzymology:
I am interested in elucidating the structure/ activity relationships between DNA processing enzymes and various damaged DNA substrates, with a goal of developing sensitive techniques for detection of DNA damage in vivo.

It has been shown that for equal exposure to ionizing radiation, the yield of DNA base lesions in vitro is at least two orders of magnitude higher than what is observed in irradiated cells . Similarly, chromatin has been shown to be 100 times less susceptible to strand breaks and base damage by ionizing radiation and oxidative stress compared to histone depleted DNA . The protective effect of histone proteins, compact higher order chromatin structures, and cellular repair processes, are likely responsible for the empirically observed differences in damage susceptibilities. This emphasizes the need for development of highly sensitive assay techniques in order to detect irradiation or oxidatively induced damage within a cellular system.
As part of my graduate work with Dr. Harold Box (State University of New York at Buffalo/ Roswell Park Memorial Cancer Institute) I characterized the structure / activity relationships between radiation damaged DNA and endonuclease P1 from Penecillium citrinum.
Nuclease P1 is an endonuclease which functions as a phosphodiesterase, cleaving the bond between the 3’-hydroxyl and 5’-phosphoryl group of adjacent nucleosides. Nuclease P1 is capable of hydrolyzing single stranded DNA and RNA completely to the level of mononucleoside 5’-monophosphates. During my studies I had found that the efficiency of nuclease P1 in hydrolyzing the phosphodiester bonds of substrates damaged by ionizing radiation or oxidative stress may be significantly altered by modifications to the 5’ terminal base. The hydrolytic activity has been shown to be reduced by several orders of magnitude with the loss of base aromaticity resulting from saturation of the 5-6 double bond of thymine when present on the 5’ terminus. Several DNA lesions were determined to be slowly hydrolyzed or completely refractory to hydrolysis by nuclease P1.
DNA is hydrolyzed completely to the level of mononucleoside 5’-monophosphates by nuclease P1. Damaged DNA species that were refractory to hydrolysis were isolated as dinucleoside monophosphates by high performance liquid chromatography(HPLC). A probabilistic model was derived to calculate the hydrolytic course of a DNA polymer by nuclease P1 in order to isolate slowly hydrolyzed species. As a result of this work, a sensitive 32P postlabeling assay has been developed for the detection of the formamido remnant of pyrimidine bases, a refractory lesion to nP1. The technique has successfully been applied in quantifying this lesion in irradiated keratinocytes. Currently I am extending this technique to assay for DNA base lesions which are slowly hydrolyzed by nP1. I plan to extend the technique to detect abasic sites within a DNA polymer. I plan to further develop this method of detection of radiation and/or oxidatively induced DNA damage using different enzyme systems, and hope to apply the techniques to detect and characterize DNA damage in vivo.

Pre-biotic chemistry and emergent properties of complex systems:

I have been working with polymerization of amino acids in simulated pre-biotic conditions with some interesting results from UV-irradiated samples of alanine and glycine in frozen aqueous solution, and also with amino acids in the presence of alpha hydroxy acids subjected to successive heating to dryness and reconstitution with water. the wet-dry cycling has shown promise in formation of polypeptides.