Professor
Department of Biochemistry and Molecular Biology
Bloomberg School of Public Health

pmiller@jhsph.edu

W3112 Hygiene Building
615 N. Wolfe Street
Baltimore, MD 21205

Office: 410-955-3489

Research in my laboratory focuses on studying mechanisms of DNA repair. We are currently studying the repair of DNA interstrand cross-links and alkyl phosphotriester lesions. DNA interstrand cross-links are formed when DNA is exposed to chemotherapeutic bifunctional alkylating agents, such as bis chloroethylnitrosourea (BCNU), that are used to treat cancer. Interstrand cross-links are also formed endogenously as the result of reaction of DNA with the products of lipid peroxidation. Alkyl phosphotriesters are one of the primary lesions formed when SN-1 type alkylating agents react with DNA. We have developed methods that enable us to synthesize short DNA duplexes that contain interstrand cross-links directly on an automated DNA synthesizer and methods to prepare duplexes that contain diastereomerically pure phosphotriester lesions. The cross-linked or phosphotriester modified duplexes are incorporated into longer DNA duplexes and plasmid DNA, which then serve as substrates for repair studies in cell free extracts and in cells, including E. coli and human tumor cells. We have found a novel reaction in mammalian cell extracts that unhooks the interstrand cross-link. This unhooking reaction is the first step required for interstrand cross-link repair. We are currently identifying the protein(s) responsible for the unhooking reaction and determining if it represents a repair pathway in mammalian cells. The overall goal of this research is to learn how interstrand cross-links and phosphotriester lesions are recognized and repaired in human tumor cell lines and in non-dividing mammalian cells.

In a separate project we are developing platinum-derivatized oligonucleotides that are capable of binding to double-stranded DNA through the formation of triple stranded complexes. Upon binding these platinum-derivatized oligonucleotides form covalent adducts with G and A residues in the DNA target duplex. Oligonucleotides of this type could be used to target genes with goal of disrupting gene function. We are currently examining the effect of these platinated oligonucleotides on DNA transcription and replication in vitro and in mammalian cells in culture. We also plan to examine the ability of cells to repair the covalent triple-stranded adducts that are formed by the platinated oligonucleotides.

Selected Publications
Smeaton, M.B., E.M. Hlavin, T. McGregor Mason, C.J. Wilds, A.M. Noronha, and P.S. Miller. (2008) Distortion-dependent unhooking of interstrand cross-links in mammalian cell extracts. Biochemistry 47:9920-9930.

McGregor Mason, T., M.B. Smeaton, J.Y. Cheung, L.A. Hanakahi, and P.S. Miller. (2008) End modification of a linear DNA duplex enhances NER-mediated excision of an internal Pt(II) lesion. Bioconjug. Chem. 19:1064-1070.

Smeaton, M.B., P.S. Miller, G. Ketner, and L.A. Hanakahi. (2007) Small-scale extracts for the study of nucleotide excision repair and non-homologous end joining. Nucleic Acids Res. 35:e152.

Prater, C.E., A.D. Saleh, M.P. Wear, and P.S. Miller. (2007)  Allosteric inhibition of HIV-1 Rev/RRE interaction by a 3'-methylphosphonate modified antisense oligo-2'-O-methylribonucleotide. Oligonucleotides 17:275-290.

Swenson, M.C., S.R. Paranawithana, P.S. Miller, and C.L. Kielkopf. (2007)  Structure of a DNA repair substrate containing an alkyl interstrand crosslink at 1.65 Å resolution. Biochemistry 46:4545-4553.

Campbell, M.A., T. McGregor Mason, and P.S. Miller. (2007)  Interactions of platinum(II) derivatized triplex forming oligonucleotides with DNA. Can. J. Chem. 85:241-248.

Prater, C.E., A.D. Saleh, M.P. Wear, and P.S. Miller. (2007) Chimeric RNase H-competent oligonucleotides directed to the HIV-1 Rev response element. Bioorg. & Med. Chem. 15:5386-5395.

Shahid, K.A., A. Majumdar, R. Alam, S-T. Liu, J.Y. Kuan, X. Sui, B. Cuenoud, P.M. Glazer, P.S. Miller, and M.M. Seidman. (2006) Triplex cross-linking of the human ß-globin gene in living cells mediated by a triple helix forming oligonucleotide. Biochemistry 45:1970-1978.

Noll, D.M., T. McGregor Mason, and P.S. Miller. (2006) Formation and repair of interstrand cross-links in DNA. Chem. Rev. 106:277-301.

Wilds, C.J., A.M. Noronha, S. Robidoux, and P.S. Miller. (2005) Synthesis and characterization of DNA duplexes containing an N3T-ethyl-N3T interstrand crosslink in opposite orientations. Nucleosides Nucleotides Nucleic Acids 24:965-969.

Noll, D.M., M. Webba da Silva, A.M. Noronha, C.J. Wilds, O.M. Colvin, M.P.Gamcsik and P.S. Miller. (2005) Structure, flexibility and repair of two differently oriented alkyl interstrand DNA cross-links. Biochemistry 44:6764-6775.

da Silva, M.W., R.G. Bierbryer, C.J. Wilds, A.M. Noronha, O.M. Colvin, P.S. Miller and M.P. Gamesik. (2005) Intrastrand base-stacking buttresses widening of major groove in interstrand cross-linked B-DNA. Bioorg. Med. Chem. 13:4580-4587.

Wilds, C.J., A.M. Noronha, S. Robidoux and P.S. Miller. (2004) Mispair-Aligned N3T-alkyl-N3T Interstrand cross-linked DNA: Synthesis and characterization of duplexes with interstrand cross-links of variable lengths. J. Amer. Chem. Soc. 126:9257-9265.

Noll, D.M., A.M. Noronha, C.J. Wilds and P.S. Miller. (2004) Preparation of interstrand cross-linked DNA oligonucleotide duplexes. Frontiers in Biosciences 9:421-437.

Prater, C.E and P.S. Miller. (2004) 3'-Methylphosponate modified oliog-2'-O-methylribonucleotides and their Tat-peptide conjugates: Uptake and stability in mouse fibroblasts in culture. Bioconjug. Chem. 15:498-507.