List of publications that are relevant to technology developed and used by Red5 Pharmaceuticals, LLC

*** denotes publications of high importance.
Publications are provided in reverse chronological order.


(41) Berdis, A.J. Current and Emerging
Strategies to Increase the Efficacy of Ionizing Radiation in the Treatment of Cancer. Expert Opinion on Drug Discovery  9,167-181.
(40) Maity, A., Choi, J.-S., Teets, T, Deligounul, N., Berdis, A J., and Gray, T. G. (2013) Cyclometalated  iridium (III) complexes with deoxyribose substituents. Chemistry– A European Journal, 19, 15924-15932.

(39) Golden, J., Motea, E., Zhang, X., Choi, J.S., Feng, Y., Xu, Y., Lee, I., and Berdis, A.J. (2013) Development and Characterization of a Non-natural Nucleoside that Displays Anticancer Activity Against Solid Tumors. ACS Chem. Biol. 8, 2452-2465.
*** This manuscript describes the chemical synthesis and biological testing of several non-natural nucleosides against hematological and adherent cancer cell lines. Animal studies demonstrate efficacy and safety of these novel nucleoside analogs.

(38) Motea, E.A., Lee, I., and Berdis, A. J. (2013) Insights into the roles of desolvation and pi-electron interactions during DNA polymerization. ChemBioChem 14, 489-499.
*** This work compares the ability of high-fidelity and low-fidelity DNA polymerase to utilize non-natural nucleotides when replicating damaged DNA. The results of this study validate that our nucleotides can be used to distinguish between each class of DNA polyrase during translesion DNA synthesis.

(37) Devadoss, B., Lee, I. and Berdis, A. J. (2013) Spectroscopic analysis of polymerization and exonuclease proofreading by a high-fidelity DNA polymerase during translesion DNA synthesis. Biochimica et Biophysica Acta, 1834,34-45.

(36)Ahmed, M. F., Wan, Q., Jha, S, Motea, E., Berdis, A., and Dealwis, C. (2012) Evaluating the therapeutic potential of a non-natural nucleotide that inhibits human ribonucleotide reductase. Mol. Cancer Therapeutics 11, 2077-2086.
*** This manuscript demonstrates that our lead compound, 5-nitroindolyl-2’-deoxyribose (5-NIdR) can produce anti-cancer effects by inhibiting the activity of ribonucleotide reductase, the enzyme that converts rNDPs to dNDPs needed for DNA replication.

(35) Choi, J.S. and Berdis, A.J. (2012) Nucleoside transporters: biological insights and therapeutic applications. Future Med. Chem. 4, 1461-1478.

(34) Motea, E.A., Lee, I., and Berdis, A.J. (2012) A Non-natural nucleoside with combined therapeutic and diagnostic activities against leukemia. ACS Chem. Biol. 7, 9 88-998.
*** This manuscript describes cell-based studies examining the therapeutic and diagnostic activity of 5-Endosine. Results from this study demonstrate that 5-endosine functions as a unique theranostic agent that selectively targets acute lymphoblastic leukemia (ALL).
(33) Craig, S., Gao, L., Lee, I., Gray, T., and Berdis, A.J. (2012) Gold-containing indoles as anticancer agents that potentiate the cytotoxic effects of ionizing radiation. J. Med. Chem. 55,2437-2451.

(32) Motea, E.A., Lee, I., and Berdis, A.J. (2012) Development of a ‘clickable’ non-natural nucleotide to visualize the replication of non-instructional DNA lesions. Nucleic Acids Res. 40, 2357-2367.

*** This manuscript describes the chemical synthesis and in vitro testing of a novel non-natural nucleotide that functions as a diagnostic probe for the replication of an abasic site. This manuscript provides the scientific platform for our diagnostic kit portfolio.

(31) Chavarria, D., Ramos-Serrano, A., Hirao, I, and Berdis, A. J. (2011) Exploring the roles of nucleobase desolvation and shape complementary during the misreplication of O6-methylguanine. Journal of Molecular Biology 412, 325-339.

(30) Saunders, L., Devadoss, B., Raja, G.V., O’Connor, J., Su, S., Wozniak, D. Hassett, D. J., Berdis, A. J., and Sutton, M.D. (2011) Epistatic roles for Pseudomonas aeruginosa MutS and DinB in Coping with Reactive Oxygen Species-Induced DNA Damage. PloS ONE  6, e18824.

(29) Motea, E., Lee, I., and Berdis, A. J. (2011) Quantifying the contributions of desolvation and pi-electron stacking during translesion DNA synthesis. Nucleic Acids Research 39, 1623-1637.

(28) Berdis, A. J. (2010) DNA polymerases: Perfect enzymes for an imperfect world. Biochim. Biophys. Acta. 1804, 1029-1031.

(27) Zhang, X., Motea, E., and Berdis, A. J.  (2010) Replication of a non-Natural Nucleobase Provides Evidence for Asymmetric DNA Polymerization. Biochemistry 49, 3009-3023.

(26) Eng, K. and Berdis, A. J. (2010) A novel non-natural nucleoside that influences P-glycoprotein activity andmediates drug resistance. Biochemistry 49, 1640-1648.

(25) Eng, K., Scouten-Ponticelli, S.K., Sutton, M., and Berdis, A. J. (2010) Selective inhibition of DNA replicase assembly by a non-natural nucleotide:
Exploiting the structural diversity of ATP-binding sites. ACS Chem. Biol. 5, 183-194.

(25) Lee, I. and Berdis, A. J.  (2010) Non-natural nucleotides as probes for the mechanism and fidelity of DNA polymerases. Biochim Biophys Acta 1804, 1064-1080.

*** This manuscript provides a comprehensive review on the use of nucleotide analogs as mechanistic probes for DNA polymerase activity.

(24) Motea, E.A. and Berdis A. J. (2010) Terminal deoxynucleotidyl transferase: The story of a misguided DNA polymerase. Biochim Biophys Acta 1804, 1151-1166.

*** This article provides a comprehensive review of the biological role of terminal deoxynucleotidyl transferase (TdT) in normal and cancer cells. Particular emphasis is placed on how TdT is an important therapeutic target against acute lymphoblastic leukemia.

(23) Berdis, A. J. (2009) Mechanisms of DNA polymerases. Chemical Reviews 109, 2862-2879.

(22) Sheriff, A., Motea, E, Lee, I., and Berdis, A. J. (2008) Mechanism and dynamics of translesion DNA synthesis catalyzed by the Escherichia coli Klenow fragment. Biochemistry 47, 8527-8537.

(21) Berdis, A. J. (2008) DNA polymerases as therapeutic targets. Biochemistry 47, 8253-8260.
***Distinguished as one of the ten most accessed papers of 2008 in Biochemistry

(20) Vineyard, D., Zhang, X., Donnelly, A., Lee, I., and Berdis A J. (2007) Optimization of non-natural nucleotides for selective incorporation opposite damaged DNA. Org. Biomol. Chem. 5, 3623-3630.

(19) Devadoss B, Lee I, and Berdis A J. (2007) Enhancing the “A-rule” of translesion DNA synthesis: promutagenic DNA synthesis using modified nucleoside triphosphates. Biochemistry 46, 13752-13761.

(18) Devadoss, B. and Berdis, A. J.  (2007) Non-natural nucleotide analogs as probes of DNA polymerase activity. Current Chemical Biology 1, 241-264.

(17) Berdis, A. J. and McCutcheon, D. (2007) The use of non-natural nucleotides to probe template-independent DNA synthesis. ChemBioChem. 8, 1399-1408.
(16) Devadoss, B., Lee, I., and Berdis, A. J. (2007) Is a thymine dimer replicated via a transient abasic site intermediate? A comparative study using non-natural nucleotides. Biochemistry 46, 4486-4498.(15) Lee, I. and Berdis, A.  (2006) Fluorescent analysis of translesion DNA synthesis by using a novel, non-natural nucleotide analogue. ChemBioChem. 7, 1990-1997.

(14) Zhang, X., Donnelly, A., Lee, I., and Berdis, A. J. (2006) Rational attempts to optimize non-natural nucleotides for selective incorporation opposite an abasic site. Biochemistry 45, 13293-13303.

(13) Zhuang, Z., Berdis, A. J., and Benkovic, S. J. (2006) An alternative clamp loading pathway via T4 clamp loader gp44/62-DNA complex. Biochemistry 45, 7976-7989.

(12) Zhang, X., Zhou, X, Lee, I., and Berdis, A.J. (2005) Hydrophobicity, shape, and -electron density during translesion DNA synthesis. Journal of American Chemical Society, 128, 143-149.

(11) Zhang, X., Lee, I., and Berdis, A. J.(2005) The use of nonnatural nucleotides to probe the contributions of shape complementarity and pi-electron surface area during DNA polymerization. Biochemistry 44, 13101-13110.

(10) Zhang, X., Lee, I., and Berdis, A. J. (2005) A potential chemotherapeutic strategy for the selective inhibition of promutagenic DNA synthesis by nonnatural nucleotides. Biochemistry 44, 13111-13121.

(9) Ignatov, M., Berdis, A.J., and Barkley, M.D. (2005) Attenuation of DNA replication by HIV-1 reverse transcriptase near the central termination sequence. Biochemistry 44, 5346-5356.

(8) Zhuang, Z., Spiering, M. M., Berdis, A. J., Trakselis, M. A., and Benkovic, S. J. (2004) ‘Screw-cap’ clamp loader proteins that thread. Nature Structural and Molecular Biology 11, 580-581.

(7) Zhang, X., Lee, I., and Berdis, A. J. (2004) Evaluating the contributions of desolvation and base-stacking during translesion DNA replication. Org. Biomol. Chem. 2, 1703-1711.

(6) Reineks, E. Z. and Berdis, A. J. (2004) Evaluating the contribution of base stacking during translesion DNA replication. Biochemistry 43, 393-404.

(5) Reineks, E. and Berdis, A. J. (2003) Evaluating the effects of enhanced processivity and metal ions on translesion DNA replication catalyzed by the bacteriophage T4 DNA polymerase. Journal of Molecular Biology 326, 435-451.

(4) Trakselis, M., Berdis, A. J., and Benkovic, S. J. (2003) Examination of the role of the clamp-loader and ATP hydrolysis in the formation of the bacteriophage T4 polymerase holoenzyme. Journal of Molecular Biology 326, 435-451.

(3) Hays, H. and Berdis, A. J. (2002) Manganese substantially alters the dynamics of translesion DNA synthesis. Biochemistry 41, 4771-4778.

(2) Berdis, A. J., Stetor, S. R., LeGrice, S. F., and Barkley, M. D. (2001) Molecular mechanism of sequence specific termination of lentiviral replication. Biochemistry 40, 12140-12149.

(1) Berdis, A. J. (2001) Dynamics of translesion DNA synthesis catalyzed by the bacteriophage T4 exonuclease-deficient DNA polymerase. Biochemistry 40, 7180-7191.