Dev P. Arya
Associate Professor
Bio-Organic and Medicinal Chemistry
Phone: (864) 656-1106
Office: 461 Hunter Laboratories
E-mail: dparya@clemson.edu
Research Interests | Publications | Other Items (Documents, Links, etc.)
Dr. Arya earned his B.Sc. (chemistry honors program) from St. Stephen’s College, Delhi; and Ph.D. (Bioorganic Chemistry) from Northeastern University, Boston. After spending his postdoctoral years in the labs of Prof. T. C. Bruice (UC Santa Barbara), he joined the faculty at Clemson University. Dr. Arya is a recipient of a National Science Foundation CAREER Award(2002) and the ACS Horace S. Isbell Award of the Division of Carbohydrate Chemistry (2007).
Research Interests
The long term interest of our lab lies in the
understanding, design, and discovery of new
motifs for the molecular recognition of
biological
macromolecules. An example of current focus
of the laboratory is to understand the features
that differentiate B-form from A-form DNA and
use this knowledge to discover and design
molecules that can specifically recognize
A-and B-form DNA. Results obtained are
expected to lead to a new pharmacophore
for major grooves of A and B-form-DNA
recognition that can be further developed to
obtain DNA specific molecules with higher
affinities and specificities. Minor groove
recognition of DNA was driven by the
structures of polyamide-DNA complexes solved during the 80s. We expect that a similar characterization of a major groove specific ligand will complete an important missing link in the goal of major groove DNA recognition by small molecules leading to the development of more sequence-specific and higher affinity molecules. Similar tools are being applied to the recognition of higher order DNA and RNA structures, such as triplexes and quadruplexes.
The laboratory is equipped to conduct synthesis, physical and structural studies of natural and designed conjugates that are capable of binding to nucleic acids and proteins. These studies are important to both fundamental understanding of macromolecule recognition and to drug development. Based on the information gained from fundamental studies of molecular recognition and supramolecular chemistry, new drug analogues can be synthesized to exhibit altered binding properties with desired biological effects. Ongoing projects combine areas of synthetic organic chemistry, physical organic chemistry, biochemistry, pharmacology, and molecular and cell biology. The interdisciplinary nature of these projects allows students to develop a strong basis for future research. The lab maintains active collaborations with biophysicists, oncologists and infectious disease experts.
[Top]
Publications
[25] Willis, B; Arya, DP; “Triple recognition of B-DNA”. Bioorg. Med. Chem. Lett. Volume: 19, Issue:17; Pages: 4974-4979.
[24] Xi, Hongjuan; Gray, David; Kumar, Sunil, et al. “Molecular recognition of single-stranded RNA: Neomycin binding to poly(A)”; FEBS Letters, Volume: 583, Issue: 13, Pages: 2269-2275.
[23] Shaw, N. N.; Xi, H.; Arya, Dev P. "Molecular recognition of a DNA:RNA hybrid: Sub-nanomolar binding by a neomycin-methidium conjugate." Bioorg. Med. Chem. Lett. 2008, 18(14), 4142-4145.
[22] Shaw, N. N.; Arya, D. P. "Recognition of the unique structure of DNA:RNA hybrids." Biochimie 2008, 90(7), 1026-1039.
[21] Aminoglycoside Antibiotics: From Chemical Biology to Drug Discovery. Arya, Dev P.; Editor. John Wiley and Sons, 2007. http://www.wiley.com/WileyCDA/WileyTitle/productCd-047174302X.html
[20] Charles, Irudayasamy; Xi, Hongjuan; Arya, Dev P. “Sequence-Specific Targeting of RNA with an Oligonucleotide-Neomycin Conjugate.” Bioconjugate Chemistry 2007, 18(1), 160-169. [PDF]
[19] Arya, D.P., Lee, Moses (Ed.) 2006 “Topics in Heterocyclic Chemistry (vol 2): Heterocyclic Antitumor Antibiotics.” Springer, New York.
[18] Willis, Bert; Arya, Dev P. “Recognition of B-DNA by Neomycin-Hoechst 33258 Conjugates.” Biochemistry 2006, 45(34), 10217-10232. [PDF]
[17] Willis, Bert; Arya, Dev P. “Major groove recognition of DNA by carbohydrates.” Current Organic Chemistry 2006, 10(6), 663-673.
[16] Napoli, S., Carbone, GM, Catapano, C., Shaw, N, Arya, D. P.; “Neomycin improves cationic lipid-mediated transfection of DNA in human cells”. Bioorg. Med.Chem.Letters. 2005, 15, 3467–3469.
[15] Xi, H.; and Arya, D.P.; “Recognition of triplex structures by Aminoglycosides”, Current Medicinal Chemistry, Aniticancer agents, an issue dedicated to the late Claude Helene, 2005, vol. 5, no. 4, pp. 327-338(12).
[14] Willis, B.; Arya, D. P. “An Expanding view of aminoglycoside-Nucleic Acid Interactions” Adv. Carb. Chem. Biochem. 2006, 60, 251-302.
[13] Charles, I.; Arya, D. P. “Synthesis of Neomycin-DNA/Peptide Nucleic Acid conjugates” J. Carb. Chem. 2005, 24, 145-160.
[12] Arya, D. P. “Aminoglycoside-Nucleic Acid Interactions: The case for neomycin” in Top. Curr. Chem. DNA Binders, Editors-Chaires, JB and Waring, M; 2005, 253, 149-178. [PDF]
[11] Arya, D. P.; Coffee, R. L.; Xue, L. From triplex to B-form duplex stabilization: reversal of target selectivity by aminoglycoside dimers. Bioorganic & Medicinal Chemistry Letters 2004, 14, 4643-4646.
[10] Arya, D. P.; Willis, B. Reaching into the major groove of B-DNA: Synthesis and nucleic acid binding of a neomycin-Hoechst 33258 conjugate. Journal of the American Chemical Society 2003, 125, 12398-12399. [PDF]
[9] Arya, D. P.; Xue, L.; Willis, B. Aminoglycoside (Neomycin) Preference Is for A-Form Nucleic Acids, Not Just RNA: Results from a Competition Dialysis Study. Journal of the American Chemical Society 2003, 125, 10148-10149.
[PDF]
[8] Davis, W. C.; Venzie, J. L.; Willis, B.; Coffee, R. L., Jr.; Arya, D. P. et al. Particle beam glow discharge mass spectrometry: Spectral characteristics of nucleobases. Rapid Communications in Mass Spectrometry 2003, 17, 1749-1758.
[7] Arya, D. P.; Xue, L.; Tennant, P. Combining the best in triplex recognition: Synthesis and nucleic acid binding of a BQQ-neomycin conjugate. Journal of the American Chemical Society 2003, 125, 8070-8071. [PDF]
[6] Arya, D. P.; Micovic, L.; Charles, I.; Coffee, R. L., Jr.; Willis, B. et al. Neomycin Binding to Watson-Hoogsteen (W-H) DNA Triplex Groove: A Model. Journal of the American Chemical Society 2003, 125, 3733-3744.
[PDF1][PDF2]
[5] Xue, L.; Charles, I.; Arya, D. P. Pyrene-neomycin conjugate: dual recognition of a DNA triple helix. Chemical Communications (Cambridge, United Kingdom) 2002, 70-71. [PDF]
[4] Charles, I.; Xue, L.; Arya, D. P. Synthesis of aminoglycoside-DNA conjugates. Bioorganic & Medicinal Chemistry Letters 2002, 12, 1259-1262.
[3] Arya, D. P.; Coffee, R. L., Jr.; Charles, I. Neomycin-Induced Hybrid Triplex Formation. Journal of the American Chemical Society 2001, 123, 11093-11094. [PDF]
[2] Arya, D. P.; Coffee, R. L., Jr.; Willis, B.; Abramovitch, A. I. Aminoglycoside-Nucleic Acid Interactions: Remarkable Stabilization of DNA and RNA Triple Helices by Neomycin. Journal of the American Chemical Society 2001, 123, 5385-5395.
[1] Arya, D. P.; Coffee, R. L. DNA triple helix stabilization by aminoglycoside antibiotics. Bioorganic & Medicinal Chemistry Letters 2000, 10, 1897-1899.
[Top]