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Dev P. Arya

Dev P. Arya Professor
Bio-Organic and Medicinal Chemistry

Phone: (864) 656-1106
Office: 461 Hunter Laboratories
E-mail: dparya at

Research Interests | Publications 

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). He has served as the Program Chair (2004-2008), Chair-Elect (2009-2010) and Chair (2010-2011) of the ACS Division of Carbohydrate Chemistry.

Research Interests

The long term interest of our lab lies in the understanding,Chemistry Photo Arya Profile
design, and discovery of new motifs for the molecular recognition of biological macromolecules for development of novel antibiotics.  We are currently using techniques at the interface of chemical biology, biophysics, medicinal chemistry, small molecule design, structural biology, assay development, and screening technologies to explore nucleic acid and enzyme targets implicated in disease.  A few current examples are listed below. 

1.  Recognition of the major groove of DNA.  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 for regulation of transcription.   Similar tools are being applied to the recognition of other higher order DNA and RNA structures, such as triplexes and quadruplexes.

2.  Recognition of the bacterial ribosome.   We are developing novel biophysical assays, synthetic methods and library screening approaches to identify small molecules that bind specifically to the bacterial and fungal ribosomal RNA over the mammalian ribosomal RNA. Lead molecules are screened for antibacterial activity, uptake, and follow up ADMET studies.

3.  New targets for antibacterial drug development.  We are currently developing libraries of compounds that can target bacterial enzymes selectively over their human counterparts.  One such enzyme target under investigation is the bacterial Topoisomerase I.   

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, biophysics, 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,  nucleic acid biophysics, physical organic chemistry, biochemistry, microbiology, 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 other biophysicists, oncologists and infectious disease experts, as evident from our collaborative papers and patents.




 71.       Nihar Ranjan, Sandra Story, Geraldine Fulcrand, Fenfei Leng, Muzammil Ahmad, Ada King, Souvik Sur, Weidong Wang, Yuk-Ching Tse-Dinh and Dev P. Arya. “Selective inhibition of E. coli RNA and DNA topoisomerase I by Hoechst 33258 derived mono and bisbenzimidazoles”.  J. Med. Chem. 2017, Jun 22;60(12):4904-4922.

72.       Watkins D, Gong C, Kellish P, Arya DP, Probing A-form DNA: A fluorescent aminosugar probe and dual recognition by anthraquinone-neomycin conjugates 2017Bioorg Med Chem.Feb 15;25(4):1309-1319.

73.       Anothai Kamphan, Changjun Gong, Krishnagopal Maiti, Souvik Sur, Rakchart Traiphol and Dev P. Arya, Utilization of Chromic Polydiacetylene assemblies as a platform to probe specific binding between drug and RNA".RSC Adv., 2017, 7, 41435-41443.!divAbstract

74.       Thamban Chandrika N, Shrestha SK, Ranjan N, Sharma A, Arya DP, Garneau-Tsodikova S. New Application of Neomycin B-Bisbenzimidazole Hybrids as Antifungal Agents. ACS Infect Dis. 2017 Dec 11. doi: 10.1021/acsinfecdis.7b00254

 75.       Ranjan N, Kellish P, King A, Arya DP. Impact of Linker Length and Composition on Fragment Binding and Cell Permeation: Story of a Bisbenzimidazole Dye Fragment. Biochemistry. 2017 Dec 12;56(49):6434-6447.

 76.      Yang CH, Liu Z, Dong D, Schacht J, Arya D, Sha SH. Front Cell Neurosci. 2017 Oct 24;11:315. Histone Deacetylase Inhibitors Are Protective in Acute but Not in Chronic Models of Ototoxicity.

 77.      Gómez Ramos LM, Degtyareva NN, Kovacs NA, Holguin SY, Jiang L, Petrov AS, Biesiada M, Hu MY, Purzycka KJ, Arya DP, Williams LD. Eukaryotic Ribosomal Expansion Segments as Antimicrobial Targets. Biochemistry. 2017 Oct 10;56(40):5288-5299.

78.       Ghosh, A.; Degtyareva, N.; Kukielski, C.; Story, S.; Bhaduri, S.; Maiti, K.; Nahar, S.; Arya, D. P.*; Maiti, S. "Small Molecule Mediated Interference in miR-21 Biogenesis to Revert Epithelial to Messenchymal Transition". MedChemComm, 2018, 9, 1147-1154.!divAbstract

79.       Rapid solid-phase syntheses and biological activities of mono- and diamino acid peptidic-aminosugar library." Kukielski, C.; Degtyareva, N.; Bhaduri, S.; Maiti, K.; Story, S.; Arya, D.P. 2018Tetrahedron, vol 74, issue 33, 4418-4428.

80.       Sayantan Bhaduri, Nihar Ranjan and Dev P. Arya, An overview of recent advances in duplex DNA recognition by small molecules, Beilstein J. Org. Chem. 201814, 1051-1086. doi:10.3762/bjoc.14.93.



61.       Watkins D, Kumar S, Green KD, Arya DP, Garneau-Tsodikova S. Influence of linker length and composition on enzymatic activity and ribosomal binding of neomycin dimers. Antimicrob Agents Chemother. 2015 Jul;59(7):3899-905. doi: 10.1128/AAC.00861-15. Epub 2015 Apr 20. 

62.       Jiang L, Watkins D, Jin Y, Gong C, King A, Washington AZ, Green KD, Garneau-Tsodikova S, Oyelere AK, Arya DP. Rapid Synthesis, RNA Binding, and Antibacterial Screening of a Peptidic-Aminosugar (PA) Library. ACS Chem Biol. 2015 May 15;10(5):1278-89. PMID:25706406.

63.       Smita NaharNihar RanjanArjun RayDev P. Arya and Souvik Maiti. “Potent inhibition of miR-27a by neomycin–bisbenzimidazole conjugates.” Chem. Sci., 2015,6, 5837-5846. Edge Article.!divAbstract

64.       Sunil Kumar, Meredith Newby Spano, Dev P. Arya.  Influence of linker length in Shape Recognition of B*DNA by Dimeric Aminoglycosides,” Bioorganic & Medicinal Chemistry, 23(13):3105 2015.

65.       Watkins D, Jiang L, Nahar S, Maiti S, Arya DP. “A pH Sensitive High-Throughput Assay for miRNA Binding of a Peptide-Aminoglycoside (PA) Library.” PLoS One. 2015 Dec 11;10(12):e0144251. doi: 10.1371/journal.pone.0144251. eCollection 2015.

66.       Sayantan Bhaduri, Meredith Newby Spano, and Dev P. Arya, Synthetic receptors for RNA recognition, 2017, in Comprehensive Supramolecular Chemistry II, vol 4: Bioinspired and Biomimetic Supramolecular Chemistry, p 71-113.

67.       Yi Jin,a Derrick Watkins,b Natalya N. Degtyareva,b Keith D. Green,c Meredith N. Spano,b Sylvie Garneau-Tsodikova,c,* and Dev P. Arya" Arginine-linked neomycin B dimers: synthesis, rRNA binding, and resistance enzyme activity", MedChem Comm, 2016, Jan 1;7(1):164-169. Epub 2015 Oct 3.!divAbstract

68.       Kumar S, Ranjan N, Kellish P, Gong C, Watkins D, Arya DP. “ Multivalency in the recognition and antagonism of a HIV TAR RNA-TAT assembly using an aminoglycoside benzimidazole scaffold. Org Biomol Chem. 2016 Feb 14;14(6):2052-6.!divAbstract

69.       Ranjan, N and Arya, DP , Linker dependent intercalation of bisbenzimidazole (Hoechst 33258) derivatives in a RNA duplex, Bioorg Med Chem Lett. 2016 Dec 15;26(24):5989-5994.

70.       Degtyareva NN, Gong C, Story S, Levinson NS, Oyelere AK, Green KD, Garneau-Tsodikova S, Arya DP. Antimicrobial Activity, AME Resistance, and A-Site Binding Studies of Anthraquinone-Neomycin Conjugates. ACS Infect Dis. 2017 Mar 10;3(3):206-215



51.       N. Ranjan, D. Watkins, D. Appella,  and D.P. Arya, Recognition of HIV-TAR RNA using neomycin-benzimidazole conjugates.", Bioorg. Med.  Chem. Lett. 2013, Oct 15;23(20):5689-93. 

52.       King, A.; Watkins, D.; Kumar, S.; Ranjan, N.; Gong, C.; Whitlock, J. and Arya.   D.P. “Characterization of  Ribosomal Binding and Antibacterial Activities Using Two Orthogonal High Throughput Capable Screens”.  Antimicrobial Agents and Chemotherapy. 2013, Oct;57(10):4717-26. [PMCID: PMC3811423]

53.       N. Ranjan, D. Watkins and D.P. Arya, An assay for human telomeric G-quadruplex DNA binding drugs.", Bioorg. Med.  Chem. Lett. 2013, Dec 15;23(24):6695-9.

54.       Ranjan, Nihar; Davis, Erik; Xue, Liang; Arya, Dev P. Dual recognition of the human telomeric G-quadruplex by a neomycin-anthraquinone conjugate. Chemical Communications. 2013, 49(51), 5796-5798.!divAbstract

55.       Ranjan, N.; Arya, D.P. Targeting C-myc G-quadruplex: dual recognition by aminosugar-bisbenzimidazoles with varying linker lengths. Molecules, 2013, Nov 18;18(11):14228-40.

56.       Kumar, S.; Newby, M.; Arya, D.P.; Shape readout of B' form DNA by carbohydrates, Biopolymers. 2014, 101, 720-32, [PMCID: PMC4112085]

57.       Kellish, P.C., Kumar, S., Mack, T.S., Spano, M.N., Hennig, M., and Arya, D.P. “Multivalent amino sugars to recognize different TAR RNA conformations”, Med Chem Comm. 2014, Jun 1;5(6):816-825.!divAbstract

58.       King, A.; Kumar, S.; Ranjan, N.; Gong, C.; Leng, F; and Arya.   D.P. “Selective inhibition of bacterial topoisomerase I by alkynyl-bisbenzimidazoles”, Med. Chem. Commun. 2014, 5, 816-825. [PMCID: PMC4112416].!divAbstract 

59.       Woo CM, Ranjan N, Arya DP, Herzon SB. Analysis of diazofluorene DNA binding and damaging activity: DNA cleavage by a synthetic monomeric diazofluorene. Angew Chem Int Ed Engl. 2014 Aug 25;53(35):9325-8. 

60.       Willis B, Arya DP. Recognition of RNA duplex by a neomycin-Hoechst 33258 conjugate. Bioorg Med Chem. 2014 Apr 1;22(7):2327-32. doi: 10.1016/j.bmc.2014.02.003. Epub 2014 Feb 18. PMID: 24630691



41.       Arya D.P. "New Approaches to Recognition of Nucleic Acid Triple Helices", Acc. Chem. Res., 2011, 44 (2), pp 134–146.

42.       Xue, L; Ranjan, N; Arya, D. P. "Synthesis and spectroscopic studies of aminoglycoside (Neomycin)-Perylene conjugate binding to Human Telomeric DNA", Biochemistry. 2011, 50, 2838-2849.

43.       Kumar, S.; Xue, L.; Arya, D.P. "Neomycin-Neomycin Dimer: An All Carbohydrate Scaffold with High Affinity for AT Rich DNA Duplexes", J. Amer. Chem. Soc. 2011, 133, 7361-7375.

44.       Kumar, S. and Arya, D. P. "Recognition of HIV TAR RNA by aminosugars", Bioorg. Med.  Chem. Lett. 2011, 21, 4788-4792. 

45.       Xi, H., Davis, E.; Xue, L., Ranjan, N; Hyde-Volpe. D. and Arya, D. P. Thermodynamics of Nucleic Acid 'Shape readout' by aminosugars, 2011, Biochemistry, 50, 9088-9113.

46.       Hamilton, P. and Arya, D. P. "Natural Product DNA major groove binders", Natural Product Reviews. 2012, 29, 134-143.!divAbstract

47.       Charles, I.; Davis, Erik; Arya, Dev P. "Efficient Stabilization of Phosphodiester (PO), Phosphorothioate (PS), and 2'-O-Methoxy (2'-OMe) DNA·RNA Hybrid Duplexes by Amino Sugars. Biochemistry. 2012, 51(27), 5496-5505.

48.       S. Kumar, P. Kellish, W.E. Robinson Jr, D. Wang, D.H. Appella, D.P. Arya, Click Dimers To Target HIV TAR RNA Conformation, Biochemistry. 2012, 51 2331-2347.

50.       Watkins, D.; Norris, F.A.; Kumar, S.; and Arya. D.P.  “A Fluorescence Based Screen for Ribosome Binding Antibiotics”.  Analytical Biochemistry. 2013, 434(2):300-7.



31.       Arya, D. P.; Shaw, N.; Xi, H. “Novel targets for aminoglycosides.” In      Aminoglycoside Antibiotics: From Chemical Biology to Drug Discovery, Arya, Dev P.; Ed. John Wiley and Sons: New Jersey, 2007; pp 289-314.

32.       Arya, D.P, Editor.; “Aminoglycoside Antibiotics: From Chemical Biology to Drug Discovery” John Wiley & Sons, 2007.

33.       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.

34.       Shaw, N. N.; Arya, D. P. "Recognition of the unique structure of DNA:RNA hybrids." Biochimie 2008, 90 (7), 1026-1039.

35.     Xi, Hongjuan; Gray, David; Kumar, Sunil, et al. “Molecular recognition of single-     stranded RNA: Neomycin binding to poly(A)”; FEBS Letters, 2009. 583,13, 2269-2275. 

36.  Willis, B; Arya, DP; “Triple recognition of B-DNA”. Bioorg. Med. Chem. Lett. 2009, 19, 17; 4974-4979.

37.       Kumar, S., Xi, H., Micovic, L., and Arya, D. P. Calorimetric and Spectroscopic Studies of Aminoglycoside Binding to a DNA Triplex. Biochimie, 2010, 92, 5, 514-529.

38.    Willis, B., and Arya, D. P. Triple Recognition of B-DNA by a Neomycin-Hoechst 33258-Pyrene Conjugate. Biochemistry, 2010, 49, 452-469.

39.       Xue, L., Xi, H., Kumar, S., Gray, D., and Arya, D. P. Probing the Recognition Surface of a DNA Triplex: Synthesis and Binding of Neomycin-Intercalator Conjugates. Biochemistry, 2010, 49 (26), 5540-5552.

40.       Ranjan, N.; Andreasen, K; Kumar, S.; Hyde-Volpe. D. and Arya, D. P. Aminoglycoside binding to Oxytricha Nova Telomeric DNA Biochemistry. 2010, 49, 9891-9903.



21.       Arya, D. P., R. L. Coffee Jr and Xue L.   “From triplex to B-form duplex stabilization: reversal of target selectivity by aminoglycoside dimers “. Bioorg. Med. Chem. Letts, 2004, 14, 18, 4643-4646.

22.       Charles, I.; Arya, D. P. “Synthesis of Neomycin-DNA/Peptide Nucleic Acid conjugates” J. Carb. Chem. 2005, 24, 145-160.

23.       Arya, D. P. “Aminoglycoside-Nucleic Acid Interactions: The case for neomycin” in Top. Curr. Chem.  DNA Binders, Editors-Chaires, JB; Waring, M; 2005, 253, 149-178.

24.       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).

25.       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.

26.       Willis, B.; and Arya, D.P.; “Major groove recognition of DNA by carbohydrates”, Curr. Org. Chem., Carbohydrates in Drug Design, 2006, 10, 663-673.

27.       Willis, B.; Arya, D. P. “An Expanding view of aminoglycoside-Nucleic Acid Interactions” Adv. Carb. Chem. Biochem.  2006, vol 60, Chapter 6, 263-314.

28.       Willis, B.; Arya, D. P.; “Recognition of B-form DNA by neomycin-Hoechst 33258 conjugates” Biochemistry. 2006, 10217-10232.

29.       Arya, D. P.;Diazo and Diazonium DNA cleavage agents: Studies on Model systems and Natural product mechanism of action”, Top. Heterocyclic Antitumor Antibiotics, Series: Topics in Heterocyclic Chemistry , Lee, Moses (Ed.). 2006, Vol. 2.

30. Charles, I.; Hongjuan Xi, and Arya, D.P.; “Sequence-Specific Recognition of RNA by neomycin-DNA conjugates”, Bioconj. Chem., 2007, 18(1) pp 160 – 169.



11.       Arya, D. P.; R. Lane Coffee Jr.  “DNA Triple Helix Stabilization by Aminoglycoside Antibiotics” Bioorg. Med.  Chem. Letts, 2000, 10,17, 1897-1899.

12.       Arya, D. P.; R. Lane Coffee Jr.; Willis, B; Abramovitch, A. “ Aminoglycoside-Nucleic Acid Interactions: Remarkable Stabilization of DNA & RNA Triple Helices by Neomycin”. J. Amer. Chem. Soc, 2001; 123(23); 5385-5395.

13.       Arya, D. P.; Coffee, R. L., Jr.; Charles, I. "Neomycin-Induced Hybrid Triplex Formation" J. Amer. Chem. Soc. 2001, 123, 11093-11094.

14.       Xue, L.; Charles, I.; Arya, D. P. "Pyrene–Neomycin Conjugate: Dual Recognition of a DNA Triple Helix" Chemical Communications 2002, 70-71.!divAbstract

15.       Arya, D. P.; I. Charles and Liang Xue.; Synthesis of Aminoglycoside-Nucleic Acid Conjugates, Bioorg. Med.  Chem. Letts, 2002, 12, 9, 1259-1262Corrigendum to ‘Synthesis of Aminoglycoside–DNA Conjugates’ [Bioorg. Med. Chem. Lett. 12 (2002) 1259], Bioorg. Med.  Chem. Letts, 2003, Volume 13, Issue 9, Page 1607.

16.       Arya, D. P.; R. Lane Coffee Jr.; Charles, I.; Willis, B; Micovic, L.; Neomycin binding to triplex Watson-Hoogsteen Groove-A Model, J. Amer. Chem. Soc. 2003, 125, 3733-3744., also see C&E News, “Triplex Selective Groove Binder”2003, March 24, p26.

17.       W. Clay Davis, Jacob L. Venzie, R. Lane Coffee, Jr., Bert Willis, Dev P. Arya, and R. Kenneth Marcus, "Particle Beam Glow Discharge Mass Spectrometry: Spectral Characteristics of Nucleobases and Oligonucleotides", Rapid. Commun. Mass Spectrom 2003, 17(15):1749-58.

18.       Arya, D. P.; Xue, L.; and Tennant, P.; Combining the Best in Triplex Recognition: Synthesis and Nucleic Acid Binding of a BQQ-Neomycin Conjugate.  J. Amer. Chem. Soc. 2003, 125, 8070-8071.

19.       Arya, D. P.; Xue, L.; and Bert Willis. “Aminoglycoside (Neomycin) Preference is for A-form Nucleic Acids, not just RNA: Results from a Competition Dialysis Study” J. Amer. Chem. Soc. 2003, 10148-10149.

20.       Arya, D. P. and Bert Willis.  “Reaching into the major groove of B-DNA, Synthesis and Nucleic Acid Binding of a neomycin-Hoechst 33258 conjugate” J. Amer. Chem. Soc. 2003, 12398-12399.

1.       Arya, D. P.; Warner, P. M.; Jebaratnam, D. J. “Development of New DNA Binding and Cleaving Molecules: Design, Synthesis and Activity of a Bisdiazonium Salt.”Tetrahedron  Lett. 1993, 34, 7823-7826.

2.       Jebaratnam, D. J.; Kugabalasooriar, S.; Chen, H.; Arya, D. P. " Azoester compounds for inducing DNA cleavage under physiological conditions."     Tetrahedron Lett. 1995, 36, 3123.

3.       Arya, D. P.; Jebaratnam, D. J. " DNA cleaving activity of 9 - diazo fluorenones and diaryl diazomethanes: Implications for the mode of action of Kinamycin antibiotics." J. Org. Chem. 1995, 60, 3268. 

4.       Jebaratnam, D. J.; Arya, D. P.; Chen, H.; Kugabalasooriar, S.; Vo, D."A  single precursor  approach  to  new  DNA cleaving  and  crosslinking  agents." Bioog. Med. Chem. Lett. 1995, 5, 1191.

5.       Arya, D. P.; Jebaratnam, D. J. “Towards  the  development  of  non-enediyne approaches  for  mimicking  enediyne  chemistry: Design, synthesis  and  activity  of  a  1,4-bisdiazonium  compound."Tetrahedron Lett. 1995, 36, 4369.

6.       Arya, D. P.; Bruice, T. C. “Replacement of the Negative Phosphodiester Linkages of DNA by Positive S-Methyl Thiourea Linkers; A Novel Approach to Putative Antisense Agents” J. Amer. Chem. Soc. 1998,120, 6619-6620.

7.       Arya, D. P.; Bruice, T. C. “Positively Charged DeoxyNucleic MethylThioureas: Synthesis and Binding Properties of Pentameric Thymidyl DeoxyNucleic Methylthiourea” J. Amer. Chem. Soc. 1998, 120, 12,419 -12,427.

8.       Arya, D. P.; Bruice, T. C. “ Kinetics and thermodynamics of pentameric thymidyl DNmt binding to short strand DNA homooligomers.” Proc. Natl. Acad. Sci. USA. 1999, 96, 4384-4389.

9.       Arya, D. P.; Bruice, T. C. “Fidelity of deoxynucleic S-methythiourea (DNmt) binding to DNA oligomers: Influence of C mismatches”. J. Amer. Chem. Soc, 1999; 121(46); 10680-10684.

10.       Arya, D. P.; Bruice, T. C. “Solid-phase synthesis of oligomeric deoxynucleic-thiourea (DNT) and deoxynucleic S-methylthiourea (DNmt): a neutral/polycationic analogue of DNA” Bioorg. Med. Chem. Letts 2000, 10, 8, 691-93.