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Dev P. Arya

Dev P. Arya Professor
Medicinal and Pharmaceutical Chemistry
Bio-Organic Chemistry

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

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.

Positions available in Arya Lab

  1. Postdoctoral position in nucleic acid biophysics. We are seeking a postdoctoral candidate with a published track record in conducting studies of molecular interactions of ligand binding to RNA/DNA using ITC, gel electrophoresis, NMR, computational studies, fluorescence, CD, and UV spectroscopy. The candidate must have strong written and verbal communication skills and be able to write professional reports and manuscripts.
  2. Postdoctoral position in nucleic acid chemistry. We are seeking a Ph.D. chemist who can perform the synthesis and purification of nucleic acids (natural and backbone modified) using solid phase chemistry. The candidate should be adept at making chemical modifications of nucleic acids. The candidate must have strong written and verbal communication skills and be able to write professional reports and manuscripts.
  3. Technician.    A bachelor or master’s level candidate with excellent organizational skills and a background in the fields of chemistry, genetics, microbiology, and/or cell biology. The candidate must have strong written and verbal communication skills and be able to write professional reports and manuscripts.

We are especially interested in candidates from diverse backgrounds, including those from groups that have been shown to be underrepresented in health-related research.

 

[Top]

Publications

[81-90]

  1. Chamberlin, J.; Story S.; Ranjan, N.; Chesser, G.; Arya, D.P. Gram-negative synergy and mechanism of action of alkynyl bisbenzimidazoles. Sci. Rep. 2019, 9, 1-19. doi 10.1038/s41598-019-48898-4.

https://www.nature.com/articles/s41598-019-48898-4

 

  1. Story, S.; Skriba, M. J.; Maiti, K.; Ranjan, N.; Degtyareva, N.; Green, K.D.; Khodaverdian, V.; Oyelere, A. K.; Garneau-Tsodikova, S.; Arya, D. P. “Synthesis, antimicrobial activity, attenuation of aminoglycoside resistance in MRSA, and ribosomal A-site binding of pyrene-neomycin conjugates.” European J Med Chem. 2019, 163, 381-393.

https://www.sciencedirect.com/science/article/pii/S0223523418309802

 

  1.  Kellish, P; Arya, D. P. “A deeper exploration of the relationship between the miR-27a and insulin resistance.” Non-coding RNA Invesig., 2018, 2, 1-5. doi: 10.21037/ncri.2018.09.06. http://dx.doi.org/10.21037/ncri.2018.09.06

 

  1. Watkins D., Maiti K., Arya D.P. Aminoglycoside Functionalization as a Tool for Targeting Nucleic Acids. In: Shank N. (eds) Non-Natural Nucleic Acids. 2019, 1973, 147-162. Print ISBN: 978-1-4939-9215-7.

https://doi.org/10.1007/978-1-4939-9216-4_9

 

  1. Ranjan, N.; Arya, D.P. A fluorescent aminosugar to rapidly screen and study RNA binders. Methods in Enzymology. 2019, 623, 291-314. https://doi.org/10.1016/bs.mie.2019.05.027

 

 [71-80]

  1. Ranjan, N.; Story, S.; Fulcrand, G.; Leng, F.; Ahmad, M.; King, A.; Sur, S.; Wang, W.; Tse-Dinh, Y.; Arya D. P. “Selective inhibition of E. coli RNA and DNA topoisomerase I by Hoechst 33258 derived mono and bisbenzimidazoles”. J. Med. Chem. 2017, 60(12):4904-4922.

http://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.7b00191

 

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

http://www.sciencedirect.com/science/article/pii/S0968089616307301

 

  1. Kamphan, A.; Gong, C.; Maiti, K.; Sur, S.; Traiphol, R.; Arya, D. P.; “Utilization of chromic polydiacetylene assemblies as a platform to probe specific binding between drug and RNA.” RSC Adv., 2017, 7, 41435-41443.

http://pubs.rsc.org/en/content/articlelanding/2017/ra/c7ra07178g#!divAbstract

 

  1. Thamban, C. N.; Shrestha S. K.; Ranjan, N.; Sharma, A.; Arya, D.P.; Garneau-Tsodikova S. ‘New Application of Neomycin B-Bisbenzimidazole Hybrids as Antifungal Agents.”

ACS Infect Dis. 2017 Dec 11. doi: 10.1021/acsinfecdis.7b00254

http://pubs.acs.org/doi/abs/10.1021/acsinfecdis.7b00254

 

  1. Ranjan, N.; Kellish, P.; King, A.; Arya, D. P. “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.

http://pubs.acs.org/doi/abs/10.1021/acs.biochem.7b00929

 

  1. Yang, C. H.; Liu, Z.; Dong, D.; Schacht, J.; Arya, D. P.; Sha, S. H. “Histone Deacetylase Inhibitors Are Protective in Acute but Not in Chronic Models of Ototoxicity.” Front Cell Neurosci. 2017, Oct 24;11:315.

https://www.frontiersin.org/articles/10.3389/fncel.2017.00315/full

 

  1. Gómez Ramos, L. M.; Degtyareva, N. N.; Kovacs, N.A.; Holguin, S. Y.; Jiang, L.; Petrov, A. S.; Biesiada, M.; Hu, M. Y.; Purzycka, K. J.; Arya, D. P.; Williams, L. D. “Eukaryotic Ribosomal Expansion Segments as Antimicrobial Targets.” Biochemistry. 2017 Oct 10;56(40):5288-5299.

http://pubs.acs.org/doi/abs/10.1021/acs.biochem.7b00703

 

  1. 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”. Med. Chem. Comm., 2018, 9, 1147-1154.

https://pubs.rsc.org/en/content/articlelanding/2018/md/c8md00092a#!divAbstract

 

 

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

https://www.sciencedirect.com/science/article/pii/S0040402018308093

 

  1. Sayantan, B.; Ranjan, N.; Arya, D.P. “An overview of recent advances in duplex DNA recognition by small molecules.” Beilstein J. Org. Chem. 2018, 14,1051–1086. doi:10.3762/bjoc.14.93.

https://www.beilstein-journals.org/bjoc/articles/14/93

 

[61-70]

  1. Watkins, D.; Kumar, S.; Green, K. D.; Arya, D. P.; 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.

http://aac.asm.org/content/59/7/3899.abstract

 

  1. Jiang, L.; Watkins, D; Jin, Y.; Gong, C.; King, A.; Washington, A. Z.; Green, K.D.; Garneau-Tsodikova, S.; Oyelere, A. K.; Arya, D. P. “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.

http://pubs.acs.org/doi/abs/10.1021/cb5010367

 

  1. Nahar, S.; Ranjan, N.; Ray, A.; Arya D. P.; Maiti, S. “Potent inhibition of miR-27a by neomycin–bisbenzimidazole conjugates.” Chem. Sci., 2015,6, 5837-5846. Edge Article.

http://pubs.rsc.org/en/content/articlelanding/2015/sc/c5sc01969a#!divAbstract

 

  1. Kumar, S.; Spano, M. N.; Arya, D. P. “Influence of linker length in Shape Recognition of B*DNA by Dimeric Aminoglycosides.” Bioorganic & Medicinal Chemistry, 2015, 23(13):3105.

http://www.sciencedirect.com/science/article/pii/S0968089615003983

 

  1. Watkins, D.; Jiang, L.; Nahar, S.; Maiti, S.; Arya, D. P. “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.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0144251

 

  1. Bhaduri, S.; Spano, M. N.; Arya, D. P. “Synthetic receptors for RNA recognition.”, 2017, in Comprehensive Supramolecular Chemistry II, vol 4: Bioinspired and Biomimetic Supramolecular Chemistry, p 71-113.

https://www.sciencedirect.com/science/article/pii/B9780124095472125508

 

 

  1. Jin, Y.; Watkins, D.; Degtyareva, N. N.; Green, K. D; Spano, M. N.; Garneau-Tsodikova, S.*; Arya, D. P. "Arginine-linked neomycin B dimers: synthesis, rRNA binding, and resistance enzyme activity." Med Chem Comm, 2016, Jan 1;7(1):164-169. Epub 2015 Oct 3.

http://pubs.rsc.org/en/Content/ArticleLanding/2016/MD/c5md00427f#!divAbstract

 

  1. Kumar S.; Ranjan, N; Kellish, P.; Gong, C.; Watkins, D.; Arya, D. P. “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.

http://pubs.rsc.org/-/content/articlelanding/2016/ob/c5ob02016f#!divAbstract

 

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

http://www.sciencedirect.com/science/article/pii/S0960894X16311246

 

  1. Degtyareva, N. N.; Gong, C.; Story, S.; Levinson, N. S.; Oyelere, A. K.; Green, K. D.; Garneau-Tsodikova, S.; Arya, D. P. “Antimicrobial Activity, AME Resistance, and A-Site Binding Studies of Anthraquinone-Neomycin Conjugates.” ACS Infect Dis. 2017 Mar 10;3(3):206-215

http://pubs.acs.org/doi/abs/10.1021/acsinfecdis.6b00176

 

[51-60]

 

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

http://www.sciencedirect.com/science/article/pii/S0960894X13009438

 

  1. King, A.; Watkins, D.; Kumar, S.; Ranjan, N.; Gong, C.; Whitlock, J.; 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]

http://aac.asm.org/content/57/10/4717.abstract

 

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

http://www.sciencedirect.com/science/article/pii/S0960894X13012365

 

  1. Ranjan, N.; Davis, E.; Xue, L.; Arya, D. P. “Dual recognition of the human telomeric G-quadruplex by a neomycin-anthraquinone conjugate.” Chemical Communications. 2013, 49(51), 5796-5798.

http://pubs.rsc.org/en/Content/ArticleLanding/2013/CC/c3cc42721h#!divAbstract

 

  1. 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.

https://www.ncbi.nlm.nih.gov/pubmed/24252993

 

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

https://www.ncbi.nlm.nih.gov/pubmed/24281844

 

  1. 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.

http://pubs.rsc.org/en/Content/ArticleLanding/2014/MD/c4md00165f#!divAbstract

 

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

http://pubs.rsc.org/en/Content/ArticleLanding/2014/MD/c4md00140k#!divAbstract

 

  1. Woo, C. M.; Ranjan, N.; Arya, D. P.; Herzon, S. B. “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.

https://www.ncbi.nlm.nih.gov/pubmed/25044348

 

  1. Willis, B.; Arya, D. P. “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

http://www.sciencedirect.com/science/article/pii/S0968089614000984

 

[41-50]

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

http://pubs.acs.org/doi/abs/10.1021/ar100113q

 

  1. 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.

http://pubs.acs.org/doi/abs/10.1021/bi1017304

 

  1. 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.

http://pubs.acs.org/doi/abs/10.1021/ja108118v

http://pubs.acs.org/doi/abs/10.1021/cen-v088n039.p050

 

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

http://www.sciencedirect.com/science/article/pii/S0960894X11008419

http://www.sciencedirect.com/science/article/pii/S0960894X11017306

 

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

http://pubs.acs.org/doi/abs/10.1021/bi201077h

 

  1. Hamilton, P.; Arya, D. P. "Natural Product DNA major groove binders", Natural Product Reviews. 2012, 29, 134-143.

http://pubs.rsc.org/en/content/articlelanding/2012/np/c1np00054c#!divAbstract

 

  1. Charles, I.; Davis, Erik; Arya, D. 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.

http://pubs.acs.org/doi/abs/10.1021/bi3004507

http://pubs.acs.org/doi/abs/10.1021/bi301245w

 

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

http://pubs.acs.org/doi/abs/10.1021/bi201657k

http://pubs.acs.org/doi/abs/10.1021/bi401088n

 

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

http://www.sciencedirect.com/science/article/pii/S0003269712006161

 

[31-40]

  1. 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.

 

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

http://pubs.acs.org/doi/abs/10.1021/ja076997o

http://pubs.acs.org/doi/abs/10.1021/jm701010a

 

  1. Shaw, N. N.; Xi, H.; Arya, D. 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.

http://www.sciencedirect.com/science/article/pii/S0960894X08005970

 

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

http://www.sciencedirect.com/science/article/pii/S0300908408001090

 

  1. Xi, H.; Gray, D.; Kumar, S.; Arya, D. P. “Molecular recognition of single-stranded RNA: Neomycin binding to poly(A)”; FEBS Letters, 2009. 583,13, 2269-2275.

http://onlinelibrary.wiley.com/doi/10.1016/j.febslet.2009.06.007/abstract

 

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

http://www.sciencedirect.com/science/article/pii/S0960894X09010300

 

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

http://www.sciencedirect.com/science/article/pii/S0300908410000489

 

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

http://pubs.acs.org/doi/abs/10.1021/bi9016796

 

  1. 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.

http://pubs.acs.org/doi/abs/10.1021/bi100071j

 

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

http://pubs.acs.org/doi/abs/10.1021/bi101517e

 

[21-30]

  1. Arya, D. P., Coffee Jr., R. L.; 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.

http://www.sciencedirect.com/science/article/pii/S0960894X0400887X

 

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

http://www.tandfonline.com/doi/abs/10.1081/CAR-200059973

 

  1. 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.

http://www.springer.com/us/book/9783540228356

 

  1. Xi, H.; 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).

http://www.ingentaconnect.com/contentone/ben/cmcaca/2005/00000005/00000004/art00003

 

  1. Napoli, S.; Carbone, G. M.; 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.

http://www.sciencedirect.com/science/article/pii/S0960894X05005202

 

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

http://www.eurekaselect.com/55718/article/major-groove-recognition-dna-carbohydrates

 

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

https://www.elsevier.com/books/advances-in-carbohydrate-chemistry-and-biochemistry/horton/978-0-12-007260-6

 

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

http://pubs.acs.org/doi/abs/10.1021/bi0609265

 

  1. 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.

 

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

http://pubs.acs.org/doi/abs/10.1021/bc060249r

 

 

[11-20]

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

http://www.sciencedirect.com/science/article/pii/S0960894X00003723

 

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

http://pubs.acs.org/doi/abs/10.1021/ja003052x

 

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

http://pubs.acs.org/doi/abs/10.1021/ja016481j

 

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

http://pubs.rsc.org/en/Content/ArticleLanding/2002/CC/b108171c#!divAbstract

 

  1. Arya, D. P.; Charles I.; Xue, L. “Synthesis of Aminoglycoside-Nucleic Acid Conjugates.” Med. Chem. Letts, 2002, 12, 9, 1259-1262.

Corrigendum to ‘Synthesis of Aminoglycoside–DNA Conjugates’ [Bioorg. Med. Chem. Lett. 12 (2002) 1259], Bioorg. Med.  Chem. Letts, 2003, Volume 13, Issue 9, Page 1607.

http://www.sciencedirect.com/science/article/pii/S0960894X02001579

http://www.sciencedirect.com/science/article/pii/S0960894X03001653

 

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

http://pubs.acs.org/doi/abs/10.1021/ja027765m

 17. Davis, W. C.; Venzie, J. L.; Coffee Jr., R.L.; Willis, B.: Arya, D. P.; Marcus, R. K. "Particle Beam Glow Discharge Mass Spectrometry: Spectral Characteristics of Nucleobases and Oligonucleotides." Commun. Mass Spectrom 2003, 17(15):1749-58.

https://www.ncbi.nlm.nih.gov/pubmed/12872280

 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.” Amer. Chem. Soc. 2003, 125, 8070-8071.

http://pubs.acs.org/doi/abs/10.1021/ja034241t

 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.” Amer. Chem. Soc. 2003, 10148-10149.

http://pubs.acs.org/doi/abs/10.1021/ja035117c

 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.” Amer. Chem. Soc. 2003, 12398-12399.

http://pubs.acs.org/doi/abs/10.1021/ja036742k

 

 

[1-10]

  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.

http://www.sciencedirect.com/science/article/pii/S0040403900614855

           

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

http://www.sciencedirect.com/science/article/pii/004040399500480Z

 

  1. 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.

http://pubs.acs.org/doi/abs/10.1021/jo00116a002

 

  1. 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.

http://www.sciencedirect.com/science/article/pii/0960894X9500193W

 

  1. 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. 

http://www.sciencedirect.com/science/article/pii/004040399500815T

 

  1. 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.

http://pubs.acs.org/doi/abs/10.1021/ja980629q

 

  1. 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.

http://pubs.acs.org/doi/abs/10.1021/ja9829416

 

  1. 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.

 

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

http://pubs.acs.org/doi/abs/10.1021/ja992871i 

 

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” Med. Chem. Letts 2000, 10, 8, 691-93.

http://www.sciencedirect.com/science/article/pii/S0960894X00000858

 

 

 

 

 

 

 

 

 

 

 


 

 

 

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