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Dr. Ambadas B. Rode
Associate Professor
  • PhD 2012, Kongju National University, Republic of Korea
  • JSPS Postdoc, Frontier Institute for Biomolecular Engineering Research, Konan University, Kobe, Japan
  • Research Assistant Professor Fellow, Frontier Institute for Biomolecular Engineering Research, Konan University, Kobe, Japan
  • Assistant Professor, Regional Centre for Biotechnology (2018-2023)
ab[dot]rode[at]rcb[dot]res[dot]in

RNA Engineering for Synthetic Biology and Drug Development

The ability to reprogram prokaryotic and eukaryotic cellular functions by modulating gene expression is central to advancing biotechnology and therapeutic applications. Synthetic biology has revolutionized the biomedical field by providing powerful genetic tools, among which synthetic riboswitches (engineered RNA regulatory elements) emerged as a promising tool. 

Synthetic riboswitches modulate gene expression in response to specific inducer molecules, mimicking the mechanism of natural riboswitches that alter RNA structure upon ligand binding. Synthetic riboswitches enable spatiotemporal control of gene expression, allowing precise and dynamic regulation of cellular responses with high specificity. 

Our lab focuses on the rational design and development of synthetic RNA switches that deliver robust and predictable regulatory functions for diverse synthetic biology applications.

Beyond synthetic biology, we also explore RNA sequence-structure-function relationships in bacterial and human non-coding RNAs (ncRNAs). These studies not only deepen our understanding of RNA-mediated regulation but also identify ncRNAs as promising therapeutic targets. 

Specifically, we design and synthesize small molecules to selectively interact with Bacterial ncRNAs for antibacterial therapies and Human ncRNAs implicated in cancer for anticancer therapies.

CURRENT FOCUS AREAS
•   Rational design and development of RNA switches as synthetic biology tool and their applications. 
•   Development of small molecules to target nucleic acid conformation for antibacterial and anticancer therapy.

  • JSPS Bridge Fellowship (2024) from Japan Society for the Promotion of Science (JSPS).
  • India EMBO Lecture Course Grant (2022) as an Organizer from European Molecular Biology Organization.
  • Ramalingaswami Re-entry Fellowship (2017).
  • Ramanujan Fellowship (2017).
  • JSPS Postdoctoral Fellowship (2015).
  • The Chemical Society of Japan (CSJ) Oral Presentation Award for the presentation at 97th Annual meeting of the chemical Society of Japan (2017).
  • ISNAC Outstanding Oral Presentation Award for the presentation at 43th International Symposium on Nucleic Acids Chemistry, Japan (2016).
  • ISNAC Outstanding Poster Presentation Award for the presentation at 40th International Symposium on Nucleic Acids Chemistry, Japan (Nov 2013).
  • SPARC Award at a Pharma Company (MNC) Pune, Maharashtra, India (Jan 2008).
  • S. Asthana, C. Suri, M. Kalia, A. Awasthi, A. Chande, A. Rode, S. Prajapat, S. Sadhu, R.Dalal, V. Bhardwaj, D. Ojha., m-Tor independent autophagy inducing small peptide and therapeutic uses thereof, Indian Patent Application No.: 202011007117, Feb-19-2020
  • S. Asthana, C. Suri, M. Kalia, A. Awasthi, A. Chande, A. Rode, S. Prajapat, S. Sadhu, R.Dalal, V. Bhardwaj, D. Ojha., AUTOPHAGY INDUCING PEPTIDES, International Patent Application No.: PCT/IN2021/050799, Feb-24-2022

Selected Publications

All Publications

  1. Kumar R, Singh R, das Chagas Almeida A, da Trindade Granato J, de Oliveira Lemos AS, Kumar K, Patil MT, da Silva AD, Rode AB, Coimbra ES, Salunke DB.Imidazo[1,2-a]pyrimidine as a New Antileishmanial Pharmacophore against Leishmania amazonensis Promastigotes and Amastigotes. ACS Omega. 2023 Oct 20;8(43):40613-40621. doi: 10.1021/acsomega.3c05441. eCollection 2023 Oct 31. PMID: 37929127
  2. Satange R, Jin P, Hou MH, Rode AB* (2023). Editorial: Non-canonical nucleic acid structures, functions and their applications for understanding human genetic diseases Front. Genet. 14:1188978.
  3. Gupta P, Khadake RM, Panja S, Shinde K, Rode AB* (2022). Alternative RNA Conformations: Companion or Combatant. Genes 13, 1930
  4. Gupta P, Ojha D, Nadimetla DN, Bhosale SV, Rode AB* (2022) Tetraphenylethene Derivatives Modulate the RNA Hairpin-G-quadruplex Conformational Equilibria in Proto-Oncogenes. ChemBioChem, e202200131
  5. Jadhav RW, Wagalgave SM, Kumbhar BV, Khadake RM, Rode AB, Bhosale SV , Bhosale SV*(2022). Aminoglycoside antibiotic kanamycin functionalized tetraphenylethylene molecular probe for highly selective detection of bovine serum albumin protein. Sci Rep., 11526
  6. Satange R, Rode AB, Hou M* (2022). Revisiting recent unusual drug-DNA complex structures: implications for cancer and neurological disease diagnostics and therapeutics. Bioorg Med Chem, 117094
  7. Pandey M, Ojha D, Bansal S, Rode AB*, Chawla G* (2021)From bench side to clinic: Potential and challenges of RNA vaccines and therapeutics in infectious diseases. Molecular Aspects of Medicine,101003
  8. Harale B, Kidwai S, Ojha D, Singh M, Chouhan D, Singh R, Khedkar V, Rode AB* (2021) Synthesis and evaluation of antimycobacterial activity of riboflavin derivatives. Bioorg Med Chem Lett. 48, 128236.
  9. Ojha D, Rode AB * (2019) Recent Advances in Aptamer Generation for Synthetic Biology Applications. Journal of Japan Society of Nucleic Acids Chemistry (JISNAC), 3:7-11
  10. Rode AB, Endoh T, Sugimoto N (2018) Crowding Shifts the Riboswitch Aptamer-FMN Recognition Mechanism from Conformational Selection to Induced Fit.Angew Chem Int Ed Engl. 57:6868
  11. Rode AB, Endoh T, Sugimoto N. (2016) tRNA Shifts the G-quadruplex-Hairpin Conformational Equilibrium in RNA towards the Hairpin Conformer. Angew Chem Int Ed Engl. 55:14319
  12. Endoh T, Rode AB, Takahashi S, Kataoka Y, Kuwahara M, Sugimoto N. (2016) Real-Time Monitoring of G-Quadruplex Formation during Transcription. Anal Chem 88:1989
  13. Rode AB, Endoh T, Sugimoto N. (2015) Tuning riboswitch-mediated gene regulation by rational control of aptamer ligand binding properties. Angew Chem Int Ed Engl. 54:909
  14. Rode AB, Endoh T, Sugimoto N. (2015) Key Tertiary Interactions in FMN Riboswitch Aptamers Required for Ligand Binding. Bull. Chem. Soc. 88: 948
  15. Rode AB, Endoh T, Tateishi KH, Takahashi S, Sugimoto N. (2013) Real-time monitoring of DNA hybridization kinetics on living cell surfaces. Chem Commun (Camb). 49:8446
  16. Rode AB, Kim J, Kim SH, Hong IS, (2012) A Highly Selective Chemodosimeter for the Rapid Detection of Hg2+ ions in Aqueous Media. Tetrahedron Lett. 20:2574
  17. Kim BM, Rode AB, Han EJ, Hong IS, Hong SH. (2012) 5-Phenylselenyl- and 5-methylselenyl-methyl-2'-deoxyuridine induce oxidative stress, DNA damage, and caspase-2-dependent apoptosis in cancer cells. Apoptosis. 17:216
  18. Rode AB, Kim BM, Park SH, Hong IS, Hong SH. (2011) Potent radiosensitizing agents: 5-methylselenyl- and 5-phenylselenyl-methyl-2'-deoxyuridine. Bioorg Med Chem Lett. 21:1154
  19. Rode AB, Thajudeen H, Chung KW, Kim YW, Hong IS (2011) Synthesis and Evaluation of Stearic Acid Derivatives as Cetane Number Improvers. Bull. Korean Chem. Soc. 32:1969
  20. Rode AB, Chung KW, Kim YW, Hong IS. (2010) Synthesis and Cetane-Improving Performance of 1, 2, 4, 5-Tetraoxane and 1, 2, 4, 5, 7, 8-Hexaoxonane Derivatives. Energy & fuels. 24:1639.
  21. Rode AB, Son SJ, Hong IS. (2010) An Efficient One-pot N-Acylation of Deoxy- and Ribo- cytidine Using Carboxylic Acids Activated in situ with 2-Chloro-4,6-dimethoxy-1,3,5-triazine. Bull. Korean Chem. Soc. 7:2064.
  22. Shinde SB, Rode AB, Dake SA, Bhosale DS, Pawar RP. (2010) An Expeditious Synthesis of Bioactive 4- Aryl-3, 4-Dihydropyrimidines Using Insitu Generated HCl. International Journal of Industrial Chemistry. 1:51.
  23. Dake SA, Kulkarni RS, Rode AB, Shinde PS, Ghumbre SK, Magarn RL, Pawar RP (2010) H2O2 /Phosphonium Ionic Liquid: An Efficient and Simple Approach for Benzyl Halides Oxidation. Lett. Org. Chem., 7, 491-494.
  24. Shinde PS, Shinde SS, Renge AS, Patil GH, Rode AB, Pawar RR (2009) An Efficient Synthesis of Raloxifene in Ionic Liquid: A Green Approach. Lett. Org. Chem. 6:10
  25. Sarda SR, Puri VA, Rode AB, Dalwale TN, Jadhav WN, Pawar RP (2007) Sulfated Tin Oxides: A Suitable Reagent for Synthesis of 2, 4-diphenyl-4, 6, 7, 8-tetrahydrochromen-5-one. ARKIVOC 16:251
Dr. Ambadas B. Rode
Associate Professor

Regional Centre for Biotechnology
NCR Biotech Science Cluster
3rd Milestone, Faridabad-Gurgaon Expressway
P.O. Box No. 3, Faridabad - 121 001
Haryana (NCR Delhi), India
E-mail: ab.rode at rcb dot res dot in
Phone: 91 129-2848788

no text ab[dot]rode[at]rcb[dot]res[dot]in
no text 91 129-2848788

Dr. Ambadas B. Rode