CSIR-Central Leather Research Institute
Dr.V.G. Vaidyanathan
Principal Scientist
Academic Qualifications
    PhD
Contact Details
Dr.V.G. Vaidyanathan
Principal Scientist
& AcSIR Coordinator - CSIR-CLRI
Advanced Materials
CSIR-Central Leather Research Institute
Adyar, Chennai – 600 020
e-mail: vaidyanathan@clri.res.in,
Phone:91 44 24437142


Qualification
 
  • Ph.D., University of Madras, India (2005) Dissertation entitled “Role of Ligand Structure in the Interaction of Chromium(III) Complexes with DNA”, Advisor: Dr. Balachandran Unni Nair, Central Leather Research Institute, Adyar, Chennai

  • M.Sc (Chemistry) University of Madras (2000)

  • B.Sc (Chemistry) University of Madras (1998)

Area of interests
 
  • Bioinorganic Chemistry
  • Biophysics.
  • Chemical Carcinogenesis
Professional Experience
 

Associate Professor, Academy of Scientific and Innovative Research (AcSIR)
Subjects Covered: Stereochemistry of Organic Compounds, Drug Discovery

 

Faculty Member (Hon), Anna University
Subjects Covered: Instrument methods of analysis

  Ramanujan Fellow, CSIR-Central Leather Research Institute, “Investigation of Chromium(III)-DNA adducts in DNA Replication/Repair Machinery: Role of Ligand Structure in Chromium (III) Toxicity” -
April 2012 to current
  Visiting Professor, Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, USA -
Sep 13 to Nov 13
 

Postdoctoral Research Fellow, Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Project entitled: “Understanding the Sequence context of aminofluorene-adducted DNA at the Replication Fork By Biochemical and Biophysical Approaches” - Sep 08 to Apr 12

  Postdoctoral Research Associate, Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Worked on the project entitled: “Development of Chemical Strategies to Probe Carcinogenesis Mechanisms” -
Sep 05 to Aug 08
Research Interest
 

(i) A High Throughput Screening Kit for COVID-19

The ongoing outbreak of the pandemic disease COVID-19 poses serious challenges to the public as it spreads throughout the world. So far, more than 4.5 million people affected and 300000 fatalities are reported till date. The screening kit to diagnose COVID-19 currently available is based on PCR and consumes much longer time. Further, the diagnosis is required at different stages and multiple times to know whether the patient is infected/recovered from the virus and incurs high cost. To overcome these issues, here we propose screening kit based on DNA aptamer that can bind specifically to RBD of spike protein present in SARS-Cov-2 virus. The rationale to target the RBD region of spike protein is that in comparison to other acute respiratory diseases such as SARS and MERS, the sequencing data shows that RBD in COVID-19 differentiates between the coronavirus genome and has a high binding affinity to angiotensin-converting enzyme (ACE-2).

(ii) DNA Aptamer Conjugated Nanoprobes for REACH Chemicals Recognition

The stringent regulations by European Union and other monitoring agencies on application of chemicals in leather and textile industries keep increasing constantly. This leads to increasing labour intense procedures that require strict compliance to the regulations for analysing the unwanted or toxic chemicals. High cost instruments such as GC-MS, ICP-MS and UPLC-MS etc are currently employed for analysis. Moreover, rigorous attention is required for development of protocol for each chemical analysis. This leads to increasing costs on manpower, maintenance and chemical reagents. Overall, the chemical analysis not only becomes more tedious but also an expensive endeavour. To overcome these issues, a greener and simplistic solution needs to be developed. In this regard, DNA aptamers will be a viable alternative for the above-mentioned methods. DNA aptamers are single-stranded oligonucleotides that bind specifically with target molecule with high affinity. Aptamers for specific targets are identifiable using Systematic Evolution of Ligands by Exponential enrichment (SELEX) methodology. These aptamers are stable compared to RNA aptamers and most widely used in the biological processes. However, studies on small molecules such as REACH chemicals or any other molecules with less than 1000 Da molecular weight are still in primitive stage. Here, our goal is to screen DNA aptamers and conjugate with nanoparticles and study its optimal sensitivity for various banned REACH chemicals.

(iii) Development of transition metal complexes as probes for detecting different DNA adducts

Transition metal complexes have been extensively studied as probes for DNA structures, photodynamic therapy and anticancer agents. However, only few studies have been reported on transition metal complexes as probes for the damaged site viz., abasic sites. The classical hypothesis of the DNA-adduct chemistry is that each DNA adduct adopts different conformations and each adduct conformation leads to multiple different mutations. The majority of toxicology research has been focused on determining the DNA adduct conformation using NMR as a key tool. Proposed models of binding of L-[Ru(phen)2(dppz)]2+ to AAF-dG adduct. (a) stacked and (b) major groove

The disadvantage of this method is (i) it requires large quantity of samples, (ii) time consuming and (iii) complexity in structural analysis. To overcome these drawbacks, we are interested in developing transition metal complexes as a tool to identify the conformations of the DNA adduct in a sequence dependent context.

(iv) Understanding the role of Cr(III) adducts in replication and repair machinery at molecular level

Chromium has been extensively used in dyes, chrome plating and leather industries. Chromium in +3 oxidation state is susceptible to form different DNA adducts including DNA interstrand crosslinks (ICLs), DNA-protein crosslinks (DPCs) as well as with DNA phosphates.  Though various reports have shown that DPCs exhibit different mutagenicity, the detailed mechanistic pathway is not yet ascertain. Our hypothesis is that the nature of adducts influence DNA replication fork progression and repair pathway in a sequence dependent manner. We use both biophysical as well as biochemical techniques to understand the mechanistic pathway.  


Professional Affiliations
  Member of American Chemical Society (ACS) / Division of Chemical Toxicology
 

Life Member of Chemical Research Society of India (CRSI)

 

Lifetime Member of Indian Society of Nanomedicine (ISNM)

Research Grant
 

As Principal Investigator (Total Grants Received: Rs. 14.6 millions)

1. Project Title: Paper-Based Plasmonic Aptamer Linked Immobilized Sorbent Assay (pALISA) for Screening COVID-19 Disease
Funded by: Science and Engineering Research Board (SERB)
Project Cost: Rs. 1.2 million
Duration: July 2020-Dec 2020

2. Project Title: A High Throughput Screening Kit for COVID-19
Funded by: Council of Scientific and Industrial Research (CSIR)
Project Cost: Rs. 2.5 million
Duration: May 2020-April 2021
 
3. Project Title: DNA aptamers based nanoprobes for REACH chemicals recognition
Funded by: DST Nanomission
Project Cost: Rs. 3.4 million
Duration: Jan 2020-Dec 2022

4. Project Title: Metal Complexes based Probes for Arylamine modified biomolecules
Funded by: Science and Engineering Research Board(SERB)
Project Cost: Rs. 2.3 million 
Duration: June 2017-May 2020

5. Project Title: Investigation of Chromium(III)-DNA adducts in DNA Replication/Repair Machinery: Role of Ligand Structure in Chromium (III) Toxicity
Funded by: Science and Engineering Research Board (SERB)
Project Cost: Rs. 5.2 million
Duration: April 2012-Mar 2017 

As Co-Principal Investigator (Co-PI)

1. Project Title: First Principle Design and Development of Multifunctional and van der Waals and Non-van der Waals solids
(PI: Dr. V.Subramanian)
Funded by: Science and Engineering Research Board (SERB)
Amount: Rs. 3.6 million
Duration: Feb 2020-Jan 2023

2. Project Title: Designing an Admittance based experimental tool to evaluate mechanical properties and stability of supported lipid bilayers , liposomes, biological cell membranes
(PI: Dr. Aruna Dhathathreyan)
Funded by: Science and Engineering Research Board (SERB)
Amount: Rs. 2.9 million
Duration: June 2018-May 2021

3. Project Title: Understanding collagen- functionalized metal/metal oxide nanostructure interactions for tuning tissue engineering applications
(PI: Dr. K.J. Sreeram)
Funded by: Funded by: Department of Biotechnology (DBT)
Amount: Rs. 2.5 million
Duration: Nov 2014-Oct 2017

Book Chapter
  Recent Advances in Gene Expression and Regulation
Title: Chromium (III): Bio-significant or Bio-toxic?
Authored by: Yamini Asthana, V.G. Vaidyanathan and B.U. Nair
Published by: Nova Publishers (2013)
Patent Filed
 

TITLE: Platinum(II) complex as Cell Staining Agent

INVENTORS:
V.G. Vaidyanathan*
V.M. Manikandamathavan
M.S.  Kiran
B.U. Nair

   

Complete List of Publications

  1. P. David Dayanidhi, T. Nandhini and V.G. Vaidyanathan (2020)
    Selective Recognition of Conformation-Specific Arylamine-DNA adduct in Frameshift Model by [Ru(phen)2(dppz)]2+
    Chem. Res. Toxicol., 3, 800-805

  2. P. David Dayanidhi and V.G. Vaidyanathan (2020)
    Switch-On Effect on Conformation-Specific Arylamine-DNA adduct by Cyclometalated Ir(III) complexes
    J. Biol. Inorg. Chem., 25, 305-310.

  3. D. Madhumitha, V.G. Vaidyanathan and D. Aruna (2020)
    Plasticity or elasticity? Relating elastic moduli with secondary structural features of mixed films of polypeptides at air/fluid and fluid/solid interfaces
    Biophys. Chem.258, 106329

  4. P. David Dayanidhi, M. Pinky Rozaria and V.G. Vaidyanathan* (2019)
    Selective Recognition of DNA Defects By Cyclometalated Ir(III) complexes”,
    Dalton Trans., DOI: 10.1039/C9DT01225G.

  5. D. Madhumitha, A. Bruntha, V.G. Vaidyanathan, N. Bhargavi, K. J. Sreeram and D. Aruna (2019)
     "Elasitc Compliance as a tool to understand Hofmeister ion specific effect in DMPC liposomes",
    Biophys. Chem., 240, 15-24.

  6. T. Nandhini, J. Indumathi, R. Mukund, V.G. Vaidyanathan* and B.U. Nair (2019)
    Photocrosslinking of Collagen using Ru(II)-polypyridyl complex functionalized Gold Nanoparticles
    Spectrochim. Acta A: Mol. Biomol. Spectrosc. 215, 196-202.

  7. T. Nandhini, V.G. Vaidyanathan and B.U. Nair (2018)
    Conformation Specific Binding of [Ru(phen)2(dppz)]2+ with Mono- and Cluster Arylamine-DNA Adducts,
    ChemistrySelect, 3, 11152-11159

  8. V.G. Vaidyanathan, D. Madhumitha, T. Nandhini and D. Aruna (2018)
    Elastic compliance of fibrillar assemblies in type I collagen
    Biophys. Chem., 240, 15-24

  9. J. Dhanya, B. Babu and V.G. Vaidyanathan* (2017)
    Effect of Chromium(III) gallate on the stabilization of collagen
    Int. J. Biol. Macromol., In press

  10. T. Nandhini, V.G. Vaidyanathan* and B.U. Nair (2016)
    Effect of Conformation of the arylamine-DNA adduct on the sensitivity of [Ru(phen)2(dppz)]2+ complex
    Inorg. Chem. Commun., 73, 64

  11. B. Babu, T. Nandhini, V.G. Vaidyanathan* and B.U. Nair (2016)
    Studies on interaction of Cr(III) polypyridyl complexes with DNA
    Inorg. Chem. Commun., 73, 124-128

  12. T. Nandhini, K.R. Anju, V. M. Manikandamathavan, V.G. Vaidyanathan* and B.U. Nair (2015)
    Interaction of Ru(II) polypyridyl complexes with DNA mismatches and abasic sites
    Dalton Trans.,44, 9044-9051

  13. V.M. Manikandamathavan, N. Duraipandy, M.S. Kiran, V.G. Vaidyanathan* and B.U. Nair (2015)
    A new Pt(II) complex for bioimaging applications
    RSC Adv.,5, 24877–24885

  14. L. Xu^, V.G. Vaidyanathan^ and B.P. Cho^ (2014)
    Real-time surface plasmon resonance study of biomolecular interactions between polymerase and bulky mutagenic lesions
    Chem. Res. Toxicol. 27, 1796-1807 (^Authors contributed equally)

  15. V.Jain, V.G. Vaidyanathan, S. Patnaik, S. Gopal and B.P. Cho (2014)
    Conformational insights into the lesion and sequence effects for arylamine-induced translesion DNA synthesis: 19F NMR, Surface plasmon resonance and primer kinetic studies
    Biochemistry, 53, 4059-4071

  16. S. Rajalakshmi, M.S. Kiran, V.G. Vaidyanathan, E.R. Azhagiya Singam, V. Subramanian and B.U.Nair (2013)
    Investigation of nuclease, protelytic and anti-proliferative effects of copper(II) complexes of thiophenylmethanamine derivatives
    Eur. J. Med. Chem., 70, 280-293

  17. V.G. Vaidyanathan, F. Liang, W. Beard, D.D. Shock, S.H. Wilson and B.P. Cho (2013)
    Insights into the Conformation of Aminofluorene-dG Adduct in a DNA Polymerase Active Site
    J Biol. Chem. 288, 23573-23585

  18. J.G. Dinorah, L. Li, V.G. Vaidyanathan, R. King, B. P. Cho, D. R. Worthen, C.O. Chichester III and N.P. Seeram (2013)
    Inhibitory Effects of the Pomegranate Polyphenol, Punicalagin, on Type-II Collagen Degradation In Vitro and Inflammation In Vivo
    Chemico-Biol. Interact., 205, 90-99

  19. V.G. Vaidyanathan*, L. Xu and B.P. Cho* (2013)
    Binding kinetics of DNA-protein interaction using surface plasmon resonance
    Nature Protocol Exchange doi:10.1038/protex.2013.054.

  20. V.G. Vaidyanathan, Yamini Asthana and B.U. Nair (2013)
    Importance of Ligand Structure in DNA/Protein Binding, Mutagenicity, Excision Repair and Nutritional Aspects of Chromium (III) Complexes
    Dalton Trans., 42, 2337-2346.

  21. V.G. Vaidyanathan, L. Xu and B.P. Cho (2012)
    Binary and ternary binding affinities between exonuclease-deficient Klenow fragment (Kf-exo−) and various arylamine DNA lesions characterized by surface plasmon resonance
    Chem. Res. Toxicol., 1568-1570.

  22. S.Sangeetha, G.Sathyaraj, M.Duraisamy,V.G.Vaidyanathan and B.U.Nair (2012)
    Structurally modified 1,10-phenanthroline based fluorophores for specific sensing of Ni2+ and Cu2+ ions
    Dalton Trans., 41, 5769-5773. (Top 10 Most Accessed Article in April 2012)

  23. V.G. Vaidyanathan and B.P.Cho (2012)
    Sequence effects on translesion synthesis of an aminofluorene-DNA adduct: conformational, thermodynamic, and primer extension kinetic studies
    Biochemistry, 51, 1983-1995.

  24. H.Dahlmann, V.G.Vaidyanathan and S.J.Sturla (2009)
    Investigating the Biochemical Impact of DNA Damage with Structure-Based Probes: Abasic Sites, Photodimers, Alkylation Adducts and Oxidative Lesions
    Biochemistry, 48, 9347-9359 (Top 20 Most Read Article Nov 2009).

  25. V.G.Vaidyanathan, P.W.Villalta and S.J.Sturla (2007)
    Identification of Covalent DNA Adducts In Vitro From a Quinone Metabolite of Pentachlorophenol
    Chem. Res. Toxicol. 20, 913-919

  26. J.Gong,V.G.Vaidyanathan, X.Yu, T.W.Kensler, L.A.Peterson and S.J.Sturla (2007)
    Depurinating Acylfulvene-DNA Adducts: Characterizing Cellular Chemical Reactions of a Selective Antitumor Agent
    J. Am. Chem. Soc., 129, 2101-2111.

  27. D.Lawrence, V.G.Vaidyanathan and B.U.Nair (2006)
    Synthesis, characterization and DNA binding studies of two mixed ligand complexes of ruthenium(II)
    J. Inorg. Biochem. 100, 1244-1251 (Top 25 hottest articles in J Inorg. Biochem).

  28. V.G.Vaidyanathan, T.Weyhermuller, B.U.Nair and J.Subramanian (2005)
    DNA Damage Induced by a Chromium (III) Schiff Base Complex is Reversible under Physiological Condition
    J. Inorg. Biochem. 99, 2248-2255.  (Top 25 hottest articles in J Inorg Biochem).

  29. V.G.Vaidyanathan and B.U.Nair (2005)
    Synthesis, Characterization and Electrochemical Studies of Mixed Ligand Complexes of Ruthenium(II) with DNA
    Dalton Trans.,17, 2842-2848.

  30. V.G.Vaidyanathan and B.U.Nair (2005)
    Platinum(II) based Molecular Light Switch for Proteins.
    Eur. J. Inorg. Chem, 18, 3756-3759.

  31. R.N.Patel, N.Singh, K.K.Shukla, J.Niclós-Gutiérrez, A.Castineiras, V.G. Vaidyanathan and B.U.Nair (2005)
    Synthesis, Characterization and biological activities of two copper(II) complexes with diethylenetriamine and 2,2′-bipyridine or 1,10-phenanthroline as ligands
    Spectrochim. Acta Part A: Mol. and Biomol. Spectroscopy, 62, 261-268 (Top 25 hottest articles in Spec. Chim. Acta).

  32. V.Uma, V.G.Vaidyanathan and B.U.Nair (2005)
    Synthesis, structure and metallonuclease activity of copper(II) complexes of terpyridine derivatives
    Bull. Chem. Soc. Jpn. 78, 845-850.

  33. V.G.Vaidyanathan and B.U.Nair (2004)
    Nucleobase Oxidation of DNA by Chromium(III) terpyridyl derivatives
    Eur. J. Inorg. Chem., 19, 1840-1846.

  34. V.G.Vaidyanathan and B.U.Nair (2003)
    Synthesis, Characterization and binding studies of Chromium(III) complex having an intercalating ligand with DNA
    J. Inorg. Biochem. 95, 334-342.

  35. V.G.Vaidyanathan and B.U.Nair (2003)
    Synthesis, Characterization and binding studies of Chromium(III) complex having tridentate ligand with DNA
    Eur. J. Inorg. Chem., 19, 3633- 3638.

  36. V.G.Vaidyanathan and B.U.Nair (2003)
    Photooxidation of DNA by Cobalt (II) tridentate complex
    J. Inorg. Biochem., 94, 121- 126.

  37. V.G.Vaidyanathan and B.U.Nair (2003)
    Oxidative Cleavage of DNA by Copper(II) tridentate complex
    J. Inorg. Biochem., 93, 271-276.

  38. V.G.Vaidyanathan and B.U.Nair (2002)
    Synthesis, Characterization and DNA binding studies of a ruthenium (II) complex
    J. Inorg. Biochem., 91, 405-412.

  39. V.G.Vaidyanathan, R.Vijayalakshmi, V.Subramanian and B.U.Nair (2002)
    Synthesis, Characterization and Binding of [Cr(naphen)(H2O)2]+ with DNA: Experimental and Modeling Study
    Bull. Chem. Soc. Jpn., 75, 1143-1149.

Honors and Awards
  • Recipient of Ramanujan Fellowship from Department of Science and Technology (DST), India (2011).

  • Recipient of "ACS Young Investigator Award-3rd Prize" from American Chemical Society (ACS) Division of Chemical Toxicology, Denver, Colorado, USA (2011)

  • Recipient of NSF “Experimental Program to Stimulate Competitive Research (EPSCoR)” Seed grant from Proteomics Division, Brown University (2009).

  • Travel Grant Award from CSIR to attend First Asian Meeting in Bioinorganic Chemistry, Okasaki, Japan (2003) (Participated as Graduate Student delegates from India).

  • Qualified as “Junior Research Fellow in National Eligibility Test (CSIR-NET)” conducted by Council of Scientific and Industrial Research (CSIR), Govt. of India (2000).

  • "Best Chemistry Student Award" in undergraduate Chemistry (1998)

PhD students

 



Nandhini T.
JRF

MSc., Chemistry (Gold Medalist)
(University of Madras - D.G. Vaishnav College)

 



David Dayanidhi P.
JRF

MSc., Chemistry
(University of Madras - Loyola College)