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Functional biointerfaces: Sensing, Electron transport and Single molecule structural biology

We are working on Nanoscale Nucleic Acid Sensors where we develop bioactive films of Xeno Nucleic Acids (XNAs) with an aim of achieving better DNA/RNA detection abilities; Nanoscale Biological Electron Transport where we assess the utility of the metalloproteins (human source) as potential molecular bioelectronic components; and Single Molecule level Structural Biology using Scanning Probe Microscopy approach - here we assess the capacity of such an approach by probing the architecture of protein supramolecular assemblies, where the protein structure could be previously unknown, and also by probing the DNA topological changes induced by drug-binding. Click here for a graphical summary of the contributions made in the last few years.

Lab News: Asmita Paul (DBT, JRF) has joined the group for reading PhD in Nanoscale Nucleic Acid Sensing. A Hearty Welcome to Asmita.

Academic Profile

Academic profile

Rupa Mukhopadhyay received B.Sc. with Honours from Presidency College (Calcutta University) and M.Sc. from IIT Kanpur. She read for her Doctoral degree under the supervision of Professor H. Allen O. Hill, FRS, in the University of Oxford, United Kingdom. After a brief sojourn at IIT Guwahati and IIT Kanpur, she moved to the Interdisciplinary Nanoscience Centre (iNANO) in Denmark and worked under the mentorship of Professor Flemming Besenbacher. She joined at IACS as an Assistant Professor in 2007 and at present, she is serving as a Senior Professor.

Research interest

Her research interest is the combined use of bio- and nano-systems to engineer surfaces for nanoscale biosensing (for PCR-independent, fluorescent label-free sensing), bioelectronics (for sustainable development) and single molecule level structural biology. This involves explorations with alternative nucleic acids as sensing probes, protein modification and assembly, and force-based microscopy/spectroscopy at single molecule level.

Group

Budhaditya Bhattacharya

Institute Fellow (JRF)
MSc
Nanoscale Nucleic Acid Sensing
bsbb2310@iacs.res.in

Asmita Paul

DBT Fellow (JRF)
MSc
Nanoscale Nucleic Acid Sensing
sbsap2663@iacs.res.in

Sourav Mondal

CSIR Fellow (SRF)
MSc
Single Molecule Structural Biology
bcsm6@iacs.res.in

Jayita Biswas

DBT Fellow (JRF)
MSc
Single Molecule Structural Biology
bsjb2497@iacs.res.in

Publication

Publications

Impact of HMGB1 binding on the structural alterations of platinum drug-treated single dsDNA molecule, Sourav Mondal, Siddhartha Banerjee, Debapriya Dey, Hiya Lahiri, Tanushree Mana, Siddhartha Sankar Jana and Rupa Mukhopadhyay*, Biochimie, 2023 (Accepted).

The XNAs - A Troubleshooter for Nucleic Acid Sensing, Tanushree Mana, Budhaditya Bhattacharya, Hiya Lahiri and Rupa Mukhopadhyay, ACS Omega, 7, 15296-15307 (2022) (Invited Minireview*).

Molecularly Resolved, Label-free Nucleic Acid Sensing at Solid-liquid Interface using Non-ionic DNA Analogues, Tanushree Mana, Jayanta Kundu, Hiya Lahiri, Sudipta Bera, Jayeeta Kolay, Surajit Sinha and Rupa Mukhopadhyay*, RSC Advances, 12, 9263-9274 (2022).

How Stable are the Collagen and Ferritin Proteins for Application in Bioelectronics? Jayeeta Kolay, Sudipta Bera and Rupa Mukhopadhyay*, PLoS One, 2021.

Nanoscale Solid-state Electron Transport via Ferritin: Implications in Molecular Bioelectronics, Tatini Rakshit, Sudipta Bera, Jayeeta Kolay and Rupa Mukhopadhyay, (invited perspective article) Nano-structures and Nano-objects, 24, 100582 (2020).

Free-energy-based gene mutation detection using LNA probes, H. Lahiri, S. Banerjee and R. Mukhopadhyay*, ACS Sensors, 4(10), 2688-2696 (2019).

Electron transport in muscle protein collagen, J. Kolay, S. Bera and R. Mukhopadhyay*, Langmuir, 35, 11950-11957 (2019).

Long-range solid-state electron transport through ferritin multilayers, S. Bera, J. Kolay, P. Pramanik, A. Bhattacharyya and R. Mukhopadhyay*, Journal of Materials Chemistry C, 7, 9038-9048 (2019).

Nanoscale Nucleic Acid Recognition at Solid-liquid Interface using Xeno Nucleic Acid Probes, H. Lahiri, S. Mishra and R. Mukhopadhyay, Langmuir, 35, 8875-8888 (2019) (Invited Feature Article*) (frontispiece).

Negative differential resistance behaviour of the iron storage protein ferritin, J. Kolay, S. Bera, T. Rakshit and R. Mukhopadhyay*, Langmuir, 34, 3126-3135 (2018).

Nanoscale on-silico electron transport via ferritins, S. Bera, J. Kolay, S. Banerjee and R. Mukhopadhyay*, Langmuir, 33, 1951-1958 (2017).

Discriminating Intercalative Effects of Threading Intercalator Nogalamycin, from Classical Intercalator Daunomycin, using Single Molecule Atomic Force Spectroscopy, T. Banerjee, S. Banerjee, S. Sett, S. Ghosh, T. Rakshit and R. Mukhopadhyay*, PLoS ONE, 11(5), e0154666. (2016).

Discriminating Unalike Single Nucleobase Mismatches using a Molecularly Resolved, Label-free, Interfacial LNA-based Assay, H. Lahiri, S. Mishra, T. Mana and R. Mukhopadhyay*, Analyst, 141, 4035-4043 (2016) (frontispiece).

Molecularly Resolved Label-free Sensing of Single Nucleobase Mismatches by Interfacial LNA Probes, S. Mishra, H. Lahiri, S. Banerjee and R. Mukhopadhyay*, Nucleic Acids Research, 44(8), 3739-3749 (2016).

Interactions of Histone Acetyltransferase p300 with the Nuclear Proteins Histone and HMGB1, as Revealed by Single Molecule Atomic Force Spectroscopy, S. Banerjee, T. Rakshit, S. Sett and R. Mukhopadhyay*, J Phys Chem B, 119(42), 13278-13287 (2015).

Regulating On-surface LNA Probe Density for the Highest Target Recognition Efficiency, Sourav Mishra, Srabani Ghosh and Rupa Mukhopadhyay*, Langmuir, 30(34), 10389-10397 (2014).

Enhancing Sensitivity in a Piezoresistive Cantilever-based Label-free DNA Detection Assay using ssPNA Sensor Probes, Srabani Ghosh, Sourav Mishra and Rupa Mukhopadhyay*, Journal of Materials Chemistry B, 2, 960-970 (2014).

Nanoscale Mechano-Electronic Behaviour of a Metalloprotein as a Variable of Metal Content; T. Rakshit, S. Banerjee, S. Mishra and R. Mukhopadhyay*, Langmuir, 29(40), 12511-12519 (2013).

Enhancing On-Surface Mismatch Discrimination Capability of PNA Probes by AuNP Modification of Gold(111) Surface; S. Ghosh, S. Mishra and R. Mukhopadhyay*;Langmuir, 29(38), 11982-11990 (2013).

Facilitating Mismatch Discrimination by Surface-Affixed PNA Probes via Ionic Regulation; S. Ghosh, S. Mishra, T. Banerjee and R. Mukhopadhyay*;Langmuir, 29(10), 3370-3379 (2013).

Maximizing Mismatch Discrimination by Surface-Tethered LNA Probes via Ionic Tuning; S. Mishra, S. Ghosh and R. Mukhopadhyay*; Analytical Chemistry, 85(3), 1615-1623 (2013). (highlighted in ‘Advances in Engineering’)

Structural features of Human Histone Acetyltransferase p300 and its complex with p53; S. Banerjee, Arif M, T. Rakshit, N. S. Roy, T. K. Kundu, S. Roy and R. Mukhopadhyay*; FEBS Letters 586, 3793–3798 (2012).

Solid-state electron transport in Mn-, Co-, holo- and Cu-Ferritins: Force-induced modulation is inversely linked to the protein conductivity; T. Rakshit and R. Mukhopadhyay*; Journal of Colloid and Interface Science 388, 282-292 (2012).

Ordered self-assembled Locked Nucleic Acid (LNA) structures on gold(111) surface with enhanced single base mismatch recognition capability; S. Mishra, S. Ghosh and R. Mukhopadhyay*; Langmuir, 28, 4325-4333 (2012).

DNA compaction by mononuclear platinum cancer drug cisplatin and the trisplatinum anticancer agent BBR3464: Differences and Similarities; T. Banerjee, P. Dubey and R. Mukhopadhyay*; Biochimie 94, 494-502, (2012).

Tuning band gap of holoferritin by metal core reconstitution with Cu, Co and Mn; T. Rakshit and R. Mukhopadhyay*; Langmuir 27, 9681-9686, (2011).

An Atomic Force Microscopy Investigation on Self-assembled Peptide Nucleic Acid Structures on Gold(111) Surface; S. Ghosh and R. Mukhopadhyay*; Journal of Colloid and Interface Science 360, 52-60, (2011).

Near-metallic Behavior of Warm Holoferritin Molecules on Gold(111) Surface, T. Rakshit, S. Banerjee and R. Mukhopadhyay*, Langmuir 26(20), 16005-16012, (2010).

Compacting effect of BBR3464, a new-generation trisplatinum anticancer agent, on DNA; T. Banerjee, P. Dubey and R. Mukhopadhyay*; Biochimie 92, 846-851, (2010).

Tunable 3D and 2D polystyrene nanoparticle assemblies using surface wettability, low volume fraction and surfactant effects; S. Pillai, A. G. Hemmersam, R. Mukhopadhyay, R. L. Meyer, S. M. Moghimi, F. Besenbacher and P. Kingshott*; Nanotechnology 20(2), article no. 025604 (2009).

A new bio-active surface for protein immobolisation via copper free “Click” between azido SAM and alkynyl Fischer carbene complex; S. Sawoo, P. Dutta, A. Chakraborty, R. Mukhopadhyay, O. Bouloussa and A. Sarkar*; Chem Commun 5957-5959, (2008).

Structural effects of nogalamycin, an antibiotic antitumour agent, on DNA; T. Banerjee and R. Mukhopadhyay*; Biochem Biophys Res Commun 374, 264-268, (2008).

Ordering of binary polymeric nanoparticles on hydrophobic surfaces assembled from low volume fraction dispersions; R. Mukhopadhyay, O. Al-Hanbali, S. Pillai, A. G. Hemmersam, R. L. Meyer, A. C. Hunter, K. J. Rutt, F. Besenbacher, S. M. Moghimi and P. Kingshott*; J Am Chem Soc 129, 13390-13391, (2007).

Femtomolar electrochemical detection of DNA-targets using metalsulfide nanoparticles; Ask J., Mukhopadhyay R., Hansen J. O., and Gothelf K.*; J Am Chem Soc 128, 3860-3861, (2006).

Cantilever sensor for nanomechanical detection of specific protein conformations; Mukhopadhyay R., Sumbayev V. V., Lorentzen M, Kjems J. Andreasen P. A. and Besenbacher F.; Nano Lett 5(12), 2385-2388, (2005).

Nanomechanical sensing of DNA sequences using piezoresistive cantilevers;Mukhopadhyay R.*, Lorentzen M, Kjems J. and Besenbacher F.; Langmuir 21(18), 8400-8408, (2005).

Structural changes of DNA induced by mono- and binuclear cancer drugs; Mukhopadhyay, R.*, Dubey, P. and Sarkar, S.; J Struct Biol 150(3), 277-283, (2005).

Synthesis and characterization of water-soluble carbon nanotubes from mustard soot; P. Dubey, D. Muthukumaran, S. Das, R. Mukhopadhyay and S. Sarkar*; Pramana 65(4), 681-697, (2005).

Oriented Immobilization of Pseudomonus Putida Putidaredoxin at gold(111)-buffer interface: A real time Scanning Tunneling Microscopy Study; Mukhopadhyay, R.*, Lo, K. K., Wong, L. L. and Hill, H. A. O.; Journal of Microscopy 213(1), 6-10, (2004).

KCTCCA, a Peptide-based Facilitator for Bioelectrochemistry; Mukhopadhyay, R.; Journal of Biosciences 29(2), 163-167, (2004).

Molecular level structural studies of metalloproteins/metalloenzymes by Scanning Tunneling Microscopy: scopes and promises, Current Science (review article); Mukhopadhyay, R.; 84(9), 1202-1210, (2003).

Surface trapping and AFM detection of DNA topological intermediates generated from an oxidative chemical nuclease; Mukhopadhyay, R., Srivatsan S. G. and Verma S.; Biochem Biophys Res Commun 308, 165-169, (2003).

A Molecular Level Study of Complex Formation between Putidaredoxin and Cytochrome P450 by Scanning Tunneling Microscopy, Mukhopadhyay, R., Lo, K. K., Wong, L. L., Pochapsky T. and Hill, H. A. O., Phys. Chem. Chem. Phys. 4, 641-646, (2002) (frontispiece).

A Scanning Tunneling Microscopy study of Clostridium Pasteurianum Rubredoxin; Mukhopadhyay, R., Meyer, J., Kyritsis, P., Davis, J. J. and Hill, H. A. O.*; J Inorg Biochem 78, 251-254, (2000).

BIOSENSORS: PAST, PRESENT AND FUTURE; Jason J. Davis, H. Allen, O. Hill, Rupa Mukhopadhyay; Biochemical Society Transactions 02/1999; 27(1): A27.3-A27.

Teaching

• ‘Biotechnology & Nanobiotechnology’ at IACS for Ph.D. students (2006-2007)

• ‘Elements of Chemical Biology’ at IACS for Ph.D. students (2011-2012)

• ‘Elements of Chemical Biology’ at IACS for Ph.D. students (2015-2016).

• 'Molecules of Life and Fundamentals of Living Systems' at IACS for Integrated MSc-PhD students (2016-2017, 2017-2018).

• 'Biophysical and Biochemical Methods' at IACS for Integrated MSc-PhD students (2016-2017, 2017-2018, 2018-2019, 2019-2020, 2020-2021) and BS-MS students (2020-2021)

• 'Nanoscale Engineering of Biological Systems' at IACS for Integrated MSc-PhD students (2017-2018, 2018-2019, 2019-2020, 2020-2021).

A number of pedagogical lectures as part of ‘Advanced Biology’ course in ‘Molecular and Cellular Imaging’ at IICB, in 2009 and 2010.

Project Students Alumni

Alumni members (PhD)

1. Dr. Trambaki Banerjee [PhD Topic: Nanoscale Analysis of the Effects of DNA - binding Cancer Drugs on DNA Topology]

2. Dr. Srabani Ghosh [PhD Topic: Peptide Nucleic Acid: Potentially Better Alternative for On - Surface DNA Dtection]

3. Dr. Tatini Rakshit [PhD Topic: Tunable Ferritin Bioelectronics at the Nanoscale]

4. Dr. Siddhartha Banerjee [PhD Topic: Structural Aspects of Proteins and Protein - Protein Assemblies at Single Molecule Level Using Scanning Microscopy Approach]

5. Dr. Sourav Mishra [PhD Topic: Locked Nucleic Acid (LNA): An Improved Alternative to DNA for Nanoscale 'On - Surface' Nucleic Acid Detection]

6. Dr. Jayeeta Kolay [PhD Topic: Protein-based Molecular Bioelectronics: Practical Aspects using Ferritin and Collagen]

7. Dr. Hiya Lahiri [PhD Topic: Molecularly Resolved, Label-Free Sensing of Gene Mutations using Locked Nucleic Acid (LNA) Probes]

8. Dr. Sudipta Bera [PhD Topic: Assessment of Suitability of Ferritin as Bioelectronic and Optical Material]

9. Dr. Tanushree Mana [PhD Topic: Molecularly Resolved Label-Free Analysis of Gene Sequences using Xeno Nucleic Acid (XNA) Probes]

Alumni members (Project students)

1. Ajoy K. Das [IACS, Kolkata] - Integrated MSc PhD project in 2007

2. Sujan Das [St. Stephens College, Delhi] - Summer Project in 2007

3. Soham Sengupta [Haldia Institute of Technology, Haldia] - B. Tech. Project in 2011

4. Arundhoti Mandal [Presidency College, Kolkata] - DST Inspire Project in 2012

5. Ankita Ray [Christ University, Bangalore] - Summer Project in 2014

6. Subham Jain [University of Rajasthan, Jaipur] - Integrated Dual Degree (B. Tech. & M. Tech.) Project in 2014

7. Krishnendu Kr. Kundu [Ballygunge Science College, Calcutta University] - Biotech RISE Summer Project in 2017

8. Subarna Chakraborty [IACS, Kolkata] - Integrated MSc PhD Project in 2017

9. Sayan Chakraborty [University of Kalyani] - Master's Project in 2021

10. Sourabh Kundu [RKMVC College, Rahara] - Summer Project in 2021

11. Anushree Chakraborty [IACS, Kolkata] - Master's Project in 2022

12. Jita Das [IACS, Kolkata] - Master's Project in 2022

Contact Us

Contact information

School of Biological Sciences

Indian Association for the Cultivation of Science

Phone:+91 33 2473 4971 [Ext. 1506 (O), 1513 (L)]

Fax: +91 33 2473 2805

E-mail : bcrm@iacs.res.in

Name : Rupa Mukhopadhyay Deptartment : School of Biological Sciences Designation : Senior Professor Contact : +91 33 2473 4971 (Ext:1506)Email : bcrm@iacs.res.in