Publications

Articles

1.  "How Do Molecular Crowders Influence Ligand Binding Kinetics with G-Quadruplex DNA? The Role of Bound Water"
   Alam, P.;#* Chand, A. K.;#* Sahu, H.;#* Rohman, M.A.; Clovis, N.S.; Sardana, D.; Puri, S.; Sen, S.*
   J. Phys. Chem. B 2025, 129, 2958 . (DOI)

2. "Effect of Divalent Cations on Polarity and Hydration at Lipid/Water Interface Probed by 4-Aminophthalimide-Based Dyes" 

Alam, P.;# Kumar, P;#* Sahu, H.;# Sardana, D.; Kundu, P.; Chand, A.; Sen, S.* 

J. Phys. Chem. B 2025, 129, 930. (DOI)

3. "Quantifying Membrane Alterations with Tailored Fluorescent Dyes: A Rapid Antibiotic Resistance Profiling Methodology"
   Dubey, A. K.; Sardana, D.; Verma, T.; Alam, P.; Chattopadhyay, A.; Nandini, S. S.; Khamari, B.; Bulagonda, E. P.;
   Sen, S.*; Nandi, D.*
   ACS Infect. Dis.  2024, 10, 2836. (DOI)

4. "Effect of Molecular Crowders on Ligand Binding Kinetics with G-quadruplex DNA Probed by Fluorescence Correlation Spectroscopy"
   Alam, P.;# Clovis, N. S.;# Chand, A. K.;# Khan, M. F.; Sen, S.*
   Methods Appl. Fluoresc. 2024, 12, 045002. (DOI)

5. "Hotspot Site Microenvironment in the Deubiquitinase OTUB1 Drives its Stability and Aggregation"
   Majumder, S.; Srivastava, M.; Alam, P.; Saha, S.; Kumari, R.; Chand, A. K.; Asthana, S.; Sen, S.; Maiti, T. K.*
   J. Biol. Chem. 2024, 300, 107315. (DOI) 
   
   
   

6. "Unusual Similarity of DNA Solvation Dynamics in High-Salinity Crowding with Divalent Cations of Varying Concentrations"
   Sardana, D.;* Alam, P.; Yadav, K.; Clovis, N. S.; Kumar, P.; Sen, S.*
   Phys. Chem. Chem. Phys. 2023, 25, 27744. (DOI)
   
   
   

7. "Molecular Crowders Modulate Ligand Binding Affinity to G-Quadruplex DNA by Decelerating Ligand Association".
   Clovis, N. S.;# Alam, P;# Chand, A. K.; Sardana, D.; Khan, M. F.; Sen, S.*
   J. Photochem. Photobiol. A 2023, 437, 114432 (Invited Article in Anunay Samanta Festschrift) (DOI)   

8. "G-Tetrad-Selective Ligand Binding Kinetics in G-Quadruplex DNA Probed with Fluorescence Correlation Spectroscopy".
   Clovis, N. S.*; Sen, S.*
   J. Phys. Chem. B 2022, 126, 6007. (DOI)
   
   
   

9. “Molecular Picture of the Effect of Cosolvent Crowding on Ligand Binding and Dispersed Solvation Dynamics in G-Quadruplex DNA”.
   Yadav, K.#; Sardana, D.#; Shweta, H.#; Clovis, N. S.; Sen, S.*
   J. Phys. Chem. B 2022, 126, 168. (Invited Article in Kankan Bhattacharyya Festschrift) (DOI)
   
   
   

10. “Graphene Quantum Dot-Based Optical Sensing Platform for Aflatoxin B1 Detection via the Resonance Energy Transfer Phenomenon”.
    Singh, A. K.; Sri, S,; Garimella, L. B. V. S.; Tarun Kumar Dhiman, T.K.; Sen, S.; Solanki, P. R.*
    ACS Appl. Bio Mater. 2022, 5, 1179. (DOI)
    
    
    

11. “DNA Damage, Cell Cycle Perturbation and Cell Death by Naphthalene Diimide Derivative in Gastric Cancer Cells”.
    Gurung, S. K.; Kumari, S. K.; Dana, S.; Mandal, K.; Sen, S.; Mukhopadhyay, P.; Mondal, N.*
    Chem. Biol. Interact. 2022, 358, 109881. (DOI)
    
    
    

12. "Structure of an Unfolding Intermediate of an RRM Domain of ETR‐3 Reveals Its Native like Fold".
    Bhatt, H.; Ganguly, A.K.; Sharma, S.; Kushwaha, G.S.; Khan, M. F.; Sen, S.; Bhavesh, N.S.*
    Biophys. J. 2020, 118, 352 (Cover Article). (DOI)
    
    
    

13. "Cdr1p Highlights the Role of the Non‐Hydrolytic ATP‐Binding Site in Driving Drug Translocation in Asymmetric ABC Pumps".
    Banerjee, A; Moreno, A.; Khan, M.F.; Nair, R.; Sharma, S.; Sen, S.; Mondal, A.K.; Pata, J.; Orelle, C.; Falson, P.*; Prasad, R.*
    BBA-Biomembrane 2019, 1862, 183131. (DOI)
    
    
    

14. "Origin of Slow Solvation Dynamics in DNA: DAPI in Minor Groove of Dickerson‐Drew DNA ".
    Sardana, D.#; Yadav, K.#; Shweta, H.; Clovis, N.S.; Alam, P.; Sen, S.*
    J. Phys. Chem. B  2019, 102, 10202 (Cover Article). (DOI)
    
    
    

15. "Role of Ser65, His148 and Thr203 in the Organic Solvent‐dependent Spectral Shift in Green Fluorescent Protein".
    Kaur, J.; Yadav, N.S.; Singh, M.K.; Khan, M.J.; Sen, S.; Dixit, A.*; Choudhury, D.*
    Photochem. Photobio. 2018, 95, 543. (DOI)
    
    
    

16. "Dynamics of Water and Ions around DNA: What is So Special About Them?".
    Shweta, H.; Sen, S.*
    J. Biosciences 2018, 43, 499 (Review Article for special issue- "Flourescence in Biology"). (DOI)
    
    
    

17. "Ras Hyper activation Versus Over expression: Lessons from Ras Dynamics in Candida Albicans ".
    Vavilala, A.P.; Victoria, G.S.; Khan, M.F.; Haokip, D.T.; Yadav, B.; Pal, N.; Sethi, S.C.; Jain, P; Singh, S. L.; Sen, S.*; Komath, S.S.*
    Sci. Rep. 2018, 8, 5248. (DOI)
    
    
    

18. "Effect of T∙T Mismatch on DNA Dynamics Probed by Minor Groove Binders: Comparison of Dynamic Stokes Shifts of Hoechst and DAPI".
    Shweta, H.; Singh, M.K.; Yadav, K.; Verma, S.D.; Pal, N.; Sen, S.*
    J. Phys. Chem. B 2017, 121, 10735 (Cover Article). (DOI)
    
    
    

19. "Probe‐location Dependent Resonance Energy Transfer at Lipid/Water Interfaces: Comparison between the Gel‐ and Fluid‐Phase of Lipid Bilayer ".
    Singh, M.K.*; Khan, M.F.; Shweta, H.; Sen, S.*
    Phys. Chem. Chem. Phys. 2017, 19, 25870 (Inside Front Cover Article). (DOI)
    
    
    

20. "Multidrug ABC Transporter Cdr1 of Candida Albicans Harbors Specific and Overlapping Binding Sites for Human Steroid Hormones Transport".
    Baghel, P.; Rawal, M.K.; Khan, M.F.; Sen, S.; Siddiqui, M.H.; Chaptal, V.; Falson, P.; Prasad, R.*
    J. BBA-Biomembrane 2017, 1859, 1778. (DOI)
    
    
    

21. "Dispersed Dynamics of Solvation in G-quadruplex DNA: Comparison of Dynamic Stokes Shifts of Probes in Parallel and Antiparallel Quadruplex Structures".
    Singh, M. K.; Shweta, H.; Sen, S.*
    Methods Appl. Fluoresc. 2016, 4, 034009 (Invited article Optics Within Life Sciences -2016 special issue: Author Spotlight). (DOI)
    
    
    

22. "New Insight into Probe-Location Dependent Polarity and Hydration at Lipid/Water Interfaces: Comparison Between Gel- and Fluid-Phases of Lipid Bilayers".
    Singh, M. K.#; Shweta, H.#; Khan, M. F.; Sen, S.*
    Phys. Chem. Chem. Phys. 2016, 18, 24185 (Inside Front-Cover Article).(DOI)
    
    
    

23. "Newly identified motifs in Candida albicans Cdr1 protein nucleotide binding domains are pleiotropic drug resistance subfamily‐specific and functionally asymmetric".
    Rawal, M.K.; Banerjee, A.; Shah, A.H.; Khan, M.F.; Sen, S.; Saxena, A.K.; Monk, B.C.; Cannon, R.D.; Bhatnagar, R.; Mondal, A.K.; Prasad R.*
    Sci. Rep. 2016, 8,  27132. (DOI)
    
    
    

24. “Quantifying Size Parameters of Water‐in‐Oil Microemulsion Droplets: Why Fluorescence Correlation is Advantageous over Light Scattering Correlation?”.
    Singh, M. K.; Khan, M. F.; Sen, S.*
    ISRAPS Bulletin 2016, 28, 40. (PDF)
    
    
    

25. “Measuring Size, Size Distribution, and Polydispersity of Water‐in‐Oil Microemulsion Droplets using Fluorescence Correlation Spectroscopy: Comparison to Dynamic Light Scattering”.
    Singh, M. K.; Khan, M. F.; Sen, S.*
    J. Phys. Chem. B 2016, 120, 1008. (DOI)
    
    
    

26. "Sequence-Dependent Solvation Dynamics of Minor-Groove Bound Ligand inside Duplex-DNA". Verma, S. D.; Pal, N.; Singh, M. K.; Sen, S.*
    J. Phys. Chem. B 2015, 119, 34 (Invited article for Biman Bagchi Festschrift issue). (DOI)
    
    
    

27. "Power-Law Solvation Dynamics in G-quadruplex DNA: Role of Hydration Dynamics on Ligand Solvation inside DNA".
    Pal, N.#; Shweta, H.#; Singh, M. K.; Verma, S. D.; Sen, S.*
    J. Phys. Chem. Lett. 2015, 6, 1754. (DOI)
    
    
    

28. "The Potent Anti-Malarial Activity of Acriflavine In Vitro and In Vivo".
    Dana, S.; Prusty, D.; Dhayal, D.; Gupta, M. K.; Dar, A.; Sen, S.; Mukhopadhyay, P.; Adak, T.; Dhar, S. K.*
    ACS Chem. Biol. 2014, 9, 2366. (DOI)
    
    
    

29. "Insight into Pleiotropic Drug Resistance ATP-binding Cassette Pump Drug Transport through Mutagenesis of Cdr1p Transmembrane Domain".
    Rawal, M. K.; Khan, M. F.; Kapoor, K.; Goyal, N.; Sen, S.; Saxena, A. K.; Lynn, A. M.; Tyndall, J. D. A.; Monk, B. C.; Cannon, R. D.; Komath, S. S.; Prasad, R.*
    J. Biol. Chem. 2013, 288, 24480. (DOI)
    
    
    

30. “Understanding Growth Kinetics of Nanorods in Microemulsion: A Combined Fluorescence Correlation Spectroscopy, Dynamic Light Scattering and Electron Microscopy Study”.
    Sharma, S.#; Pal, N.#; Choudhury, P.; Sen S.*; Ganguli, A.K.*
    J. Am. Chem. Soc. 2012, 134, 19677. (DOI)
    
    
    

31. "Probe Position-Dependent Counterion Dynamics in DNA: Comparision of Time-Resolved Stokes Shift of Groove-bound to Base-Stacked Probes in the Presence of Different monovalent Counterions".
    Verma, S. D.; Pal, N.; Singh, M. K.; Sen, S.*
    J. Phys. Chem. Lett., 2012, 3, 2621. (DOI)
    
    
    

32. "Understanding Ligand Interaction with Different Structures of G-Quadruplex DNA: Evidence of Kinetically Controlled Ligand Binding and Binding-Mode Assisted Quadruplex Structure Alteration".
    Verma, S. D.; Pal, N.; Singh, M. K.; Shweta, H.; Khan, M. F.; Sen, S.*
    Anal. Chem., 2012, 84, 7218. (DOI)
    
    
    

33. "Fluorescence Correlation Spectroscopy: An Efficient Tool for Measuring Size, Size-Distribution and Polydispersity of Microemulsion Droplets in Solution".
    Pal, N.; Verma, S. D.; Singh, M. K.; Sen, S.*
    Anal. Chem., 2011, 83, 7736. (DOI)
    
    
    

34. "Probe Position-Dependence of DNA Dynamics: Comparision of Time-Resolved Stokes Shift of Groove-bound to Base-Stacked Probes".
    Pal, N.; Verma, S. D.; Sen, S.*
    J. Am. Chem. Soc., 2010, 132, 9277. (DOI)
    
    
    

35. "Current Perspective on Ultrafast Dynamics in DNA". Sen, S.*; Verma, S. D.; Pal, N.
    ISRAPS Bulletin, 2010, 22, 53. (Review) (PDF)
    
    
    

36. "Dynamics of Water and Ions Near DNA: Comparison of Simulation to Time-Resolved Stokes Shift Experiments". Sen, S.; Andreatta, D.; Ponomarev, S. Y.; Beveridge, D. L.; Berg, M. A.*
    J. Am. Chem. Soc. 2009, 131, 1724. (DOI)
    
    

Book Chapters

37. “Dynamics of Water and Ions near DNA: Perspective from Time‐Resolved Fluorescence Stokes Shift Experiments and Molecular Dynamics Simulation”. Shweta, H.; Pal, N.; Singh, M.K.; Verma, S.D.; Sen, S.*
    Reviews in Fluorescence 2017, Springer. (DOI)
    
    
    

38. “New Family of Fluorescent Probes for Characterizing Depth‐Dependent Static and Dynamic Properties of Lipid/Water Interfaces”. Singh, M.K.; Shweta, H.; Sen, S.*
    Analysis of Membrane Lipids 2020, Springer. (DOI)    
    
    
    

Sobhan's publications before joining JNU

39. "Half-hydration” at the air/water interface revealed by heterodyne-detected electronic sum frequency generation spectroscopy, polarization second harmonic generation, and molecular dynamics simulation". Watanabe, H.; Yamaguchi, S.; Sen, S.; Morita, A.; Tahara, T.*
    J. Chem. Phys. 2010, 132, 144701. (DOI)
    
    
    

40. "Different Molecules Experience Different Polarities at the Air/Water Interface". Sen, S.; Yamaguchi, S.; Tahara, T.*
    Angew. Chem. Int. Ed. 2009, 48, 6439. (DOI)
    
    
    

41. "Ultrafast Dynamics in DNA: “Fraying” at the End of the Helix". Andreatta, D; Sen, S.; Lustres, J. L. P; Kovalenko, S. A.; Ernsting, N. P.; Murphy, C. J.; Coleman, R. S.; Berg, M. A.*
    J. Am. Chem. Soc. 2006, 128, 6885. (DOI)
    
    
    

42. "Role of Monovalent Counterions in the Ultrafast Solvation Dynamics of DNA". Sen, S.; Gearheart, L.; Rivers, E.; Coleman, R. S.; Murphy, C. J.; Berg, M. A.*
    J. Phys. Chem. B 2006, 110, 13248. (DOI)
    
    
    

43. "Effect of Protein Binding on Ultrafast DNA Dynamics: Characterization and Measurement of a Complex with APE1". Sen, S.; Paraggio, N. A.; Gearheart, L.; Connor, E.E.; Issa, A.; Coleman, R. S.; Wilson III, D. M.; Wyatt, M.; Berg, M. A.* 
    Biophysical J. 2005, 89, 4129. (DOI)
    
    
    

44. "Solvation Dynamics in Dimyristoyl-Phosphatidylcholine Entrapped Inside a Sol-Gel Matrix". Halder, A.; Sen, S.; Burman, A. D.; Patra, A.; Bhattacharyya, K.*
    J. Phys. Chem. B 2004, 108, 2309. (DOI)
    
    
    

45. "Solvation Dynamics in Protein-Surfactant Aggregate. TNS in HSA-SDS". Mukherjee, S.; Sen, P.; Halder, A.; Sen, S.; Dutta, P.; Bhattacharyya, K.*
    Chem. Phys. Lett. 2003, 379, 471. (DOI)
    
    
    

46. "Solvation Dynamics in Protein-Surfactant Complex". Dutta, P.; Sen, P.; Halder, A.; Mukherjee, S.; Sen, S.; Bhattacharyya, K.*
    Chem. Phys. Lett. 2003, 377, 229. (DOI)
    
    
    

47. "Solvation Dynamics of 4-amiopthalimide in a Polymer (PVP)-Surfactant (SDS) Aggregate". Dutta, P.; Sukul, D.; Sen, S.; Bhattacharyya, K.*
    Phys. Chem. Chem. Phys. 2003, 5, 4875. (DOI)
    
    
    

48. "Isomerization and Fluorescence Depolarization of Merocyanine 540 in Polyacrylic Acid. Effect of pH". Sukul, D.; Sen, S.; Dutta, P.; Bhattacharyya, K.*
    Proc. Indian Acad. Sci. (Chem. Sci.) 2002, 114, 501.(PDF)
    
    
    

49. "Solvation Dynamics of a Probe Covalently Bound to a Protein and in an AOT Microemulsion: 4-(N-Bromoacetylamino)-Phthalimide". Mandal, D.; Sen, S.; Sukul, D.; Bhattacharyya, K.; Mandal, A. K.; Banerjee, R.; Roy, S.*
    J. Phys. Chem. B 2002, 106, 10741. (DOI)
    
    
    

50. "Excited State Proton Transfer of 1-Naphthol in Hydroxypropylcellulose/Sodium Dodecyl Sulfate System". Dutta, P.; Halder, A.; Mukherjee, S.; Sen, P.; Sen, S.; Bhattacharyya, K.*
    Langmuir 2002, 18, 7867. (DOI)
    
    
    

51. "Solvation Dynamics in Bile Salt Aggregates". Sen, S.; Dutta, P.; Mukherjee, S.; Bhattacharyya, K.*
    J. Phys. Chem. B 2002, 106, 7745. (DOI)
    
    
    

52. "Femtosecond studies of solvation dynamics of DCM in micelles". Mandal, D.; Sen, S.; Bhattacharyya, K.; Tahara, T.*
    Chem. Phys. Lett. 2002, 359, 77. (DOI)
    
    
    

53. "Solvation dynamics of TNS in polymer (PEG)-surfactant (SDS) aggregate". Dutta, P.; Sen, S.; Mukherjee, S.; Bhattacharyya, K.*
    Chem. Phys. Lett. 2002, 359, 15. (DOI)
    
    
    

54. "Solvation Dynamics in the Water Pool of Aerosol Sodium Dioctylsulfosuccinate Microemulsion: Effect of Polymer". Sen, S.; Dutta, P.; Sukul, D.; Bhattacharyya, K.*
    J. Phys. Chem. A 2002, 106, 6017. (DOI)
    
    
    

55. "Solvation Dynamics in Aqueous Polymer Solution and in Polymer-Surfactant Aggregate". Sen, S.; Sukul, D.; Dutta, P.; Bhattacharyya, K.*
    J. Phys. Chem. B 2002, 106, 3763. (DOI)
    
    
    

56. "Photoisomerization of merocyanine 540 in polymer-surfactant aggregate". Sen, S.; Sukul, D.; Dutta, P.; Bhattacharyya, K.*
    Proc. Indian Acad. Sci. (Chem. Sci.) 2002, 114, 83. (PDF)
    
    
    

57. "Slow Solvation Dynamics of Dimethylformamide in a Nanocavity. 4-Aminophthalimide in beta-Cyclodextrin". Sen, S.; Sukul, D.; Dutta, P.; Bhattacharyya, K.*
    J. Phys. Chem. A 2001, 105, 10635. (DOI)
    
    
    

58.  "Fluorescence Anisotropy Decay in Polymer-Surfactant Aggregates". Sen, S.; Sukul, D.; Dutta, P.; Bhattacharyya, K.*
    J. Phys. Chem. A 2001, 105, 7495. (DOI)
    
    
    

59. "Solvation dynamics of DCM in Human Serum Albumin". Pal, S. K.; Mandal, D.; Sukul, D.; Sen, S.; Bhattacharyya, K.*
    J. Phys. Chem. B 2001, 105, 1438. (DOI)
    
    
    

60. "Solvation Dynamics of DCM in Dipalmitoyl Phosphatidylcholine Lipid". Pal, S. K.; Sukul, D.; Mandal, D.; Sen, S.; Bhattacharyya, K.*
    Tetrahedron 2000, 56, 6999. (DOI)
    
    
    

61. "Solvation Dynamics of DCM in Micelles". Pal, S. K.; Sukul, D.; Mandal, D.; Sen, S.; Bhattacharyya, K.* 
    Chem. Phys. Lett. 2000, 327, 91. (DOI)
    
    
    

62. "Excited State Proton Transfer as a Probe for Polymer – Surfactant Interaction". Sukul, D.; Pal, S. K.; Mandal, D.; Sen, S.; Bhattacharyya, K.*
    J. Phys. Chem. B 2000, 104, 6128. (DOI)
    
    
    

63. "Solvation Dynamics of Coumarin 480 in Sol – Gel Matrix". Pal, S. K.; Sukul, D.; Mandal, D.; Sen, S.; Bhattacharyya, K.*
    J. Phys. Chem. B 2000, 104, 2613. (DOI) 

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*Corresponding author(s), #Equal Author Contributions