Publications

2022

(25)  S. Patra, J. B. Claude, and J. Wenger, "Fluorescence brightness, photostability, and energy transfer enhancement of immobilized single molecules in zero-mode waveguide nanoapertures", ACS Photonics., 9 (6), 2109-2118 (2022). IF 7.0

Studied the influence of Zero-Mode Waveguide (ZMW) nanoaperture on the single immobilized Cy3B and Alexa 647 fluorophores, detailing the interplay between brightness, lifetime, photobleaching time, total number of emitted photons and Förster resonance energy transfer (FRET). 

2021

(24) S. Patra, J. B. Claude, J. V. Naubron, and J. Wenger, "Fast interaction dynamics of G-quadruplex and RGG-rich peptides unveiled in zero-mode waveguides", Nucleic Acids Res., 49 (21), 12348-12357 (2021). IF 16.971  

Studied biomolecular interaction dynamics on the single molecule level at physiologically relevant µM concentrations.  

2020

(23) M. Baibakov, A. Barulin, P. Roy, J. B. Claude, S. Patra, and J. Wenger, Zero-mode waveguides can be made better: fluorescence enhancement with rectangular aluminum nanoapertures from the visible to the deep ultraviolet , Nanoscale Adv. 2 (9), 4153-4160 (2020). IF 4.38  

Demonstrated that rectangular shaped metallic nanostructures (Zero-Mode Waveguide) further improves the detection of single molecule fluorescence over their circularly shaped counterparts and therefore, opens new possibilities to achieve brighter fluorescence emission, faster lifetime and smaller detection volume. 

(22) S. Patra, M. Baibakov, J. B. Claude, and J. Wenger, Surface passivation of zero-mode waveguide nanostructures:  benchmarking protocols and fluorescent labels, Sci. Rep. 10, 5235 (2020). (IF 4.122)

A benchmark study optimizing both the choice of the fluorescent dye and the surface passivation protocol that are highly significant to expand the use of ZMWs for single molecule fluorescence applications.

(21) M. Baibakov, S. Patra, J. B. Claude, and J. Wenger, Long-Range Single-Molecule Förster Resonance Energy Transfer between Alexa Dyes in Zero-Mode Waveguides, ACS Omega, 5, 6947-6955 (2020). (IF: 2.87) 

Demonstrated that single molecule FRET enhancement inside ZMW is quite general and does not depend on the type of fluorescent dyes used.

2019

(20) A. Barulin, J. B. Claude, S. Patra, N. Bonod, and J. wenger, Deep UV plasmonic enhancement of single protein autofluorescence in zero-mode waveguides, Nano Lett. 19, 7434-7442 (2019). (IF : 12.279)

We report the first demonstration of single protein UV fluorescence enhancement using aluminum zero-mode waveguides nanoapertures.

(19) A. Barulin, J. B. Claude, S. Patra, A. Moreau, J. Lumeau and J. Wenger, Preventing Aluminum Photocorrosion for Ultraviolet Plasmonics, J. Phys. Chem. Lett., 10, 5700-5707 (2019). (IF : 7.329)  

We show that the aluminum photocorrosion is related to the nonlinear absorption by water in the UV range leading to the production of hydroxyl radicals. Different corrosion protection approaches are tested using scavengers for reactive oxygen species and polymer layers deposited on top of the aluminum structures.

(18) M. Baibakov, S. Patra, J. B. Claude, A. Moreau, J. Lumeau and J. Wenger, Extending Single-Molecule Förster Resonance Energy Transfer (FRET) Range beyond 10 Nanometers in Zero-Mode Waveguides, ACS Nano, 13, 8469-8480 (2019). (Equal contribution) (IF : 14.588)

First demonstration that the single molecule FRET can be detected beyond 10 nm barrier limit using a subwavelength size (80-200 nm) nanoaperture milled in an aluminium film.

(17) L. Li, M. Dwivedi, S. Patra, N. Erwin, S. Möbitz, R. Winter, Probing Colocalization of N‐Ras and K‐Ras4B Lipoproteins in Model Biomembranes, ChemBioChem, 20, 1190-1195 (2019). (IF : 2.593)

(16)    S. Patra, V. Schuabb, I. Kiesel, J. M. Knop, R. Oliva, R. Winter, Exploring the effects of cosolutes and crowding on the volumetric and kinetic profile of the conformational dynamics of a poly dA loop DNA hairpin: a single-molecule FRET study, Nulceic Acids Res. 47, 981-996 (2019). (IF : 11.501)

Demonstration of rugged conformatonal landscape of a DNA hairpin in a native like crowded environment using single molecule FRET.

2018

(15) J. M. Knop, S. Patra, B. Harish, C. A. Royer, R. Winter, The Deep Sea Osmolyte Trimethylamine N‐Oxide and Macromolecular Crowders Rescue the Antiparallel Conformation of the Human Telomeric G‐Quadruplex, Chem. Eur. J. 24, 14346-14351 (2018). (equal contribution) (IF : 5.160)

(14)  S. Patra, C. Anders, P. H. Schummel, R. Winter, Antagonistic effects of natural osmolyte mixtures and hydrostatic pressure on the conformational dynamics of a DNA hairpin probed at the single-molecule level, Phys. Chem. Chem. Phys. 20, 13159-13170 (2018). (IF : 3.567)

We show that the deep sea shrimp osmolyte mixture that is largely composed of TMAO is able to rescue the DNA hairpin from unfolding even up to about 1000 bar, the maximum pressure encountered in the deep sea. This work demonstrates the great potential of compatible osmolytes to combat deteriorating effects of high hydrostatic pressures on the conformational dynamics of biomolecules.

2017

(13)  S. Patra, C. Anders, N. Erwin, R. Winter, Osmolyte effects on the conformational dynamics of a DNA hairpin at ambient and extreme environmental conditions, Angew. Chem. Int. Ed., 129, 5127-5131 (2017). (IF : 12.959)

First demonstration of single molecule FRET study of biomolecular conformational dynamics at high pressure enabled by a flexible fused silica microcapillary. 

(12)  M. Gao, C. Held, S. Patra, L. Arns, G. Sadowski, R. Winter, Crowders and cosolvents—major contributors to the cellular milieu and efficient means to counteract environmental stresses, ChemPhysChem, 18, 2951-2972 (2017). (IF : 3.144)

In this review, we have discussed the recent experimental and theoretical studies on the  characterization of cosolvent and crowding induced effects in biologically relevant systems, approaching even the complexity of living organisms. In particular, we focus on cosolvent and crowding effects on the conformational equilibrium and folding kinetics of proteins and nucleic acids as well as on enzymatic reactions, including their effects on the temperature and pressure dependence of these processes. 

(11)  N. Erwin, S. Patra, M. Dwivedi, K. Weise, R. Winter, Influence of isoform-specific Ras lipidation motifs on protein partitioning and dynamics in model membrane systems of various complexity, Biol Chem., 398, 547–563 (2017). (IF : 3.014)

(9)   S. Patra, N. Erwin, R. Winter, Translational dynamics of lipidated Ras proteins in the presence of crowding agents and compatible osmolytes, ChemPhysChem, 17, 2164-2169 (2016). (IF : 3.144)

(8)  S. Seth, N. Mondal, S. Patra, A. Samanta, Fluorescence Blinking and Photoactivation of All-Inorganic Perovskite Nanocrystals CsPbBr3 and CsPbBr2I, J. Phys. Chem. Lett., 7, 266-271 (2016). (IF : 7.329)

In this article, we have conclusively established the mechanism behind photoactivation and photocorrosion of the quantum dots.

2012

(3)  S. Patra, A. Samanta, Microheterogeneity of some imidazolium ionic liquids as revealed by fluorescence correlation spectroscopy and lifetime studies, J. Phys. Chem. B, 116, 12275-12283 (2012). (IF : 2.923)

(2)  S. Patra, K. Santhosh, A. Pabbathi, A. Samanta, Diffusion of organic dyes in bovine serum albumin solution studied by fluorescence correlation spectroscopy, RSC Advances, 2, 6079-6086 (2012). (IF : 3.119)

2011

(1)  K. Santhosh, S. Patra, S. Soumya, D. C. Khara, A. Samanta, Fluorescence Quenching of CdS Quantum Dots by 4‐Azetidinyl‐7‐Nitrobenz‐2‐Oxa‐1, 3‐Diazole: A Mechanistic Study, ChemPhysChem, 12, 2735-2741 (2011). (IF : 3.075)