Early Stage Research Projects

ESR: Anastasiia Sapunova 

Host institution: Istituto Italiano di Tecnologia ;  Main supervisors: Denis Garoli

Objectives: Based on the pioneering results obtained by the PIs at IIT (Garoli) on the successful application of plasmonic nanopore for single molecule spectroscopies and trapping, this project aims at optimizing, validating and exploiting hybrid plasmonic nanopores. The JR will mainly work on the design and simulation of the plasmonic nanostructures, considering planar and 3D designs. Noble metals, 2D materials and magnetic materials will be integrated in the designs. The simulations will explore how the electromagnetic field can be localized and phenomena such as enhanced spectroscopies, thermophoresis, optical and magnetic forces. In collaboration with JR2 the designed structures will be fabricated in clean-room facilities. The designed and prepared samples will be shared with the other JRs in order to perform translocation control and single molecule detection

Expected Results: To have validated plasmonic nanopore approaches for single molecule spectroscopy. To have a full comprehension of the physical phenomena that can be obtained in a hybrid plasmonic nanopore.

ESR: Shukun Weng

Host institution: Istituto Italiano di Tecnologia ;  Main supervisors: Denis Garoli

Objectives: This project aims at the fabrication of inorganic nanopores with integrated plasmonic and magneto-optical structures, such as nanoantennas and designs that act as optical tweezers. The design concept of such functional nanopores will also comprise the integration of biomolecules toward hybrid structures.  The JR will mainly work on the design and fabrication of the plasmonic nanostructures, which will also be extended to large arrays. The planar and 3D designs developed by JR1 that include noble metals, 2D materials and magnetic materials will provide the bases for this fabrication. The designed and prepared samples will be shared with the other JRs in order to perform translocation control and single molecule detection

Expected Results: To have reproducible methods to fabricate hybrid plasmonic nanopore arrays for single molecule spectroscopy.

ESR: to be defined

Host institution: University of Leipzig ;  Main supervisors: Ralf Seidel

Objectives: Aim of this project is the development of hollow DNA-based hybrid nanostructures for optimized optical sensing applications (SERS, fluorescence spectroscopy) and analyte molecule trapping/manipulation. Advanced spectroscopy based on surface enhanced EM fields requires metallic nanostructures that support strong localized field enhancement together with specific placement of analyte molecules. With the help of the recently developed (at ULEI) construction kit to fabricate complex metal nanostructures using modular DNA origami structures as molds, the JR will synthesize plasmonic metal nanostructures with localized strong field enhancement (e.g. rod-like structures with gaps, cavities, pores) and characterize their performance in sensing applications in order to find optimal designs. Beyond this, JR will integrate in these structures specific binding sites for analyte molecules (e.g. conjugated proteins, DNA-binding proteins, nucleic acids) to allow a specific placement of the analyte molecules at the sites of strong field enhancement. Furthermore methods to place the analyte molecules in specific orientations inside the plasmonic nanostructures in order to increase the reliability and reproducibility of optical sensing applications will be established. Finally, the JR will adapt the hybrid nanostructure platform to integrate nanopores prepared by JR1 and JR2 in the surrounding DNA scaffold such that it can be integrated with hybrid nanopore sensing applications to provide nanopores with DNA-tailored diameters as well as magnetic manipulation

Expected Results: Tailored hollow metal nanostructures with specific presentation of analyte molecules exhibiting an improved performance in optical sensing applications. Robust methodology to fabricate nanopores for hybrid sensing applications.

ESR: Nageswar Reddy Sanamreddy

Host institution: CIC nanoGUNE ;  Main supervisors: Paolo Vavassori

Objectives: Realization of a magneto-plasmonic tweezer for single molecule nanopore translocation control; Use of EM fields (suitable wavelengths or magnetic field sources) in order to control the moment of nanoparticles functionalized with biomolecules. The JR will combine a single nanotrap with a functionalized nanostructure for enhanced spectroscopy thanks to magneto-plasmonic structures combined with nanopores. The JR will verify the reduced speed of translocation firstly by monitoring the blockade current though the nanopore in different configurations. Then the optimization of the signal-to-noise-ratio from fluorescent and Raman spectroscopies experiments will be performed with nanotrap and check the predicted dependence with the translocation speed. The nanopores samples will be prepared in collaboration with IIT and CNRS

Expected Results: Will establish the first-ever magneto-plasmonic platform for single molecule trapping. Will control the translocation of nanoparticles and biomolecules with external magnetic field and combine this with electro-optical single entity detection. 

ESR: Malavika Kayyil-Veedu

Host institution: CNRS Marsille ;  Main supervisors: Jerome Wenger

Objectives: The aim of this project will be to exploit the intrinsic UV autofluorescence of proteins (due to their natural aromatic aminoacids) to achieve single molecule detection in a label-free manner. The JR will develop a nanopore platform able to trap single entities by means of magnetic force and/or in combination with plasmonic nano-optical trapping using the red laser. The spectroscopy approach will be combined with dedicated aluminium nanopores to (i) enhance the deep-UV autofluorescence signal, (ii) monitor translocation and (iii) screen the background. To investigate possible conformational changes of the protein, the JR will learn how to combine the deep-UV approach with a conventional fluorescence labelling and detection using fluorescent dyes in the red spectral range. This multimodal approach will bring additional information without impairing the UV detection. 

Expected Results: Controlled single protein translocation through the nanopore detected label-free in the deep-UV and confirmed by red fluorescent dye signal. Influence of the UV laser on the protein conformation and potential structural damages. Role of energy transfer between the dyes. Demonstration of plasmonic trapping at the single protein level. 

ESR: to be defined

Host institution: University of Milano Bicocca ;  Main supervisors: Sergio Brovelli

Objectives: Key for effective single molecule spectroscopy studies on biomolecules, both isolated and coupled to plasmonic structures, is having a clear, comprehensive understanding of the photophysical processes. These include the energetics and kinetics of fundamental radiative and nonradiative processes (i.e. fluorescence, phosphorescence, intersystem crossing, phonon coupling) as well as the effects of external factors such as temperature, magnetic fields and dielectric environments. These might, in fact impact the excited states dynamics and modify the coupling with plasmonic effects by, for instance, causing substantial spectral shifts due to singlet-triplet transfer, phononic or solvatochromic effects. Therefore, JR6 will be focused on the in-depth spectroscopic investigation of the target biomolecules and nanostructures so as to provide fundamental insights onto their optical properties and experimental guidelines for tailored single molecule studies in collaboration with the other partners.

Expected Results: The activity by JR6 will envisage cw and ultrafast transient optical absorption and ultrafast emission spectroscopy to monitor the luminescence spectra and kinetics in a wide range of time (ps-cw) and energy (UV-NIR) in controlled conditions of temperature (5-300K), magnetic fields (up to 5T) and electrochemical environments controlled via custom spectro-electrochemical equipment. The ensemble studies will then be coupled to single molecule investigations by coupling the above spectroscopic facilities with a dedicated single molecule spectroscopy setup to monitor emission flickering/blinking behaviours as well as possible conformational effects that do not emerge in ensemble experiments. The data thereby collected will enable JR6 to draw comprehensive mechanistic models describing the excited state dynamics/kinetics of all target DNA nanostructures both at the ensemble and single particle levels that will feed both the materials preparation, NP design/fabrication and subsequential translocation and single molecule analysis efforts. 

ESR: Shrobona Banerjee

Host institution: University of Berlin ;  Main supervisors: Janina Kneipp

Objectives: This project will contribute to our understanding of the mechanism of molecule transition through nanopores by providing details on the interaction of proteins and nucleic acids with the nanopores. This aim will be reached by selectively probing the molecule-nanopore interaction in a multi-wavelength approach to surface-enhanced Raman scattering (SERS), including its two-photon excited analogue, surface-enhanced hyper Raman scattering (SEHRS). The project will build on a decade of research in the Kneipp group (UBER) on multi-modal enhanced vibrational spectroscopy that has been focusing on protein interactions in the past few years. Here, our existing knowledge on molecule-nanostructure interactions will be transferred and extended to experiments with different types of hybrid solid nanopores (from IIT) and structures fabricated using DNA and protein nanotechnology (ULEI).

Expected Results: Different points of interaction of individual protein molecules will be identified for specific excitation conditions, due to spatial variation of enhanced fields at the nanopores. The latter will be confirmed by state-of-the-art simulation results. Demonstration of label-free single molecule translocation through the nanopore using a range of excitation wavelengths. Identification of specific functional groups of the molecules and thereby molecular orientation in different nanopores. 

ESR: Archana Sivaraman

Host institution: TU DELFT ;  Main supervisors: Chirlmin Joo

Objectives: Here we will develop a new single-molecule protein analysis platform. The JR8, supervised by Joo group at TUDELFT will read out the sequence of a subset of residues on a target substrate by using single-molecule FRET combined with aptamer technology and identify different so-called proteoforms (many different protein forms arising from alternative splicing and post-translational modifications). This technique will make use of transient binding of aptamers labelled with fluorophores to build FRET fingerprints. A library of aptamers will be labeled and screened against biomarker proteins. Single-molecule FRET fingerprints will be acquired by immobilizing acceptor-labeled to labeled proteins of interest on the surface and adding donor-labeled aptamers. This knowledge will be transferred to the CAM, CNRS, ULEI, UBER and IIT groups for opto-electrical sensing of a protein using fluorescence, nanopores, and DNA origami. Fluorescently-labeled aptamers will be immobilized on DNA origami which will be mounted on nanopores. FRET signals will be boosted by surface plasmon resonance and read together with electrical signals using a setup by the other members of the network.

Expected Results: Will establish the first-ever single-molecule FRET based protein analysis using aptamers. Will identify different proteoforms of biomarkers including isoforms and protein translational modification at the single-molecule level. 

ESR: Simon Brauburger

Host institution: University of Cambridge ;  Main supervisors: Ulrich Keyser

Objectives: The identification of both single-nucleotide polymorphisms in short DNA and RNA molecules including possible modifications on the bases is of paramount importance for the analysis and understanding of biological systems, cancer detection and pharmacokinetics. The JR9 will use the electro-optical nanopores to detect the individual spectral and electrical fingerprints of RNA and DNA molecules with 20-30 nucleotides in lengths These short nucleic acids remain challenging to identify with standard sequencing techniques. The electro-optical nanopores will use the additional optical read-out to detect single nucleotide differences in short DNA and RNA by using SERS detection. The spectral fingerprinting will enable rapid-label free readout.

Expected Results:  A novel technique that can readout the chemical structure of short DNA and RNA molecules. The readout will be completely label-free and yield a transformational technique in detection of short biomolecules in the life sciences. 

ESR: Ehsan Semsar Parapari

Host institution: Elements S.r.l ;  Main supervisors: Federico Thei; Denis Garoli; Sergio Brovelli

Objectives: To engineer the nanopore system in order to obtain a high signal-to-noise ratio in electro-optical measurements; To integrate these smart nanostructures with on chip electronics and photodetectors for electro-optical data reading.

Solid-state nanopore arrays will be connected to the multichannel amplifiers (16ch) developed by the JR in ELE. Tests on the nanopore current readout combined to the optical readout will be done on samples prepared in collaboration with IIT. The JR will work to optimize the measurement controls and parameters to maximize the signal-to-noise ratio to improve the readout reliability. The design of the new microelectronics for nanopore current readout and optical readout will be done using suitable EDA tools. Chip prototyping using CMOS-MEMS and mixed signal process will be fabricated at suitable foundries using the MPW scheduling. Chip assembly into proper packaging able to host microelectronics, optoelectronics and microfluidic will be developed. Electronics board with PC data interface to host the new chips will be developed to realize the physical platform for experimental test.

Expected Results: Integrated device able to host nanopore chips for single molecule electro-optical measurements.

ESR: to be defined

Host institution: University of Leipzig ;  Main supervisors: Frank Cichos

 Objectives: The project aims at designing hybrid DNA-origami plasmonic structures to provide a reversible local melting of DNA for conformational control of larger DNA origami structures. The structure shall allow in the long-run the design of nanopore systems that have a fast-switchable permeability and trapping capability for objects in the nanopore and allow to switch between different sensing methods (e.g. optical spectroscopy). In combination with multiparticle plasmonic coupling and electrokinetic driving this could also lead to controlled ratchet-like translocation of objects through the nanopore. 

Expected Results: A hybrid plasmonic DNA-origami structure that allows thermal switching of conformation that can be used to control the permeability and the sensing methods of DNA-origami nanopores