*** I'm hiring! ***
1) Undergraduate or graduate students for individual investigation, rotation, honor's theses or sophomore research projects. Students not nececerrily have to have a Physics background, but Chemistry, Biochemistry, computer science and molecular biology is also highly welcome. Students just need to have a broader interest in single-molecule biophysics, molecular biology or biochemistry. Several projects are available depending on the student's backgrounds. Inquire fro more information.
2) PhD projects: Several projects are available for students from various backgrounds including physics, chemistry (polymer chemistry, physical chemistry, or biochemistry), and biology (molecular), bioengineering or related subjects.
If you are not admitted to a graduate program at Kent State, yet: Please be aware that at US universities, students need to be accepted to a graduate program, do some courses and pass “candidacy exams” prior to starting full-time research for their PhD project. Typically, you will also be a teaching assistant in a course or lab during the semester. If your previous degree is not in Physics, you may also check the graduate programs of the "Biomedical Sciences" program, particularly the Cell & Molecular Biology program, or the Material Science Graduate Program.
Why Building with DNA?
DNA is a unique polymer. It is the information storage molecule of all known life forms, and can be used to build up almost arbitrary structures and patterns out of DNA. These structures can be functionalized with a large variety of inorganic nanoparticles, small molecules or large biomolecules such as proteins and antibodies. Our group is leveraging this programmability to engineer nanoarchitectures and tools for applications in biophysics, structural biology, nanophotonics and nanomedicine. Moreover, we are developing scalable “next-generation DNA synthesis” methods.
DNA-Lipid Nanodiscs as Tools for Single-Molecule Cryo-EM of Membrane proteins
A main focus of our group is to develop molecular tools that allow to study membrane proteins (MPs), which are among the most important, but least understood components of cells. All cells are surrounded by lipid membranes that are almost impermeable for water, salts or nutrients that cells need. For this reason, a large number of membrane protein(MPs) are inserted into the membranes that control cellular functions such as material transport, sensing, intercellular communication, cell adhesion, and energy conversion. MPs are also the targets for many therapeutic drug molecules. Knowledge of the molecular structure of MPs is necessary to understand the underlying molecular mechanisms of their function and can guide the development of therapeutic drugs for many common diseases. However, MPs are difficult to study and therefore the molecular structure of most MPs is still unknown. The goal of this project is to develop broadly applicable new tools using DNA nanotechnology that will facilitate solving MP structures with cryo-electron microscopes. .
Update 3/2021: Our lab recently received an NSF EAGER award for developing our DNA-lipid nanodiscs into tools for single-molecule cryo-EM tools for membrane proteins.
Update 8/2021: We received a major 5-year award from the National Institutes of Health (NIGMS R35) for this project.
Other Research Interests
DNA-Based Plasmonic Devices
The field of plasmonics exploits the interaction of light with nanoscale metallic structures to confine, guide and manipulate light on scales below the diffraction limit. Plasmonic structures exhibit significant potential for applications including quantum optics, sensing, and short-distance optical communication (a). Towards this goal, we demonstrated the precise, robust, and high-yield assembly of gold nanoparticles on DNA origami templates (b).
More recently, we realized energy propagation through such a self-assembled waveguide to a fluorescent nanodiamond and out coupling of energy. We analyzed the waveguiding at a single-device level by electron energy loss spectroscopy (c) and cathodoluminescence imaging spectroscopy. Our work visually demonstrates the realization of nanometer-precise light manipulation and energy conversion. .
Finally, these closely spaced gold nanoparticles create a strong plasmonic hotspot for the sensing of molecules. [Nano Lett. 2019].
Triangulated DNA Origami and Nanomechanical Actuators
In the macroscopic world, stiff and material-efficient structures such as construction cranes and high voltage transmission towers are usually built from triangulated wireframe structures. We extended the DNA origami concept to generate a series of triangulated trusses. These provide defined cavities that we seek to fill with functional elements.
By introducing single-stranded regions edges of the wireframe trusses, the structures are heavily deformed due to the entropic spring forces contracting the single-stranded region. The gaps can be filled by a gap filling polymerase (such as the T4 polymerase) or the addition of the missing oligonucleotides, thus creating a nanomechanical actuator.
Outlook: This principle shall be the basis for stimuli-responsive mechanical nano devices in photonics or for applications in molecular biology. Moreover, we wish to determine biophysical properties such as their bending and torsional stiffness with super-resolution microscopy or optical tweezers.
An important goal in nanomedicine is the synthesis of smart designer nanoparticles, which show a lower renal clearance compared to conventional drugs and increase specificity to malignant cells. Cancer stem cells (CSCs) are responsible for drug resistance, tumor recurrence, and metastasis in several cancer types, making their eradication a primary objective in cancer therapy. In a collaboration project lead by Dr. Goncalves-Schmidt, gold nanorods were functionalized with nestin-binding peptides that specifically recognize Glioblastoma multiforme stem cells for photothermal therapy. and .
Outlook: Building up on our experience with gold nanoparticle based cell uptake, we will develop sophisticated and more complex functionalized DNA structures for drug delivery or as diagnostic and therapeutic devices.
Stabilizing DNA Structures for Nanomedicine
A main drawback of structural DNA nanotechnology is the instability of structures in biological environments. We developed a protection strategy based on block copolymer micellization which stabilizes DNA structures in biological or low-salt environments.
Outlook: We will use this protection to enhance DNA-based nanomedicines.
“Next-Generation” DNA Synthesis Methods
Synthetic oligonucleotides (short single-stranded DNA) and genes (long double-stranded DNA) are the main cost factor for many studies in DNA nanotechnology, genetics and synthetic biology. Inexpensive chip-synthesized oligonucleotide libraries can contain hundreds of thousands of distinct sequences, however only at sub-femtomole quantities per strand. We developed a selective oligonucleotide amplification method based on rolling circle amplification (RCA) with a 10-1000-fold cost-reduction compared to synthetic oligonucleotides or competing amplification methods such as PCR.
Outlook: We have recently extended our method for de novo gene synthesis. This will allow us to design custom scaffolds, and testing design principles that influence the folding kinetics and yields.
Current group members:
- Praneetha Sundar Prakash (research assistant, PhD candidate Biomedical Sciences PhD Program)
- Soumya Chandrasekhar (research assistant, PhD candidate, Chemical Physics Interdisciplinary Program)
- Draven Houser (PhD candidate, Physics)
|Years||Name||Job/Degree||Next Career Step|
|2019||Prof. Yusuke Sato||Postdoc||Assistant Professor, Tohoku University, Sendai|
|2019||Dr. Parastoo Maleki||Postdoc||Postdoc at University of Texas, Austin|
|2019||Alamgir Kabir||Master's||PhD student, Toledo|
|2020-2021||Daniel Hollis||High School Intern||Physics student at KSU, Film maker|
|2019-2021||Brady Weber||Research Assistant||Medicine student, Case Western, Cleveland|
|2013-2018||at cfaed / TU Dresden|
|2014-2017||Dr. Fatih Nadi Gür||PhD.||Postdoc at LMU Munich|
|2014-2018||Dr. Michael Matthies||Master's and PhD.||Postdoc at Arizona State University|
|2014-2018||Dr. Nayan P. Agarwal||Master's and PhD.||Postdoc at Massachussets Institute of Technology|
|2015-2018||Dr. Bastian Joffroy||PhD.||Staff Scientist at DKMS Dresden|
|2015-2019||Dr. Katarina Iric||PhD.||Postdoc at TU Dresden|
|2014-2015||Hafesudeen Sahabudeen||Master's||PhD candidate at TU Dresden|
|2014-2016||Simon Ahrens||Technician||Paternity leave|
|2014-2015||Yavuz Uca||Master's||PhD candidate at Charite Berlin|
|2015-2016||Jingjing Ye||Master's||PhD candidate at U. Leipzig|
|2015-2016||Eric Wiener||Master's||PhD candidate at U. Leipzig|
|2017||Ashwin Karthick||Winter intern||PhD candidate Aalto University|
|2016-2017||Shikhar Gupta||Master's||PhD candidate at Leipzig University|
|2016-2017||Foram M. Joshi||Master's||PhD candidate at TU Dresden|
|2017-2018||Olga Aftenieva||Master's||PhD candidate at TU Dresden|
|2017-2018||Kristin Joffroy||Technitian||Staff Scientist at DKMS Dresden|
|2017-2018||Prof. Dr. Diana Goncalves-Schmidt||Postdoc||Assistant Professor for organic chemistry, Kent State University|
|2018||Chloe Jones||Summer intern||PhD candidate|
For more information, I recommend this 3-hour lecture (iBiology) by William Shih:
or a current review on structural DNA nanotechnology such as:
Fall 2021: Introduction into Single-Molecule Biophysics (in person if possible)
Students who don't need this course for credit could audit. Please inquire by email.
- 2018: Outstanding Mentor Award by the Dresden International PhD Program