Physisorptions of Biomolecules

Understanding Physical Adsorption of Biomolecules on Graphene-based Surfaces

Graphene-based surfaces have been an important subject of research as active biocompatible surfaces due to their excellent mechanical strength, large surface area, and controlled modification of surface polarity. Recently, many studies have reported the successful results for the promising applications using DNA or protein – graphene surfaces complexes, such as biosensors and drug delivery devices. It is known that oxidation rate of graphene surface acts as one of the key contributors because it can either improve or deteriorate sequencing and detection abilities, biocompatibility, stability, and performance of the aforementioned applications. However, understanding of how surface polarity affects bio-molecules structure is unclear and has shown an incomplete agreement among previous experimental studies. Molecular dynamics (MD) simulations are the computation modeling that can provide an atomistic description of structure and dynamics of biomolecules under various conditions. During this research period, I have focused on the comprehensive characterization of two promising systems using MD simulations: DNA and silk proteins, in order to systematically elucidate the effect of surface polarity on biomolecular structure and dynamics.

Effect of Graphene Oxidation Rate on Single Stranded DNA

8. 2013 - 2. 2017, Financially supported by NSF-CAREER (CMMI-1150682)
This research has collaborated with Dr. Barry Farmer (NC State, NC)

First, in the case of DNA on graphene surfaces with different oxidations, I found three important regimes for DNA adsorption which depends on surface oxidation rates: (1) On graphene surface with negligible or low oxidation rate, DNA becomes completely unfolded and unstable on the surface due to strong hydrophobic driven interactions between DNA and the surface; (2) in contrast, on the surfaces with moderate oxidation rate, conformational of folded DNA was maintained well since functional groups sticking out from the surface can sterically prevent DNA from hydrophobic driven interactions.; (3) on the surface with high oxidation rate, however, strong electrostatic driven interactions by functional groups can deteriorate the structural stability of DNA (Figure Right). For more details, see two references [1] and [2].

Effect of Graphene Oxidation Rate on Proteins & Peptides

8. 2013 - 2. 2017, Financially supported by NSF-CAREER (CMMI-1150682)
This research has collaborated with Dr. Vladimir Tsukruk (Georgia Tech, GA), and Dr. Kristin Krantzman (College of Charleston, SC)

Second, in the case of silk proteins on graphene surfaces, my recent work in collaboration with the experimental group (Dr. Tsukruk and his group at Georgia Tech) revealed that the graphene surface with moderate oxidation rate can not only preserve the structure of the protein but also can restore ordered silk structure from disrupted bio-molecular chains. In contrast, as observed in DNA work, silk structure also tended to be disrupted when hydrophobic interactions are the dominant factor for protein – surface interactions, such as the case of silk protein on graphene surface with negligible or low oxidation rate. This study enables a better surface selection with respect to the surface polarity. For example, the surface with low oxidation rate can be used for the applications that require a destabilization or denaturation process such as antimicrobial filters; on the other hand, the graphene surface with moderate oxidation rate should be used for the applications that require enhanced the structural stability of the biological materials including nanocarriers for drug delivery.

Overall, my research in this field has provided a comprehensive picture of the role of surface polarity on biomolecule structures and successfully provided rational strategies to the experiments. I adamantly believe that fine tuning graphene surface based on the results of my study can pave the way towards the development or design of many novel applications using bio-molecule – surface nanocomposite. So far, I have published four research paper in regards to this research topic (see [1] – [4] Journal Paper section below).

Structure and dynamics of DNA under various conditions are another essential factors for various technological applications using DNA – surface complexes. Recently, computational modeling has attracted research interest for understanding behaviors of DNA under various conditions because it is extremely hard to predict the dynamics of these flexible and nanoscale biopolymers by using experimental approach. As a researcher who specialized in computation modeling and the simulations of DNA, I participated in writing two review articles in regards to prediction of structural properties of DNA using various computational modeling techniques (see [5] and [6] in Journal Paper section below). I also believe that these review articles can be helpful for those who started research for DNA using the computation approach.

Journal Paper

#: Brief explanation about the paper

[1] Ho Shin Kim, Sabrina. M. Huang, and Yaroslava. G. Yingling. “Sequence-dependent interaction of single stranded DNA with graphitic flakes: atomistic molecular dynamics simulations”, MRS Advances 1, 25 (2016): 1883-1889 #DNA on graphene surface, early study#

[2] Ho Shin Kim, Barry L. Farmer, and Yaroslava G. Yingling. “Effect of graphene oxidation rate on adsorption of poly-thymine single stranded DNA”, Accepted by Advanced Materials Interfaces 4, 8, (2017): 1601168#Effect of surface oxidation on DNA#, Featured on journal cover

[3] Anise M. Grant, Ho Shin Kim, Trisha L. Dupnock, Kesong Hu, Yaroslava G. Yingling, and Vladmir V. Tsukruk. “Silk fibroin–substrate interactions at heterogeneous nanocomposite interfaces”, Vladmir V. Tsukruk. “Silk fibroin–substrate interactions at heterogeneous nanocomposite interfaces”, Advanced Functional Materials 26, 35 (2016): 6380-6392 #Silk protein – surface interactions# Featured on journal cover

[4] Brandon Roark, Anna Ivanina, Jose Castaneda, Ho Shin Kim, Shriram Jawahar, Mathias Viard, Strahinja Talic, Yaroslava Yingling, Marcus Jones, Kirill Afonin. "Fluorescence blinking as an output signal for programmable biosensing", ACS Sensors, 1, 11 (2016): 1295-1300 #Study on DNA bio-sensing: Experiment and Computation#

[5] Nan K. Li, Ho Shin Kim, Jessica A. Nash, Mina Lim, and Yaroslava G. Yingling. "Progress in molecular modelling of DNA materials." Molecular Simulation, 40, (2014): 1-7 #Review article about computation modeling of DNA#

[6] Jessica A. Nash, Albert L. Kwansa, James S. Peerless, Ho Shin Kim, and Yaroslava G. Yingling. “Advances in molecular modeling of nanoparticle-nucleic acid interfaces, Bioconjugate Chemistry, 28, 1 (2017): 3-10 #Review article about computation modeling of DNA on the particles#, Featured on journal cover

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