We have thousands of apps on our computers and cell phones to serve our daily life and work. They are built by the programming languages in the information world. There are also thousands of molecular apps in our body to keep us healthy. They are programmed by the molecular languages of biomolecular systems in cells and across the cells. However, we are still far from understanding and designing those molecular apps.
A fundamental question we are motivated to answer is can we design those biomolecule apps as we develop apps in our cell-phone and computer? If we achieved this, we then can develop molecular robots to fight against diseases, molecular tools for advanced bio-analysis, novel biomaterials, and eventually even to program life. The key challenges toward this goal are to understand and manipulate complex biomolecular systems in biology. Biological systems are composed of billions of molecules (e.g., DNA, RNA, proteins) that encode different layers of information (e.g., primary sequence information, structure information by folding, function information for cellular activities). The molecular systems in the complex biological environment are the cornerstone to understanding life and developing cutting-edge technologies to advance human healthcare. We are a group of scientists working on biomolecular design to address challenges in bio-nanotechnology, bio-analysis with advanced sequencing and bio-imaging, and synthetic biology.
A fundamental question we are motivated to answer is can we design those biomolecule apps as we develop apps in our cell-phone and computer? If we achieved this, we then can develop molecular robots to fight against diseases, molecular tools for advanced bio-analysis, novel biomaterials, and eventually even to program life. The key challenges toward this goal are to understand and manipulate complex biomolecular systems in biology. Biological systems are composed of billions of molecules (e.g., DNA, RNA, proteins) that encode different layers of information (e.g., primary sequence information, structure information by folding, function information for cellular activities). The molecular systems in the complex biological environment are the cornerstone to understanding life and developing cutting-edge technologies to advance human healthcare. We are a group of scientists working on biomolecular design to address challenges in bio-nanotechnology, bio-analysis with advanced sequencing and bio-imaging, and synthetic biology.
Cells have their neighbors and will affect each other. Traditional biological analysis will blend all the cells in a tissue sample and the spatial information is missing. To understand the disease and cellular function with insights, we need to use “GPS” to create a map and track each cell within its local context. Along this direction, I’ll develop novel tools to facilitate the reading of spatial information in the biological context with DNA advanced multiplexed imaging. I'll develop method that significantly expands the multiplexity by using advanced DNA design to visualize biology (e.g., genomics, transcriptomics, and proteomics). The method will transform the way to illuminate biology spatially with unprecedented speed and information to understand biology with precision at the single-cell level and scalable at the tissue scale. The comprehensive spatial biological information will facilitate our understanding of tissue function and human diseases.
References :
1. Fan Hong, Jocelyn Y. Kishi, Ryan N. Delgado, Jiyoun Jeong, Sinem K. Saka, Hanquan Su, Constance L. Cepko, Peng Yin. Thermal-plex: Fluidic-free, rapid sequential multiplexed imaging with DNA encoded thermal channels. Nature Methods, 2023, in press
1. Fan Hong, Jocelyn Y. Kishi, Ryan N. Delgado, Jiyoun Jeong, Sinem K. Saka, Hanquan Su, Constance L. Cepko, Peng Yin. Thermal-plex: Fluidic-free, rapid sequential multiplexed imaging with DNA encoded thermal channels. Nature Methods, 2023, in press
References:
- Youngeun Kim, Adam B Yaseen, Jocelyn Y Kishi, Fan Hong, Sinem K Saka, Kuanwei Sheng, Nikhil Gopalkrishnan, Thomas E Schaus, Peng Yin. Single-stranded RPA for rapid sensitive detection of SARS-Cov-2 RNA. MedRxiv.
- Fan Hong, Duo Ma, Kaiyue Wu, Lida A. Mina, Rebecca C. Luiten, Yan Liu, Hao Yan*, Alexander A. Green*. Precise and Programmable Detection of Mutations Using Ultraspecific Riboregulators, Cell, 2020, 180, 1–15
- Xiaowen Ou, Fan Hong, et al, Fan Xia*, A highly sensitive and facile graphene oxide-based nucleic acid probe: Label-free detection of telomerase activity in cancer patient's urine using AIEgens, Biosensors and Bioelectronics, 2016, 89, 417-421.
References:
- Fan Hong, Jocelyn Y. Kishi1, Ryan N. Delgado, Jiyoun Jeong, Sinem K. Saka, Hanquan Su, Constance L. Cepko, Peng Yin*. Thermal-plex: Fluidic-free, rapid sequential multiplexed imaging with DNA encoded thermal channels. Nature Methods, 2023, In press.
- Fan Hong, Duo Ma, Kaiyue Wu, Lida A. Mina, Rebecca C. Luiten, Yan Liu, Hao Yan*, Alexander A. Green*. Precise and Programmable Detection of Mutations Using Ultraspecific Riboregulators, Cell, 2020, 180, 1018-1032.
- Fan Hong, John Shreck, Petr Sulc, Understanding DNA interactions in crowded environments with a coarse-grained model, Nucleic Acid Research, 2020,48,10726.
- Fan Hong, Shuoxing Jiang, Xiang Lan, Raghu Pradeep Narayanan, Petr, Sulc, Fei Zhang, Yan Liu, Hao Yan, Layered-Crossover Tiles with Precisely Tunable Angles for 2D and 3D DNA Crystal Engineering, J. Am. Chem. Soc. 2018, 140, 14670-14676.
- Fan Hong, Fei Zhang, Yan Liu, Hao Yan, DNA origami: scaffolds for creating high order structures. Chemical Review, 2017, 117, 12584-12640
- Fan Hong, Shuoxing Jiang, Tong Wang, Yan Liu, Hao Yan, 3D Framework DNA origami structure with layered crossover motifs. Angew Chem Int Ed, 2016,55, 12832-12835.