| NSF Org: |
CBET Division of Chemical, Bioengineering, Environmental, and Transport Systems |
| Recipient: |
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| Initial Amendment Date: | December 28, 2017 |
| Latest Amendment Date: | December 28, 2017 |
| Award Number: | 1733575 |
| Award Instrument: | Standard Grant |
| Program Manager: |
Nora Savage
nosavage@nsf.gov (703)292-7949 CBET Division of Chemical, Bioengineering, Environmental, and Transport Systems ENG Directorate for Engineering |
| Start Date: | January 1, 2018 |
| End Date: | December 31, 2018 (Estimated) |
| Total Intended Award Amount: | $130,000.00 |
| Total Awarded Amount to Date: | $130,000.00 |
| Funds Obligated to Date: |
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| History of Investigator: |
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| Recipient Sponsored Research Office: |
1608 4TH ST STE 201 BERKELEY CA US 94710-1749 (510)643-3891 |
| Sponsor Congressional District: |
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| Primary Place of Performance: |
476 Stanley Hall Berkeley CA US 94720-1762 |
| Primary Place of
Performance Congressional District: |
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| Unique Entity Identifier (UEI): |
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| Parent UEI: |
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| NSF Program(s): | Nanoscale Interactions Program |
| Primary Program Source: |
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| Program Reference Code(s): |
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| Program Element Code(s): |
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| Award Agency Code: | 4900 |
| Fund Agency Code: | 4900 |
| Assistance Listing Number(s): | 47.041 |
ABSTRACT
Proteins form the core arsenal of life, in signaling how living organisms behave, grow, and interact with their environment. To accomplish this range of biological functions, proteins have evolved remarkable attributes to interact specifically with other proteins, or with DNA. Recent discoveries have shown that certain conserved protein sequences have evolved the ability to "walk" along DNA in search of their target sites to enable this site-specific activity. The extraordinary speed and precision with which proteins accomplish this task remains a mystery, one that could have many benefits for engineering if the molecular precision of protein-DNA interactions could be reproduced in nanoscale synthetic systems. The research team will synthesize and characterize novel nanoscale materials that will behave like natural proteins in their ability to "walk" along DNA. This work could enable better understanding of how to design enzymes for bio-energy applications, antibodies for biological nanosensors, and protein-DNA interactions that drive all underlying cell processes. As a core component of the proposed research, the primary investigator will collaborate with Society for the Advancement of Chicanos and Native Americans in Science program at UC Berkeley to recruit two undergraduate students representing minority communities to the primary investigator's lab.
Brownian 1D diffusion of proteins along DNA enables protein-mediated cellular processes to occur on biologically-relevant timescales. Recent discoveries in protein biophysics have identified conserved sequences to facilitate 1-dimensional Brownian motion along DNA to expedite the target search process to a biologically-relevant timescale. Synthetic nanostructures have not been well-explored as bio-mimetic tools. Now that the "blueprints" for 1-dimensional Brownian diffusion are less elusive, the investigators propose an orthogonal study to apply these blueprints from biophysics to bioengineering. Here, the investigators seek to exploit these evolved features of site-specific proteins' 1-dimensional diffusion along DNA to build synthetic peptoid-based molecular machines. To-date, the study of synthetic motors has relied on the input of external sources of energy (chemical, photonic, etc). The investigators seek to exploit random (Brownian) mobility as a tool to build molecular translocators from synthetic bio-mimetic structures. Ultimately, the prediction is that the synthetic "Brownian machines" might carry molecular cargo, of potential applicability to fundamental and applied molecular and cellular research alike. This project combines high- resolution single-molecule fluorescence microscopy with robotic peptoid synthesis to develop a new class of synthetic materials capable of exploiting electrostatics for synthetic molecular machines. This work could be akin to the proof-of-principle exploratory research in scaffold-and-staple DNA-assembly that led to the field of DNA Origami. As a member of the underrepresented scientist community, the PI is both a strong supporter, and active leader in organizations supporting underrepresented scientists. This research effort will be integrated with the UC Berkeley Latino/a American Graduate Students in Engineering and Science program at Berkeley, and the Society for the Advancement of Chicanos and Native Americans. Prof. Landry will also organize and host the first nanobiosciences conference in Cuba, in collaboration with Prof. Dionisio Zaldivar Silva, Dean of the Faculty of Chemistry at the University of Havana Cuba. This NanoMEDD conference in Havana will be held using extramural funding that has already been secured.
PROJECT OUTCOMES REPORT
Disclaimer
This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.
The purpose of our project was to discover if synthetically-produced polymers could have life-like properties. There exist many processes in biology that are governed by molecular motion (i.e. drug delivery, protein inhibition-based therapies, cellular transcription and translation) that remain elusive and nearly impossible to replicate synthetically. Specifically, proteins are known to interact loosely with DNA through 1-dimensional sliding and hopping mechanisms to identify specific DNA binding sequences. This motion is based on Brownian diffusion (random movement) that driven along the 1-D track of DNA by electrostatic interactions, an efficient process that has been optimized by evolution of protein-DNA interactions. In this project, we sought to explore if man-made synthetic polymers could be engineered to exhibit 1-D diffusion along DNA trajectories, similarly or perhaps even more efficiently than proteins. In the first aim of the award, we synthesized a peptide sequence GVQSLKRRRCF, a conserved sequence within a larger adenovirus protein that had been shown to undergo 1D diffusion along DNA with high efficiency. We also synthesized a peptoid variant of the aforementioned peptide sequence with robotic solid-phase synthesis, for which our protocol is described in our recent peptoid synthesis publication (Chio et al. Nano Letters 2019). Next, we tagged both the peptide and the peptoid with a fluorescent marker, to enable tracking the peptide and peptoid as they interact with DNA in a glass microfluidic slide. Lastly, we designed microfluidic chambers to enable the creation of DNA bridges extended along the microscope slide surface, for introduction of fluorescently-labeled peptide and peptoids. Interestingly, we find that our synthetic peptoid diffuses along DNA bridges when the charges on the peptoid are similar to the charges in the peptide. Our figure shows the DNA bridges next to trajectories of the peptoid tracked by single-particle-tracking software. Our results suggest 1) that synthetic polymers can be made to behave as biologically-relevant protein counterparts, and 2) that the properties evolved from peptides for 1-D diffusion along DNA can be replicated in a synthetic polymer. Our project results inspire future work in designing other polymers with different lengths, charges, and structures, to explore if synthetic peptoids might enable new diffusive behaviors along DNA. Additionally, the PI has put together a proposal for a scientific Session at the SACNAS (Society for the Advancement of Chicanos and Native Americans in Science) National Conference. The goal of this session is to expose students to cutting-edge research led by a panel of 3 diverse faculty members, and to mentor students through informal discussion. Each speaker will provide an overview of their personal and academic experience, and as a result of this session, students will increase their science identity, draw parallels to their own personal and academic experiences, learn about competitive funding opportunities, and become more knowledgeable in the science approaches being used to create or investigate therapeutic solutions.
Last Modified: 04/29/2019
Modified by: Markita P Landry
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