Skip to Main Content
 

Global Search Box

 
 
 
 

Files

File List


Dissertation_Karna_final.pdf (5.66 MB)

ETD Abstract Container

Abstract Header

Synthesis and Characterization of DNA Origami Nanosprings to Study Cellular Functions

Karna, Deepak
http://orcid.org/0000-0003-3370-0997
http://rave.ohiolink.edu/etdc/view?acc_num=kent1721050065253433

Abstract Details

2024, PHD, Kent State University, College of Arts and Sciences / Department of Chemistry and Biochemistry.
DNA origami structures have provided versatile tools in a wide variety of applications. Due to higher stability, tunability and mechanical strength compared to single stranded or double stranded DNA, origami-based DNA nanostructures have garnered special interest in the scientific community. Many of these biomedical applications exploit mechanical properties and therefore, need a discrete tool/method to analyze the dynamic structural changes in these nanoassemblies. Herein, we synthesized different origami based nanosprings and mechanically characterized their properties and eventually applied them to halt the cancer cell motions. To that end, the nanosprings were synthesized from 6 helix bundles of DNA with specific bridge elements made up of either i-motifs, or G-quadruplexes or duplex DNAs. The bridge elements served as junctions which pulled/pushed nearby elements to bend the structures; multiple of which exhibited a coiled spring. To characterize the mechanical properties, we employed optical tweezers as a single molecule force manipulation tool that record the extension behaviors under tensile force in real time, assisting to compute spring constant, kinetics, recoil and uncoil distances, and pitch of nanosprings. With the strength 17 times more than previous nanosprings, these nanostructures were exploited to modulate cell migrations. To that end, we modified nanosprings with arginyl-glycyl-aspartate (RGD) domains with a spacing such that when the nanospring is coiled, the RGD ligands trigger the clustering of integrin molecules, which changes cell motions. The coiling or uncoiling of the nanospring is controlled, respectively, by the formation or dissolution of pH responsive i-motifs. Results showed significant inhibition to the migration of HeLa cells in acidic extracellular environment under the influence of nanosprings. Likewise, to divulge the structural-property relationship and the modulation factors behind the long-range, higher order arrangement of subunits in a mesoscale assembly, we synthesized two reversible forms of nanosprings using G-quadruplexes and duplex DNA such that the orientational flipping of their backbones could be achieved. Simulation results and AFM images analysis provided insights on the origin of chiral helicity in mesoscale assemblies, and also paved a direction to develop topologically based caging/uncaging strategies for delivering druggable compounds.
Hanbin Mao (Committee Chair)
Sanjaya Abeysirigunawardena (Committee Member)
Yao-Rong Zheng (Committee Member)
Thorsten-Lars Schmidt (Committee Member)
Manabu Kurokawa (Other)
181 p.
Biochemistry; Biology; Biophysics; Cellular Biology; Chemistry
DNA origami; Nanosprings; Cell migration; Optical tweezers; Mesoscale; Chirality

Recommended Citations

Citations

  • Karna, D. (2024). Synthesis and Characterization of DNA Origami Nanosprings to Study Cellular Functions [Doctoral dissertation, Kent State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=kent1721050065253433

    APA Style (7th edition)

  • Karna, Deepak. Synthesis and Characterization of DNA Origami Nanosprings to Study Cellular Functions. 2024. Kent State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=kent1721050065253433.

    MLA Style (8th edition)

  • Karna, Deepak. "Synthesis and Characterization of DNA Origami Nanosprings to Study Cellular Functions." Doctoral dissertation, Kent State University, 2024. http://rave.ohiolink.edu/etdc/view?acc_num=kent1721050065253433

    Chicago Manual of Style (17th edition)

kent1721050065253433
114
© 2024, all rights reserved.
This open access ETD is published by Kent State University and OhioLINK.