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DNA-Based Materials: From Single Molecules to Liquid Crystals

Gyawali, Prabesh
http://orcid.org/0000-0002-4140-0073
http://rave.ohiolink.edu/etdc/view?acc_num=kent1646138053940038

Abstract Details

2022, PHD, Kent State University, College of Arts and Sciences / Department of Physics.
We performed single-molecule studies to investigate the impact of several prominent small molecules (the oxazole telomestatin derivative L2H2-6OTD, pyridostatin, and Phen-DC 3) on intermolecular G-quadruplex (i-GQ) formation between two guanine-rich DNA strands that have 3-GGG repeats in one strand and 1-GGG repeat in the other (3+1 GGG), or 2-GGG repeats in each strand (2+2 GGG). Such structures are not only physiologically significant but have recently found use in various biotechnology applications, ranging from DNA-based wires to chemical sensors. Understanding the extent of stability imparted by small molecules on i-GQ structures has implications for these applications. The small molecules resulted in different levels of enhancement in i-GQ formation, depending on the small molecule and arrangement of GGG repeats. The largest enhancement we observed was in the 3+1 GGG arrangement, where i-GQ formation increased by an order of magnitude, in the presence of L2H2-6OTD. On the other hand, the enhancement was limited to three-fold with Pyridostatin (PDS) or less for the other small molecules in the 2+2 GGG case. By demonstrating detection of i-GQ formation at the single-molecule level, our studies illustrate the feasibility to develop more sensitive sensors that could operate with limited quantities of materials. In another study, although its mesomorphic properties have been studied for many years, only recently has the molecule of life begun to reveal the true range of its rich liquid crystalline (LC) behavior. End-to-end interactions between concentrated, ultra-short DNA duplexes – self-assembling to form longer aggregates that then organize into LC phases – and the incorporation of flexible single-stranded “gap” regions in otherwise fully-paired duplexes – leading to the first convincing evidence of an elementary lamellar (smectic-A) phase in DNA solutions – are two exciting developments that have opened new avenues for discovery. In this dissertation, we used a combination of optical microscopy and synchrotron small-angle x-ray scattering to characterize the nature and temperature dependence of elementary lamellar ordering in concentrated solutions of various “gapped” DNA (GDNA) constructs. We examine symmetric GDNA constructs consisting of two 48 base-pair duplex segments bridged by an unpaired, single-stranded sequence (“gap”) of 2 – 20 thymine bases. Two distinct, elementary smectic layer structures are observed for DNA concentration in the range 220 - 270 mg/ml. One exhibits an interlayer periodicity comparable to two duplex lengths (“bilayer” structure), and the other has a period similar to a single duplex length (“monolayer” structure). The GDNA with a 20T gap exhibits a “bilayer" structure, with four observable diffractions, and, when heated to a temperature between 30 °C to 35 °C melts into the cholesteric phase. At a concentration of about 260 mg/ml, the GDNA constructs with a gap length of 10T or shorter (<10T) exhibit the “monolayer” structure with two observable diffraction peaks, which predominate upon heating to 40 °C. We discuss models for the two-layer structures and mechanisms for their stability. We also report results for novel asymmetric “gapped” constructs and for constructs with terminal overhangs. These results further test and support the model layer structures and illustrate the rich liquid crystalline phases formed by gapped DNA structures.
Hamza Balci (Committee Chair)
Samuel Sprunt (Committee Member)
Michael Tubergen (Committee Member)
Sanjaya Abeysirigunawardena (Committee Member)
Antal Jákli (Committee Member)
197 p.
Physics
G-quadruplex; small molecule; single-molecule; FRET; biosensor, “gapped” DNAp, smectic liquid crystal, phase transitions, SAXS

Recommended Citations

Citations

  • Gyawali, P. (2022). DNA-Based Materials: From Single Molecules to Liquid Crystals [Doctoral dissertation, Kent State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=kent1646138053940038

    APA Style (7th edition)

  • Gyawali, Prabesh. DNA-Based Materials: From Single Molecules to Liquid Crystals. 2022. Kent State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=kent1646138053940038.

    MLA Style (8th edition)

  • Gyawali, Prabesh. "DNA-Based Materials: From Single Molecules to Liquid Crystals." Doctoral dissertation, Kent State University, 2022. http://rave.ohiolink.edu/etdc/view?acc_num=kent1646138053940038

    Chicago Manual of Style (17th edition)

kent1646138053940038
275
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This open access ETD is published by Kent State University and OhioLINK.