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DNA-based Materials: From Single Molecules to Liquid Crystals.

紀錄類型:	書目-電子資源 : Monograph/item
正題名/作者:	DNA-based Materials: From Single Molecules to Liquid Crystals./
作者:	Gyawali, Prabesh.
出版者:	Ann Arbor : ProQuest Dissertations & Theses, : 2022,
面頁冊數:	198 p.
附註:	Source: Dissertations Abstracts International, Volume: 83-10, Section: B.
Contained By:	Dissertations Abstracts International83-10B.
標題:	Physics. -
電子資源:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=29133270
ISBN:	9798209889335

DNA-based Materials: From Single Molecules to Liquid Crystals.
Gyawali, Prabesh.

DNA-based Materials: From Single Molecules to Liquid Crystals. - Ann Arbor : ProQuest Dissertations & Theses, 2022 - 198 p.

Source: Dissertations Abstracts International, Volume: 83-10, Section: B.

Thesis (Ph.D.)--Kent State University, 2022.

This item must not be sold to any third party vendors.

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 ºC to 35 ºC 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 ºC. 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.

ISBN: 9798209889335Subjects--Topical Terms:

516296
Physics.
Subjects--Index Terms:

G-quadruplex

DNA-based Materials: From Single Molecules to Liquid Crystals.
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245 1 0 $a DNA-based Materials: From Single Molecules to Liquid Crystals.
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300 $a 198 p.
500 $a Source: Dissertations Abstracts International, Volume: 83-10, Section: B.
500 $a Advisor: Balci, Hamza;Sprunt, Samuel.
502 $a Thesis (Ph.D.)--Kent State University, 2022.
506 $a This item must not be sold to any third party vendors.
520 $a 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 ºC to 35 ºC 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 ºC. 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.
590 $a School code: 0101.
650 4 $a Physics. $3 516296
650 4 $a Molecular physics. $3 3174737
650 4 $a Molecular biology. $3 517296
650 4 $a Biophysics. $3 518360
653 $a G-quadruplex
653 $a Small molecule
653 $a Single-molecule
653 $a FRET
653 $a Biosensor
653 $a "Gapped" DNAp
653 $a Smectic liquid crystal
653 $a Phase transitions
653 $a SAXS
653 $a Liquid crystalline behavior
653 $a Fluorescence resonance energy transfer
690 $a 0605
690 $a 0786
690 $a 0307
690 $a 0609
710 2 $a Kent State University. $b College of Arts and Sciences / Department of Physics. $3 3431437
773 0 $t Dissertations Abstracts International $g 83-10B.
790 $a 0101
791 $a Ph.D.
792 $a 2022
793 $a English
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=29133270