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Programming DNA for Molecular-scale ...

Shah, Shalin Nitinkumar.

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Programming DNA for Molecular-scale Temporal Barcoding and Enzymatic Computation.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Programming DNA for Molecular-scale Temporal Barcoding and Enzymatic Computation./
Author:	Shah, Shalin Nitinkumar.
Published:	Ann Arbor : ProQuest Dissertations & Theses, : 2020,
Description:	141 p.
Notes:	Source: Dissertations Abstracts International, Volume: 81-11, Section: B.
Contained By:	Dissertations Abstracts International81-11B.
Subject:	Computer science. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=27740649
ISBN:	9798645444747

Programming DNA for Molecular-scale Temporal Barcoding and Enzymatic Computation.
Shah, Shalin Nitinkumar.

Programming DNA for Molecular-scale Temporal Barcoding and Enzymatic Computation. - Ann Arbor : ProQuest Dissertations & Theses, 2020 - 141 p.

Source: Dissertations Abstracts International, Volume: 81-11, Section: B.

Thesis (Ph.D.)--Duke University, 2020.

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

DNA, the blueprint of life, is more than a carrier of genetic information. It offers a highly programmable substrate that can be used for computing, nanorobotics, and advanced imaging techniques. In this work, we use the programmable nature of synthetic DNA to engineer two novel applications. In the first part, DNA is programmed to improve the multiplexing capabilities of a fluorescence microscope while in the second part, we design a novel DNA computing architecture that uses a strand displacing polymerase enzyme. This thesis is a collection of 2 experimental papers, 2 theory papers, and 1 software paper. The general theme of this thesis is to exploit the programmable nature of DNA to develop new applications for the wider field of molecular biology, nanoimaging, and computer engineering.Optical multiplexing is defined as the ability to study, detect, or quantify multiple objects of interest simultaneously. There are several ways to improve optical multiplexing, namely, using orthogonal wavelengths, multiple mesoscale geometries, orthogonal nucleic acid probes, or a combination of these. Most traditional techniques employ either the geometry or the color of single molecules to uniquely identify (or barcode) different species of interest. However, these techniques require complex sample preparation and multicolor hardware setup. In this work, we introduce a time-based amplification-free single-molecule barcoding technique using easy-to-design nucleic acid strands. A dye-labeled complementary reporter strand transiently binds to the programmed nucleic acid strands to emit temporal intensity signals. We program the DNA strands to emit uniquely identifiable temporal signals for molecular-scale fingerprinting. Since the reporters bind transiently to DNA devices, our method offers relative immunity to photobleaching. We use a single universal reporter strand for all DNA devices making our design extremely cost-effective. We show DNA strands can be programmed for generating a multitude of uniquely identifiable molecular barcodes. Our technique can be easily incorporated with the existing orthogonal methods that use wavelength or geometry to generate a large pool of distinguishable molecular barcodes thereby enhancing the overall multiplexing capabilities of single-molecule imaging. The proposed project has exciting transformative potential for nanoscale applications in fluorescence microscopy and cell biology since the development of temporal barcodes would allow for applications such as sensing miRNAs which are largely associated with disease diagnosis and therapeutics.The regulation of cellular and molecular processes typically involves complex biochemical networks. Synthetic nucleic acid reaction networks (both enzyme-based and enzyme-free) can be systematically designed to approximate sophisticated biochemical processes. However, most of the prior experimental protocols for chemical reaction networks (CRNs) relied on either strand-displacement hybridization or restriction and exonuclease enzymatic reactions. These resulting synthetic systems usually suffer from either slow rates or leaky reactions. This work proposes an alternative architecture to implement arbitrary reaction networks, that is based entirely on strand-displacing polymerase reactions with nonoverlapping I/O sequences. First, the design for a simple protocol that can approximate arbitrary unimolecular and bimolecular reactions using polymerase strand displacement reactions is presented. Then these fundamental reaction systems are used as modules to show large-scale applications of the architecture, including an autocatalytic amplifier, a molecular-scale consensus protocol, and a dynamic oscillatory system. Finally, we engineer an in vitro catalytic amplifier system as a proof-of-concept of our polymerase architecture since such sustainable amplifiers require careful sequence design and implementation.

ISBN: 9798645444747Subjects--Topical Terms:

523869
Computer science.
Subjects--Index Terms:

Computational imaging

Programming DNA for Molecular-scale Temporal Barcoding and Enzymatic Computation.
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300 $a 141 p.
500 $a Source: Dissertations Abstracts International, Volume: 81-11, Section: B.
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520 $a DNA, the blueprint of life, is more than a carrier of genetic information. It offers a highly programmable substrate that can be used for computing, nanorobotics, and advanced imaging techniques. In this work, we use the programmable nature of synthetic DNA to engineer two novel applications. In the first part, DNA is programmed to improve the multiplexing capabilities of a fluorescence microscope while in the second part, we design a novel DNA computing architecture that uses a strand displacing polymerase enzyme. This thesis is a collection of 2 experimental papers, 2 theory papers, and 1 software paper. The general theme of this thesis is to exploit the programmable nature of DNA to develop new applications for the wider field of molecular biology, nanoimaging, and computer engineering.Optical multiplexing is defined as the ability to study, detect, or quantify multiple objects of interest simultaneously. There are several ways to improve optical multiplexing, namely, using orthogonal wavelengths, multiple mesoscale geometries, orthogonal nucleic acid probes, or a combination of these. Most traditional techniques employ either the geometry or the color of single molecules to uniquely identify (or barcode) different species of interest. However, these techniques require complex sample preparation and multicolor hardware setup. In this work, we introduce a time-based amplification-free single-molecule barcoding technique using easy-to-design nucleic acid strands. A dye-labeled complementary reporter strand transiently binds to the programmed nucleic acid strands to emit temporal intensity signals. We program the DNA strands to emit uniquely identifiable temporal signals for molecular-scale fingerprinting. Since the reporters bind transiently to DNA devices, our method offers relative immunity to photobleaching. We use a single universal reporter strand for all DNA devices making our design extremely cost-effective. We show DNA strands can be programmed for generating a multitude of uniquely identifiable molecular barcodes. Our technique can be easily incorporated with the existing orthogonal methods that use wavelength or geometry to generate a large pool of distinguishable molecular barcodes thereby enhancing the overall multiplexing capabilities of single-molecule imaging. The proposed project has exciting transformative potential for nanoscale applications in fluorescence microscopy and cell biology since the development of temporal barcodes would allow for applications such as sensing miRNAs which are largely associated with disease diagnosis and therapeutics.The regulation of cellular and molecular processes typically involves complex biochemical networks. Synthetic nucleic acid reaction networks (both enzyme-based and enzyme-free) can be systematically designed to approximate sophisticated biochemical processes. However, most of the prior experimental protocols for chemical reaction networks (CRNs) relied on either strand-displacement hybridization or restriction and exonuclease enzymatic reactions. These resulting synthetic systems usually suffer from either slow rates or leaky reactions. This work proposes an alternative architecture to implement arbitrary reaction networks, that is based entirely on strand-displacing polymerase reactions with nonoverlapping I/O sequences. First, the design for a simple protocol that can approximate arbitrary unimolecular and bimolecular reactions using polymerase strand displacement reactions is presented. Then these fundamental reaction systems are used as modules to show large-scale applications of the architecture, including an autocatalytic amplifier, a molecular-scale consensus protocol, and a dynamic oscillatory system. Finally, we engineer an in vitro catalytic amplifier system as a proof-of-concept of our polymerase architecture since such sustainable amplifiers require careful sequence design and implementation.
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653 $a DNA hybridization kinetics
653 $a Machine learning
653 $a Markov chains
653 $a Time series analysis
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