Nucleic Acid hairpins have been a subject of study for the last four decades. They are composed of single strand that is
hybridized to itself, and the central section forming an unhybridized loop. In nature, they stabilize single stranded RNA, serve as nucleation
sites for RNA folding, protein recognition signals, mRNA localization and regulation of mRNA degradation. On the other hand,
DNA hairpins in biological contexts have been studied with respect to forming cruciform structures that can regulate gene expression.
The use of DNA hairpins as fuel for synthetic molecular devices, including locomotion, was proposed and experimental demonstrated in 2003. They
were interesting because they bring to the table an on-demand energy/information supply mechanism.
The energy/information is hidden (from hybridization) in the hairpin’s loop, until required.
The energy/information is harnessed by opening the stem region, and exposing the single stranded loop section.
The loop region is now free for possible hybridization and help move the system into a thermodynamically favourable state.
The hidden energy and information coupled with
programmability provides another functionality, of selectively choosing what reactions to hide and
what reactions to allow to proceed, that helps develop a topological sequence of events.
Hairpins have been utilized as a source of fuel for many different DNA devices. In this thesis, we program four different
molecular devices using DNA hairpins, and experimentally validate them in the
laboratory. 1) The first device: A
novel enzyme-free autocatalytic self-replicating system composed entirely of DNA that operates isothermally. 2) The second
device: Time-Responsive Circuits using DNA have two properties: a) asynchronous: the final output is always correct
regardless of differences in the arrival time of different inputs.
b) renewable circuits which can be used multiple times without major degradation of the gate motifs
(so if the inputs change over time, the DNA-based circuit can re-compute the output correctly based on the new inputs).
3) The third device: Activatable tiles are a theoretical extension to the Tile assembly model that enhances
its robustness by protecting the sticky sides of tiles until a tile is partially incorporated into a growing assembly.
4) The fourth device: Controlled Amplification of DNA catalytic system: a device such that the amplification
of the system does not run uncontrollably until the system runs out of fuel, but instead achieves a finite
amount of gain.
Nucleic acid circuits with the ability
to perform complex logic operations have many potential practical applications, for example the ability to achieve point of care diagnostics.
We discuss the designs of our DNA Hairpin molecular devices, the results we have obtained, and the challenges we have overcome
to make these truly functional.
","abstract_html":"<p>Nucleic Acid hairpins have been a subject of study for the last four decades. They are composed of single strand that is </p><p>hybridized to itself, and the central section forming an unhybridized loop. In nature, they stabilize single stranded RNA, serve as nucleation</p><p>sites for RNA folding, protein recognition signals, mRNA localization and regulation of mRNA degradation. On the other hand, </p><p>DNA hairpins in biological contexts have been studied with respect to forming cruciform structures that can regulate gene expression.</p><p>The use of DNA hairpins as fuel for synthetic molecular devices, including locomotion, was proposed and experimental demonstrated in 2003. They</p><p>were interesting because they bring to the table an on-demand energy/information supply mechanism. </p><p>The energy/information is hidden (from hybridization) in the hairpin’s loop, until required.</p><p>The energy/information is harnessed by opening the stem region, and exposing the single stranded loop section.</p><p>The loop region is now free for possible hybridization and help move the system into a thermodynamically favourable state.</p><p>The hidden energy and information coupled with </p><p>programmability provides another functionality, of selectively choosing what reactions to hide and </p><p>what reactions to allow to proceed, that helps develop a topological sequence of events. </p><p>Hairpins have been utilized as a source of fuel for many different DNA devices. In this thesis, we program four different </p><p>molecular devices using DNA hairpins, and experimentally validate them in the</p><p>laboratory. 1) The first device: A </p><p>novel enzyme-free autocatalytic self-replicating system composed entirely of DNA that operates isothermally. 2) The second</p><p>device: Time-Responsive Circuits using DNA have two properties: a) asynchronous: the final output is always correct </p><p>regardless of differences in the arrival time of different inputs.</p><p>b) renewable circuits which can be used multiple times without major degradation of the gate motifs </p><p>(so if the inputs change over time, the DNA-based circuit can re-compute the output correctly based on the new inputs).</p><p>3) The third device: Activatable tiles are a theoretical extension to the Tile assembly model that enhances </p><p>its robustness by protecting the sticky sides of tiles until a tile is partially incorporated into a growing assembly. </p><p>4) The fourth device: Controlled Amplification of DNA catalytic system: a device such that the amplification</p><p>of the system does not run uncontrollably until the system runs out of fuel, but instead achieves a finite</p><p>amount of gain.</p><p>Nucleic acid circuits with the ability </p><p>to perform complex logic operations have many potential practical applications, for example the ability to achieve point of care diagnostics.</p><p>We discuss the designs of our DNA Hairpin molecular devices, the results we have obtained, and the challenges we have overcome</p><p>to make these truly functional.</p>","abstract_has_math":false,"creators":["Garg, Sudhanshu"],"institution":null,"degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Reif, John H"],"committee_chairs":[],"committee_members":[],"year":2016,"date_issued":"2016","date_published":"2016","updated_at":"2026-07-24T02:07:17Z","subjects":["Computer science","autocatalytic","catalytic","circuits","DNA","strand displacement"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/10161/12175","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Reif, John H"]},{"key":"dc:creator","label":"Author","values":["Garg, Sudhanshu"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2016-06-06T14:37:08Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2016-06-06T14:37:08Z"]},{"key":"dc:date.issued","label":"Date","values":["2016"]},{"key":"dc:type","label":"Dc Type","values":["Dissertation"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Computer science","autocatalytic","catalytic","circuits","DNA","strand displacement"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://hdl.handle.net/10161/12175"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Nucleic Acid hairpins have been a subject of study for the last four decades. They are composed of single strand that is
hybridized to itself, and the central section forming an unhybridized loop. In nature, they stabilize single stranded RNA, serve as nucleation
sites for RNA folding, protein recognition signals, mRNA localization and regulation of mRNA degradation. On the other hand,
DNA hairpins in biological contexts have been studied with respect to forming cruciform structures that can regulate gene expression.
The use of DNA hairpins as fuel for synthetic molecular devices, including locomotion, was proposed and experimental demonstrated in 2003. They
were interesting because they bring to the table an on-demand energy/information supply mechanism.
The energy/information is hidden (from hybridization) in the hairpin’s loop, until required.
The energy/information is harnessed by opening the stem region, and exposing the single stranded loop section.
The loop region is now free for possible hybridization and help move the system into a thermodynamically favourable state.
The hidden energy and information coupled with
programmability provides another functionality, of selectively choosing what reactions to hide and
what reactions to allow to proceed, that helps develop a topological sequence of events.
Hairpins have been utilized as a source of fuel for many different DNA devices. In this thesis, we program four different
molecular devices using DNA hairpins, and experimentally validate them in the
laboratory. 1) The first device: A
novel enzyme-free autocatalytic self-replicating system composed entirely of DNA that operates isothermally. 2) The second
device: Time-Responsive Circuits using DNA have two properties: a) asynchronous: the final output is always correct
regardless of differences in the arrival time of different inputs.
b) renewable circuits which can be used multiple times without major degradation of the gate motifs
(so if the inputs change over time, the DNA-based circuit can re-compute the output correctly based on the new inputs).
3) The third device: Activatable tiles are a theoretical extension to the Tile assembly model that enhances
its robustness by protecting the sticky sides of tiles until a tile is partially incorporated into a growing assembly.
4) The fourth device: Controlled Amplification of DNA catalytic system: a device such that the amplification
of the system does not run uncontrollably until the system runs out of fuel, but instead achieves a finite
amount of gain.
Nucleic acid circuits with the ability
to perform complex logic operations have many potential practical applications, for example the ability to achieve point of care diagnostics.
We discuss the designs of our DNA Hairpin molecular devices, the results we have obtained, and the challenges we have overcome
to make these truly functional.
"]},{"key":"dc:title","label":"Title","values":["Programming Molecular Devices using Nucleic Acid Hairpins"]}]}],"canonical_facts":{"dc:contributor.advisor":["Reif, John H"],"dc:creator":["Garg, Sudhanshu"],"dc:date.accessioned":["2016-06-06T14:37:08Z"],"dc:date.available":["2016-06-06T14:37:08Z"],"dc:date.issued":["2016"],"dc:description.abstract":["Nucleic Acid hairpins have been a subject of study for the last four decades. They are composed of single strand that is
hybridized to itself, and the central section forming an unhybridized loop. In nature, they stabilize single stranded RNA, serve as nucleation
sites for RNA folding, protein recognition signals, mRNA localization and regulation of mRNA degradation. On the other hand,
DNA hairpins in biological contexts have been studied with respect to forming cruciform structures that can regulate gene expression.
The use of DNA hairpins as fuel for synthetic molecular devices, including locomotion, was proposed and experimental demonstrated in 2003. They
were interesting because they bring to the table an on-demand energy/information supply mechanism.
The energy/information is hidden (from hybridization) in the hairpin’s loop, until required.
The energy/information is harnessed by opening the stem region, and exposing the single stranded loop section.
The loop region is now free for possible hybridization and help move the system into a thermodynamically favourable state.
The hidden energy and information coupled with
programmability provides another functionality, of selectively choosing what reactions to hide and
what reactions to allow to proceed, that helps develop a topological sequence of events.
Hairpins have been utilized as a source of fuel for many different DNA devices. In this thesis, we program four different
molecular devices using DNA hairpins, and experimentally validate them in the
laboratory. 1) The first device: A
novel enzyme-free autocatalytic self-replicating system composed entirely of DNA that operates isothermally. 2) The second
device: Time-Responsive Circuits using DNA have two properties: a) asynchronous: the final output is always correct
regardless of differences in the arrival time of different inputs.
b) renewable circuits which can be used multiple times without major degradation of the gate motifs
(so if the inputs change over time, the DNA-based circuit can re-compute the output correctly based on the new inputs).
3) The third device: Activatable tiles are a theoretical extension to the Tile assembly model that enhances
its robustness by protecting the sticky sides of tiles until a tile is partially incorporated into a growing assembly.
4) The fourth device: Controlled Amplification of DNA catalytic system: a device such that the amplification
of the system does not run uncontrollably until the system runs out of fuel, but instead achieves a finite
amount of gain.
Nucleic acid circuits with the ability
to perform complex logic operations have many potential practical applications, for example the ability to achieve point of care diagnostics.
We discuss the designs of our DNA Hairpin molecular devices, the results we have obtained, and the challenges we have overcome
to make these truly functional.
"],"dc:identifier.uri":["https://hdl.handle.net/10161/12175"],"dc:subject":["Computer science","autocatalytic","catalytic","circuits","DNA","strand displacement"],"dc:title":["Programming Molecular Devices using Nucleic Acid Hairpins"],"dc:type":["Dissertation"]},"updated_at":"2026-07-24T02:07:17Z"}