DNA-BASED STIMULI-RESPONSIVE NANOTECHNOLOGY AND MATERIALS

Joonas Ryssy

DNA-BASED STIMULI-RESPONSIVE NANOTECHNOLOGY AND MATERIALS

Julkaisun otsikon käännös: DNA-BASED STIMULI-RESPONSIVE NANOTECHNOLOGY AND MATERIALS

Joonas Ryssy

Neurotieteen ja lääketieteellisen tekniikan laitos

Tutkimustuotos: Doctoral Thesis › Collection of Articles

Abstrakti

Tässä väitöskirjassa tutkitaan erilaisia DNA-pohjaisia ärsykkeille herkkiä järjestelmiä. Tässä työssä esitellyt järjestelmät antavat plasmonisia vasteita uudelleen järjestäytyessään rakenteellisesti ulkoisen ärsykkeen seurauksesta. DNA on monipuolinen biomolekyyli, jolla on kyky reagoida ympäristön ärsykkeisiin. Tässä väitöskirjassa käytimme kolmea eri ulkopuolista ärsykettä: valoa, pH:ta ja pieniä molekyylejä. Nämä ärsykkeet indusoivat erilaisia rakenteellisia muutoksia saaden aikaan plasmonisia vasteita. Ensimmäiseksi, DNA:n luontaista kykyä reagoida pH:n muutokseen hyödynnettiin Hoogsteen-sidoksen ja DNA:n kolmoissidosten itseohjaavuuden avulla. Kolmoissidos oli yhdistettynä DNA origamipohjaisiin kiraalisiin plasmonisiin metamolekyyleihin, jotka kykenivät vaihtamaan konfiguraatiota. Kolmoissidos toimi täten siltana lukiten DNA-origami rakenteen plasmonisesti intensiiviseen tilaan. Kolmoissidoksen tilaa hallittiin valoherkän väliaineen avulla, joka sisälsi protonoitua merosyaniinia. Täten DNA-origami-pohjaisia metamolekyylejä voitiin hallita ulkopuolisella näkyvällä valolla ilman valoherkkiä modifikaatioita DNA:ssa itsessään. Toiseksi, toimme DNA nanoteknologian kohti makroskaalan sovelluksia konjugoimalla kultananosylintereitä DNA:n avulla synteettiseen polymeeri verkostoon luoden hybridi DNA hydrogeelin. Tässä kultananosylinterit eivät vain toimineet plasmonisina vasteina vaan myös ärsykkeiden vastaanottimina. Kultananosylinterit olivat suunniteltu absorboimaan valoa punaisen valon aallonpituusalueella sekä toimimaan lämpöelementteinä. DNA:n luontaista lämpöherkkyyttä käytettiin tuomaan palautuvia dynaamisia valolle herkkiä ominaisuuksia hydrogeeliin. Ulkoinen valoärsyke mahdollisti rakenteellisten muutoksien laukaisemisen järjestelmässä edullisesti, vakaasti, kohdennetusti ja ilman syntyvää jätettä. Hydrogeeli ilmaisi palautuvia plasmonisia vasteita näkyvän valon muodossa. Kolmanneksi esittelimme DNA-origami-pohjaisia kiraalisia metamolekyylejä. Nämä metamolekyylit olivat funktionalisoitu DNA-aptameeri silloilla origamien käsien välissä muodostaen antureita. Kohdemolekyylin sitoutuminen kaksoisaptameeri siltaan sai aikaan rakenteellisia muutoksia, jotka vaikuttavat kultananosylentereiden välittämään kiraaliseen plasmoniseen vasteeseen. Seulomalla referenssi analyytit ja komplementtijuosteet alustaa käytettiin karakterisoimaan aptameeri-kohde affiniteettia. Yleisesti, tämä väitöskirja tuo esille DNA:n käyttöä rakennusmateriaalina nanorakenteissa ja ärsykkeille alttiissa materiaaleissa.

Julkaisun otsikon käännös	DNA-BASED STIMULI-RESPONSIVE NANOTECHNOLOGY AND MATERIALS
Alkuperäiskieli	Englanti
Pätevyys	Tohtorintutkinto
Myöntävä instituutio	Aalto-yliopisto
Ohjaaja	Kuzyk, Anton, Vastuuprofessori
Kustantaja	Aalto University
Painoksen ISBN	978-952-64-1124-8
Sähköinen ISBN	978-952-64-1125-5
Tila	Julkaistu - 2023
OKM-julkaisutyyppi	G5 Artikkeliväitöskirja

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http://urn.fi/URN:ISBN:978-952-64-1125-5

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Seitsonen, J. (Manager) & Rissanen, A. (Other)
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@phdthesis{736bba4862184a4eb9004641dbd223c6,

title = "DNA-BASED STIMULI-RESPONSIVE NANOTECHNOLOGY AND MATERIALS",

abstract = "This thesis is a study of various stimuli-responsive DNA-based systems. The systems presented here take advantage of the advances in DNA nanotechnology to provide plasmonic outputs due to structural reconfiguration in response to external stimuli. DNA is a versatilebiomolecule with responsiveness to specific environmental cues. We utilized three different environmental cues, pH, light, and small molecules, to induce structural changes in the designed system that led to changes in the gold nanorod-based plasmonic outputs. First, the inherent pH-responsiveness of DNA was used in the form of Hoogsteen bonding and triplex self-assembly. The triplex self-assembly was coupled with a structural reconfiguration of DNA origami-based chiral plasmonic metamolecules. When formed, the triplex acted as a bridge to bring forth an intense chiral plasmonic state. The state of the triplex was controlled through a photoresponsive medium containing protonated merocyanine, MCH+. Therefore, a DNA-based chiral plasmonic system could be rapidly actuated with external visible-light stimulus without any light-responsive modifications on the DNA itself. Next, we brought DNA nanotechnology towards macro-scale applications by conjugating DNA-functionalized gold nanorods into synthetic polymer networks to create a hybrid DNA hydrogel. Here, gold nanorods did not only act as plasmonic optical reporters but also as stimuli-responsive elements. The gold nanorods were designed to absorb light in the visible-light spectrum's red region and act as heating elements. The inherent thermoresponsiveness of DNA was used to implement dynamic reversible light responses into the hydrogel system. The external visible-light stimulus provided an inexpensive, robust, spatial, and waste-free method to trigger structural changes. The hybrid hydrogel exhibited reversible plasmonic optical output in the form of visible colors. Third, we introduced DNA origami-based chiral plasmonic metamolecules functionalized with DNA aptamer bridges between the origami arms as a sensing platform. The binding of a target to the duplexed aptamer bridge brought structural changes that affected the gold nanorod-mediated chiral plasmonic signal. By adequately screening the reference analytes and complementary strand designs, the platform was utilized to characterize aptamer-target affinity. Overall, this thesis highlights the utility of DNA for the fabrication of nanostructures and materials with programmable stimuli responses.",

keywords = "self-assembly, DNA origami, stimuli-responsive materials, chiral plasmonics, active plasmonics, light-responsiveness, self-assembly, DNA origami, stimuli-responsive materials, chiral plasmonics, active plasmonics, light-responsiveness",

author = "Joonas Ryssy",

year = "2023",

language = "English",

isbn = "978-952-64-1124-8",

series = "Aalto University publication series DOCTORAL THESES",

publisher = "Aalto University",

number = "8",

address = "Finland",

school = "Aalto University",

}

TY - BOOK

T1 - DNA-BASED STIMULI-RESPONSIVE NANOTECHNOLOGY AND MATERIALS

AU - Ryssy, Joonas

PY - 2023

Y1 - 2023

N2 - This thesis is a study of various stimuli-responsive DNA-based systems. The systems presented here take advantage of the advances in DNA nanotechnology to provide plasmonic outputs due to structural reconfiguration in response to external stimuli. DNA is a versatilebiomolecule with responsiveness to specific environmental cues. We utilized three different environmental cues, pH, light, and small molecules, to induce structural changes in the designed system that led to changes in the gold nanorod-based plasmonic outputs. First, the inherent pH-responsiveness of DNA was used in the form of Hoogsteen bonding and triplex self-assembly. The triplex self-assembly was coupled with a structural reconfiguration of DNA origami-based chiral plasmonic metamolecules. When formed, the triplex acted as a bridge to bring forth an intense chiral plasmonic state. The state of the triplex was controlled through a photoresponsive medium containing protonated merocyanine, MCH+. Therefore, a DNA-based chiral plasmonic system could be rapidly actuated with external visible-light stimulus without any light-responsive modifications on the DNA itself. Next, we brought DNA nanotechnology towards macro-scale applications by conjugating DNA-functionalized gold nanorods into synthetic polymer networks to create a hybrid DNA hydrogel. Here, gold nanorods did not only act as plasmonic optical reporters but also as stimuli-responsive elements. The gold nanorods were designed to absorb light in the visible-light spectrum's red region and act as heating elements. The inherent thermoresponsiveness of DNA was used to implement dynamic reversible light responses into the hydrogel system. The external visible-light stimulus provided an inexpensive, robust, spatial, and waste-free method to trigger structural changes. The hybrid hydrogel exhibited reversible plasmonic optical output in the form of visible colors. Third, we introduced DNA origami-based chiral plasmonic metamolecules functionalized with DNA aptamer bridges between the origami arms as a sensing platform. The binding of a target to the duplexed aptamer bridge brought structural changes that affected the gold nanorod-mediated chiral plasmonic signal. By adequately screening the reference analytes and complementary strand designs, the platform was utilized to characterize aptamer-target affinity. Overall, this thesis highlights the utility of DNA for the fabrication of nanostructures and materials with programmable stimuli responses.

AB - This thesis is a study of various stimuli-responsive DNA-based systems. The systems presented here take advantage of the advances in DNA nanotechnology to provide plasmonic outputs due to structural reconfiguration in response to external stimuli. DNA is a versatilebiomolecule with responsiveness to specific environmental cues. We utilized three different environmental cues, pH, light, and small molecules, to induce structural changes in the designed system that led to changes in the gold nanorod-based plasmonic outputs. First, the inherent pH-responsiveness of DNA was used in the form of Hoogsteen bonding and triplex self-assembly. The triplex self-assembly was coupled with a structural reconfiguration of DNA origami-based chiral plasmonic metamolecules. When formed, the triplex acted as a bridge to bring forth an intense chiral plasmonic state. The state of the triplex was controlled through a photoresponsive medium containing protonated merocyanine, MCH+. Therefore, a DNA-based chiral plasmonic system could be rapidly actuated with external visible-light stimulus without any light-responsive modifications on the DNA itself. Next, we brought DNA nanotechnology towards macro-scale applications by conjugating DNA-functionalized gold nanorods into synthetic polymer networks to create a hybrid DNA hydrogel. Here, gold nanorods did not only act as plasmonic optical reporters but also as stimuli-responsive elements. The gold nanorods were designed to absorb light in the visible-light spectrum's red region and act as heating elements. The inherent thermoresponsiveness of DNA was used to implement dynamic reversible light responses into the hydrogel system. The external visible-light stimulus provided an inexpensive, robust, spatial, and waste-free method to trigger structural changes. The hybrid hydrogel exhibited reversible plasmonic optical output in the form of visible colors. Third, we introduced DNA origami-based chiral plasmonic metamolecules functionalized with DNA aptamer bridges between the origami arms as a sensing platform. The binding of a target to the duplexed aptamer bridge brought structural changes that affected the gold nanorod-mediated chiral plasmonic signal. By adequately screening the reference analytes and complementary strand designs, the platform was utilized to characterize aptamer-target affinity. Overall, this thesis highlights the utility of DNA for the fabrication of nanostructures and materials with programmable stimuli responses.

KW - self-assembly

KW - DNA origami

KW - stimuli-responsive materials

KW - chiral plasmonics

KW - active plasmonics

KW - light-responsiveness

KW - self-assembly

KW - DNA origami

KW - stimuli-responsive materials

KW - chiral plasmonics

KW - active plasmonics

KW - light-responsiveness

M3 - Doctoral Thesis

SN - 978-952-64-1124-8

T3 - Aalto University publication series DOCTORAL THESES

PB - Aalto University

ER -

DNA-BASED STIMULI-RESPONSIVE NANOTECHNOLOGY AND MATERIALS

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