4 research outputs found
Reprogramming the assembly of unmodified DNA with a small molecule
The ability of DNA to store and encode information arises from base pairing of the four-letter nucleobase code to form a double helix. Expanding this DNA âalphabetâ by synthetic incorporation of new bases can introduce new functionalities and enable the formation of novel nucleic acid structures. However, reprogramming the self-assembly of existing nucleobases presents an alternative route to expand the structural space and functionality of nucleic acids. Here we report the discovery that a small molecule, cyanuric acid, with three thymine-like faces reprogrammes the assembly of unmodified poly(adenine) (poly(A)) into stable, long and abundant fibres with a unique internal structure. Poly(A) DNA, RNA and peptide nucleic acid all form these assemblies. Our studies are consistent with the association of adenine and cyanuric acid units into a hexameric rosette, which brings together poly(A) triplexes with a subsequent cooperative polymerization. Fundamentally, this study shows that small hydrogen-bonding molecules can be used to induce the assembly of nucleic acids in water, which leads to new structures from inexpensive and readily available materials
Reprogramming and manipulating DNA assembly using simple self-assembly principles
Supramolecular chemistry is the "chemistry of molecular information". Information stored in the structural features of molecules is recognized and processed at the supramolecular level and drives the ever more complex organization of matter â from the formation of simple host-guest complexes, to the assembly of viral capsids and the emergence of life itself. The work presented in this thesis uses basic principles governing intermolecular interactions to manipulate the assembly of DNA, a molecule that exemplifies the concept of information storage in its structure. In Chapter 2, simple molecular recognition principles are applied to expand the DNA base-pairing alphabet. A small molecule, cyanuric acid, with three thymine-like faces, is determined to reprogram the assembly of poly(adenine) strands into micron-long fibers with a unique internal structure. Adenine residues and cyanuric acid molecules are shown to associate into hexameric rosettes that bring about the formation of poly(adenine) triplexes and subsequent polymerization into nanofibers. Fundamentally, this finding demonstrates that a small molecule can induce nucleic acid assembly, giving rise to a new type of structure from inexpensive, readily available materials. Further examination of the mechanisms involved in nanofiber formation in Chapter 3 uncovers that the supramolecular polymerization of poly(adenine) strands proceeds through a cooperative mechanism. A new methodology to analyse thermal hysteresis profiles provides a quantitative understanding of the kinetics and thermodynamics of the assembly process. In addition, key parameters influencing assembly are identified and can be tuned to modify nanofiber properties in potential nanomaterials applications. While hydrogen bonding and Ï-stacking interactions dominate the co-assembly of poly(adenine) and cyanuric acid described in Chapters 2 and 3, a different combination of intermolecular interactions is used to manipulate the long-range assembly of DNA nanostructures into ordered networks in Chapter 4. Blunt-ended DNA tiles, or tiles lacking complementary single-stranded portions at the duplex ends, with and without a cholesterol anchoring moiety, are interfaced with lipid bilayers, a soft support with composition-dependent properties. The balance of pi-stacking interactions between DNA duplex ends, cholesterol-mediated nanostructure anchoring, electrostatic DNA binding to the bilayer surface, and the fluid nature of the lipid bilayer enable the formation of dynamic materials with long-range order and tunable morphology on a cell membrane-like support. In turn, these lattices represent a tool for organizing materials such as nanoparticles or proteins at a biological interface, with potential applications in cellular recognition, development of model systems for study of membrane proteins or plasmonics. Altogether, this thesis demonstrates that information encoded in molecular building blocks and the interplay between intermolecular interactions can be used to manipulate the assembly and long-range organization of DNA to achieve new structures and higher complexity.La chimie supramolĂ©culaire est aussi appelĂ©e la « chimie de l'information molĂ©culaire ». L'information structurelle des molĂ©cules est reconnue et traitĂ©e au niveau supramolĂ©culaire, entraĂźnant ainsi la complexification de l'organisation de la matiĂšre â de la formation de simples composĂ©s d'inclusion Ă l'Ă©mergence de la vie elle-mĂȘme. Le travail prĂ©sentĂ© dans cette thĂšse applique les principes fondamentaux rĂ©gissant les interactions intermolĂ©culaires pour manipuler l'assemblage de l'ADN, un archĂ©type du stockage de l'information dans la structure molĂ©culaire. Dans le Chapitre 2, des principes Ă©lĂ©mentaires de reconnaissance molĂ©culaire sont appliquĂ©s pour Ă©largir l'alphabet d'appariement de bases d'ADN. L'acide cyanurique, une petite molĂ©cule Ă trois faces de type thymine, est utilisĂ© pour reprogrammer l'assemblage de brins de poly(adĂ©nine) en fibres d'une longueur de l'ordre du micromĂštre avec une structure interne unique. Nos rĂ©sultats indiquent que l'association des unitĂ©s d'adĂ©nine et d'acide cyanurique forme des rosettes hexamĂ©riques, entraĂźnant ainsi la formation de triple-hĂ©lices de poly(adĂ©nine) et leur polymĂ©risation subsĂ©quente en nanofibres. Fondamentalement, cette dĂ©couverte dĂ©montre qu'une petite molĂ©cule peut induire l'assemblage de brins d'ADN, formant ainsi une nouvelle structure Ă partir de matĂ©riaux peu coĂ»teux et abondants. Dans le Chapitre 3, des Ă©tudes visant les mĂ©canismes impliquĂ©s dans la formation des nanofibres rĂ©vĂšlent que la polymĂ©risation supramolĂ©culaire des brins de poly(adĂ©nine) avec l'acide cyanurique passe par un mĂ©canisme coopĂ©ratif. Une nouvelle mĂ©thodologie d'analyse de profils d'hystĂ©rĂšse thermique fournit une comprĂ©hension quantitative plus approfondie de la cinĂ©tique et de la thermodynamique du processus d'assemblage. Certains paramĂštres clĂ©s qui influencent l'assemblage sont Ă©galement identifiĂ©s et peuvent ĂȘtre modifiĂ©s afin d'ajuster les propriĂ©tĂ©s des nanofibres et de dĂ©velopper des applications potentielles en tant que nanomatĂ©riaux. Alors que les liaisons hydrogĂšne et les interactions entre cycles aromatiques dominent le co-assemblage de poly(adĂ©nine) et d'acide cyanurique dĂ©crit dans les Chapitres 2 et 3, une combinaison diffĂ©rente d'interactions intermolĂ©culaires est utilisĂ©e pour manipuler l'assemblage de tuiles d'ADN en rĂ©seaux ordonnĂ©s Ă grande Ă©chelle dans le 4e Chapitre. Ainsi, des tuiles d'ADN Ă extrĂ©mitĂ©s franches, c'est-Ă -dire sans ajout de portions d'ADN complĂ©mentaire aux extrĂ©mitĂ©s, sont modifiĂ©es avec une molĂ©cule de cholestĂ©rol servant d'ancre hydrophobe. L'Ă©tude de l'interface entre ces tuiles, modifiĂ©es ou non, et des bicouches lipidiques, supports souples avec des propriĂ©tĂ©s dĂ©pendantes de la composition, est entreprise. L'Ă©quilibre des interactions entre cycles aromatiques joignant les extrĂ©mitĂ©s des duplex, l'ancrage de la nanostructure mĂ©diĂ© par le cholestĂ©rol et les liaisons Ă©lectrostatiques de l'ADN Ă la surface de la bicouche permet de construire des matĂ©riaux dynamiques ordonnĂ©s Ă grande Ă©chelle, permettant aussi d'obtenir des morphologies ajustables. Ă leur tour, ces rĂ©seaux reprĂ©sentent un outil pour organiser des matĂ©riaux tels que des nanoparticules ou des protĂ©ines Ă une interface biologique, avec des applications potentielles dans la reconnaissance cellulaire, le dĂ©veloppement de systĂšmes modĂšles pour l'Ă©tude de protĂ©ines membranaires ou les systĂšmes plasmoniques. En somme, cette thĂšse dĂ©montre que l'information structurelle codĂ©e dans des blocs de construction molĂ©culaires et un juste Ă©quilibre d'interactions intermolĂ©culaires peuvent ĂȘtre utilisĂ©s pour manipuler l'assemblage de l'ADN et son organisation Ă plus grande Ă©chelle
Long-Range Ordering of Blunt-Ended DNA Tiles on Supported Lipid Bilayers
Long-range ordering of DNA crossover
tiles with blunt ends on lipid
bilayers is investigated using atomic force microscopy. âBlunt-endedâ
tiles do not have single-stranded complementary ends, and thus instead
of assembling via base-pairing, they can interact by Ï-stacking
of their duplex ends. This work demonstrates that the balance of base
Ï-stacking interactions between the ends of DNA duplexes, cholesterol-mediated
DNA anchoring, and electrostatic DNA binding to supported lipid bilayers
(SLBs) presents an opportunity to build dynamic materials with long-range
order on a soft support. The tiles are shown to organize into novel
tunable surface packing morphologies on the micrometer scale. This
work focuses on three-point star (3PS) tiles that are either unmodified
or modified with a cholesterol unit and investigates their interactions
on supported lipid bilayers. On fluid bilayers, the cholesterol tiles
form extended hexagonal arrays with few defects, while the unmodified
tiles do not bind. In contrast, both modified and unmodified tiles
bind to gel-phase bilayers and produce arrays of new organized morphologies.
With increasing tile concentration, we observe a range of motifs,
that progressively favor tileâtile packing over duplex-end
Ï-stacking. These structures can selectively pattern domains
of phase-separated lipid bilayers, and the patterning is also observed
for four-arm cross-tiles. Dynamic blunt end contacts promote error
correction and network reconfiguration to maximize favorable interactions
with the substrate and are required for the observed tile organization.
These results suggest that small blunt-ended tiles can be used as
a platform to organize oligonucleotides, nanoparticles, and proteins
into extensive networks at the interface with biologically relevant
membrane systems or other soft surface materials for applications
in cellular recognition, plasmonics, light harvesting, model systems
for membrane protein assemblies, or analytical devices