Triplex‐DNA‐Nanostrukturen: von grundlegenden Eigenschaften zu Anwendungen

Abstract

Triplex‐Nukleinsäuren sind ein Teil des umfangreichen “Struktur‐Werkzeugkastens”, der für die Entwicklung von Nanostrukturen und Materialien auf DNA‐Basis eingesetzt wird. Dieser Aufsatz behandelt die Verwendung von DNA‐Triplexen für die Konstruktion von Sensorplattformen und molekularen Schaltern. Daneben behandeln wir die pH‐induzierte, schaltbare Assoziation und Dissoziation von Triplex‐DNA‐verbrückten Nanostrukturen. Dazu gehören die Aggregation/Deaggregation von Nanopartikeln, die reversible Oligomerisierung von Origamikacheln oder DNA‐Zyklen und die Verwendung von Triplex‐DNA‐Strukturen als Funktionseinheiten zum Aufbau von pH‐responsiven Systemen und Materialien. Beispiele hierfür sind Halbleiter‐beladene DNA‐stabilisierte Mikrokapseln und DNA‐funktionalisierte Farbstoff‐beladene Metall‐organische Gerüste (MOFs) sowie die pH‐induzierte Freisetzung der Beladungen. Auch stimuliresponsive Hydrogele auf DNA‐Basis, die unter Verwendung von Triplex‐Nukleinsäuren reversible pH‐induzierte Hydrogel‐zu‐Lösung‐Übergänge durchlaufen und die Verwendung von Triplex‐DNA zum Herstellen von Formgedächtnis‐Hydrogelen werden behandelt. Schließlich wird ein Ausblick auf zukünftige Anwendungen und Perspektiven für Triplex‐Nukleinsäuren gegeben.

Dynamic Reconfigurable DNA Nanostructures, Networks and Materials

“…In addition to the base‐pair stabilization of duplex nucleic acid structures and dictated dynamic strand displacement of duplex nucleic acids by appropriate fuel‐/anti‐fuel strands, [2] the structural information embedded in the biopolymer includes the sequence‐guided reconfiguration of single strands into secondary structures in the presence of auxiliary triggers. Examples include the pH‐induced reconfiguration of cytosine‐rich strands into i‐motif structures (pH<5.5) and their separation at neutral pH values, [3] the K + ‐ion (or Sr 2+ , Pb 2+ ) stimulated stabilization of guanosine‐rich strands into G‐quadruplex assemblies and their separation in the presence of crown ethers (CE), [1, 4] the auxiliary strand‐induced formation of T‐A ⋅ T or C‐G ⋅ C + triplex structures and their pH‐stimulated separation or auxiliary‐strand displacement, [5] the metal‐ion (Ag + or Hg 2+ ) stabilization of C‐mismatched or T‐mismatched duplexes by C‐Ag + ‐C or T‐Hg 2+ ‐T bridges and their dissociation in the presence of ligands, e.g., cysteine, [6] and the stabilization and destabilization of duplex nucleic acids by photoisomerizable intercalators, such as trans / cis ‐azobenzene units [7] . In addition, duplex nucleic acid structures provide instructive information towards enzyme‐driven transformations on the nucleic acid scaffolds.…”

Topologically Triggered Dynamic DNA Frameworks

“…Structural information includes instructive base‐pair hybridization, [1] and dictating strand‐displacement principles, [2] topological reconfiguration properties, in the presence of auxiliary triggers, and capacities to assemble supramolecular structures, in the presence of auxiliary ligands, ions or nucleic acids strands [3] . These include, for example, the reversible reconfiguration of guanosine‐rich strands into G‐quadruplexes, [4] in the presence of ions (e. g., K + ions or Sr 2+ ions), and their separation by crown ethers, the pH‐induced and reversible reconfiguration of cytosine‐rich strands into i‐motif structures, [5] or the formation of supramolecular triplex structures consisting of T−A ⋅ T or C−G ⋅ C + bridges and their separation by pH or strand displacement processes [6] . Functional information encoded in the nucleic acid strands includes sequence‐specific recognition and binding properties towards low‐molecular‐weight substrates or macromolecular ligands, such as proteins (e. g. aptamers), [7] or sequence dictated catalytic properties, such as cofactor‐dependent DNAzymes, [8] hemin/G‐quadruplex DNAzymes [9] or DNAzyme‐aptamer conjugates mimicking native enzymes (e. g. nucleozymes) [10] .…”

DNAzyme- and light-induced dissipative and gated DNA networks

“…17 For example, the fuel strand displacement of duplex nucleic acids and the separation of the displaced duplex with an anti-fuel strand, 9b,18 the K + -ion stimulated reconfiguration of guanosine-rich strands into G-quadruplexes and their separation with crown ether, 19 the pH-controlled formation and dissociation of T-A . T complexes 20 or the lightinduced stabilization of duplex DNA by photoisomerizable intercalator such as trans/cis-azobenzene units 21 represent sequence-dictated structural switching of nucleic acids. These sequence-guided functions of nucleic acids were widely applied to develop DNA machines 22 and devices, to design materials of switchable stiffness properties for shape-memory and selfhealing applications, 23 to prepare DNA-modified nanocarriers for controlled drug release, 24 to use the DNA as a material for logic gate operations and logic circuits 25 and to apply nucleic acid as building blocks of reconfigurable dynamic networks.…”