Cationic Comb-Type Copolymers for Boosting DNA-Fueled Nanomachines

Abstract

For the better applications and developments of DNA nanomachines, their responding kinetics, output, and sequence-selectivity need to be improved. Furthermore, the DNA nanomachines currently have several limitations in operating conditions. Here we show that a simple addition of a cationic comb-type copolymer, poly(l-lysine)-graft-dextran, produces the robust and quick responses of DNA nanomachines under moderate conditions including physiologically relevant conditions even at very low strand concentrations (nanomoles per liter range) through hybrid stabilization and DNA strand exchange acceleration.

Nukleinsäure‐basierte molekulare Werkzeuge

“…[26] Die Geschwindigkeit von Strangverdrän-gungsreaktionen wird darüber hinaus von der Gegenwart bestimmter kationischer Polymere beeinflusst, was bereits für den Betrieb von DNA-Nanomaschinen genutzt wurde (siehe Abschnitt 3.3). [27] 2.1.3. Mechanische Eigenschaften von Einzel-und Doppelsträngen…”

“…[152] Unter Verwendung von Poly(l-lysin-graftdextran) konnten sie das Antwortverhalten und die Leistung der DNA-Pinzette, aber auch anderer Nukleinsäurebauteile verbessern. [27] Ein interessanter Ansatz zur Steuerung der Bewegung von DNA-Nanobauteilen besteht in der Verwendung von DNA-Basen, die von Asanuma et al [96] sowie Ogura et al [98] mit dem photoschaltbaren Molekül Azobenzol modifiziert wurden. Azobenzol lässt sich aus seiner trans-in seine cisKonfiguration schalten, wenn man es mit Licht der Wellenlänge 330-350 nm bestrahlt, wogegen Wellenlängen von 440-460 nm das Molekül wieder in seine trans-Form zurück-schalten.…”

Biological nano-functionalization of titanium-based biomaterial surfaces: a flexible toolbox

“…'Fuel 1' hybridizes to the initial state of the nanomotor, thus inducing motion. The recovery of the initial state is then propelled by adding 'fuel 2' (Alberti & Mergny 2003;Choi et al 2007). Such nanomotors can also be driven by other processes like metal ion complexation, as used by Fahlman et al (2003) for quadruplexes stabilized by Sr 2þ and destabilized by EDTA.…”

Fullerene Attachment Enhances Performance of a DNA Nanomachine

“…We are interested in developing biocompatible molecules with controllable, accurate and reproducible molecular motor functions. Our objective was to follow in detail the molecular conformation changes occurring in a DNA motif using three-dimensional molecular analysis by small angle x-ray scattering (SAXS).As in previous work, we have chosen to use the i-motif DNA (DNA) switch driven by pH changes [6,7] that does not require any additional ''fuel'' molecules [8,9] and avoids the accumulation of waste products that can limit the machine lifetime.[9] In mildly acidic conditions (pH 5), the 21mer single strand DNA forms a compact, folded i-motif conformation due to intramolecular noncanonical base pair interactions between a protonated and an unprotonated cytosine residue (i.e., a C þ :C base-pair) as shown in Figure 1a.[10] When the pH value is raised to 8, the DNA opens to a random coil. Fullerene (C 60 ) have been attached to both end-sides (5 0 and 3 0 ) of the DNA strand to improve the DNA nanomachine performance, in particular to facilitate a stronger ''lock'' in the open and closed states by proton exchange as shown in Figure 1b.…”

“…[9] In mildly acidic conditions (pH 5), the 21mer single strand DNA forms a compact, folded i-motif conformation due to intramolecular noncanonical base pair interactions between a protonated and an unprotonated cytosine residue (i.e., a C þ :C base-pair) as shown in Figure 1a. [10] When the pH value is raised to 8, the DNA opens to a random coil.…”