Enzyme-free synthesis of cyclic single-stranded DNA constructs containing a single triazole, amide or phosphoramidate backbone linkage and their use as templates for rolling circle amplification and nanoflower formation

Abstract

Three different chemical cyclisation reactions yield biocompatible cyclic oligonucleotide templates for use in RCA and DNA nanoflower formation.

Biomolecular Densely Grafted Brush Polymers: Oligonucleotides, Oligosaccharides and Oligopeptides

“…[11] While highly promising therapeutically,negatively charged oligonucleotides suffer from serious limitations such as poor cellular penetration, reduced bioavailability,a nd susceptibility to hydrolysis in the presence of nucleases.These inherent downsides of oligonucleotides greatly compromise their effectiveness both in vitro and in vivo and have hindered translation to the clinic. Several approaches towards engineering the structure of oligonucleotides have been developed, giving rise to spherical nucleic acids, [12] cyclic oligonucleotides, [13] and polymer-oligonucleotide bioconjugates. [9b, 14] Among these structural variations,o ligonucleotide brush polymers hold potential due to their densely packed threedimensional architecture and ability to display oligonucleotide side chains in amultivalent fashion.…”

Artificial nucleic acid backbones and their applications in therapeutics, synthetic biology and biotechnology

“…A combinatorial approach for the discovery of splint-templated chemical ligations has been reported to identify DNA-compatible reactions to ligate terminally functionalised ONs [57]. Moreover, the generation of artificial backbone mimics has been shown for bridging 5 0 -S-phosphorothioester linkages (Ps) [58], PA [59][60][61][62], AM [61], urea [63], SQAM [63], TL1 [64] and TL3 [61]. Indeed, copper-catalysed azide-alkyne cycloaddition (CuAAC) to form TL3 was reported for the assembly of whole genes [12,65] and long RNA [9,10] from azide and alkyne modified shorter ONs.…”

Expanding the chemical functionality of DNA nanomaterials generated by rolling circle amplification

“…Through design of the circular template, DNFs can be programmed to contain specific functionalities such as aptamers for cell targeting ( 14 ), immuno-stimulatory regions ( 18 ), DNAzymes for targeted RNA degradation ( 19 ), and drug loading sequences ( 17 ). The size of the particles can be controlled to a degree by altering the amplification time ( 17 ), adjusting the Mg 2+ concentration ( 20 ), or by condensing the resulting particles ( 21 ). DNFs can be prepared that contain proteins, including enzymes, for intracellular delivery and catalytic enhancement ( 22 ), and the inorganic core of the particles can be altered by changing the reaction buffer ( 23 , 24 ).…”