Simulation-guided engineering of an enzyme-powered three dimensional DNA nanomachine for discriminating single nucleotide variants

Abstract

Development of an enzyme-powered three dimensional DNA nanomachine for discriminating single nucleotide variants through simulation-guided engineering and noncovalent DNA catalysis.

A bipedal DNA nanowalker fueled by catalytic assembly for imaging of base-excision repairing in living cells

“…The progressive movement of DNA nanowalkers provides the possibility of executing multiple tasks or signal amplication, affording valuable platforms in molecular transportation, biosensors and biosynthesis. 1-3 Current DNA nanowalkers have been engineered to travel in landscapes of different dimensionalities with varying driving energy fueled by nuclease, [4][5][6] DNAzymes, [7][8][9] or toehold-mediated strand displacement. [10][11][12] DNA walkers traversing three-dimensional (3D) tracks confer increased capacity in mimicking complicated biological systems and achieving efficient signal amplication.…”

Enhanced SNP-sensing using DNA-templated reactions through confined hybridization of minimal substrates (CHOMS)

“…12,13 The need to achieve more costeffective, faster analysis and higher single nucleotide resolution continues to drive technological developments. 14 Recent examples include amendments to existing technologies such as molecular beacons, 15,16 melting analysis, 17,18 environmentally sensitive uorescent nucleobases, [19][20][21][22][23][24] and strand displacement probes 25,26 or new technologies such as polymerase-amplied release of ATP (POLARA) 27 or graphene-based biosensors for real-time kinetic monitoring of hybridization. 28 The analysis of SNVs requires technologies with the highest nucleotide resolution to ascertain the polymorphism or variation.…”

A photo zipper locked DNA nanomachine with an internal standard for precise miRNA imaging in living cells

“…The I 580 /U 658 for single base mismatched miRNA 21 was slightly higher due to approximate thermodynamic energy with miRNA 21. 11 Live cell imaging of miRNA 21 with the PZ-DNA nanomachine HeLa cells, with high miRNA 21 expression prole, were chosen as the model cells to demonstrate the feasibility of the PZ-DNA nanomachine for in situ visualization of intracellular miRNA.…”

“…DNA nanomachines are articially designed DNA self-assembly structures based on sequence specic interactions. [1][2][3][4] With DNA reaction strands compacted in the synthesized nano-structures, [5][6][7][8] DNA nanomachines accelerate cascade hybridization reactions by converting tiny triggers like nucleic acids, [9][10][11][12] proteins 5,13 and pH [14][15][16] into autonomous mechanical motions and resulting outputs, such as the conformational change of DNA assemblies. Self-quenched DNA nanomachines have been constructed by conjugating both uorescent molecules and quenchers to DNA strands with close distance in between, [17][18][19] and the machine motion triggered by a specic target resulted in the continuous conguration change of the DNA strands with amplied uorescence recovery in a short time, which efficiently enhanced the target signal and was applied as a signal amplication strategy for bioanalysis and imaging.…”