Construction of a Multiple-Aptamer-Based DNA Logic Device on Live Cell Membranes via Associative Toehold Activation for Accurate Cancer Cell Identification

Abstract

The ability to accurately identify and isolate cells is the cornerstone of precise disease diagnosis and therapies. A single-step cell identification method based on logic analysis of multiple surface markers will have unique advantages because of its accuracy and efficacy. Herein, using multiple DNA aptamers for cancer biomarker recognition and associative toehold activation for signal integration and amplification as two molecular keys, we have successfully operated a cell-surface device that can perform AND Boolean logic analysis of multiple biomarkers and precisely label the target cell subtype in large populations of similar cells via the presence or absence of different biomarkers. Our approach can achieve single-step cancer cell identification and isolation with excellent sensitivity and accuracy and thus will have broad applications in biological science, biomedical engineering, and personalized medicine.

A DNAzyme-amplified DNA circuit for highly accurate microRNA detection and intracellular imaging

“…The efficiency of DNAzyme amplication could be improved by integrating its functional sequence with other amplication means. 12,13 Besides DNAzymes, the catalytic DNA circuit, including the hybridization chain reaction (HCR) [14][15][16] and catalyzed hairpin assembly (CHA), 17,18 is also emerging as a typical enzyme-free amplication strategy. The HCR mediates the target-initiated autonomous cross-opening of hairpin reactants for assembling long nicked dsDNA copolymers.…”

A localized molecular automaton for in situ visualization of proteins with specific chemical modifications

“…In conclusion, unlike prior studies mainly focusing on computing cell identity by performing DNA reactions at the global cell membrane, [11][12][13] we have built a localized molecular automaton capable of in situ assessment of the chemical modication characteristics of the target protein on the cell surface. The automaton has harnessed different types of exquisite DNA nanotechnology to choreograph the anticodingcoding sequential propagation algorithm, achieving the visualization of a protein subtype with dual MOIs.…”

“…On this basis, the key obstacle is how to link these protein-localized interactions in isolation into an information propagation pathway, which will terminate by a signal switch to indicate the existence of a particular protein subtype with a given modication pattern on the cell surface. In this context, DNA nanodevices, which can operate sophisticated computation at the molecular level in a complex biological environment, [10][11][12][13][14] offer a robust, elegant and versatile tool, owing to the predictable hybridization and programmable assembly of DNA. For example, several innovative cell discrimination platforms have been developed by combining DNA strand displacement cascade with antibody 11 -or aptamer 12 based recognition for the evaluation of cell surface markers.…”

An Intelligent DNA Nanorobot for Autonomous Anticoagulation

“…Nucleic acids,a sm olecular carriers with predictable structures,programmable hybridization, and excellent ability for encoding information, are promising materials for building molecular devices with integrated biocomputing capabilities. [1][2][3][4][5][6][7][8] With the aid of DNAn anotechnology,D NA-based nanorobots have been used as logical sensing probes on cell membranes, [9][10][11][12] autonomous molecular machines for molecular cargo sorting, [13,14] stimuli-responsive delivery vehicles for biocomputing, [15][16][17][18][19][20] and for targeted cancer therapy. [21][22][23] In this respect, these task-specific DNAn anorobots show great potentials to be utilized as molecular tools that surpass all state of the art theragnostic platforms.…”

“…[15,21,[30][31][32] Furthermore,autonomous nanorobots that can respond to multiple disease markers show enhanced theragnostic intelligence levels with the ability to logically analyze the inputs. [9,10,30] In both cases,the presence of stimuli triggers the activation of nanorobots,w hereas only the absence of stimuli stops the function control of the nanorobots.However, the development of future personalized theragnostic tools leads to the urgency of higher level of intelligence where the nanorobots could regulate their functions in response to ap recise concentration of stimuli instead of merely the presence of stimuli. Since stimuli and targets are commonly present in steady concentrations under normal conditions, nanorobots that are able to autonomously perform their functions based on ac oncentration-triggered threshold control show ag reat potential for am ore efficient and safer therapeutic strategy.One application scenario for the abovementioned theragnostic tools is to autonomously regulate the blood coagulation cascade that involves multiple enzymes and cofactors.The central molecule is human a-thrombin that directly controls blood coagulation by converting fibrinogen to fibrin.…”