Antibody-powered nucleic acid release using a DNA-based nanomachine

Abstract

A wide range of molecular devices with nanoscale dimensions have been recently designed to perform a variety of functions in response to specific molecular inputs. Only limited examples, however, utilize antibodies as regulatory inputs. In response to this, here we report the rational design of a modular DNA-based nanomachine that can reversibly load and release a molecular cargo on binding to a specific antibody. We show here that, by using three different antigens (including one relevant to HIV), it is possible to design different DNA nanomachines regulated by their targeting antibody in a rapid, versatile and highly specific manner. The antibody-powered DNA nanomachines we have developed here may thus be useful in applications like controlled drug-release, point-of-care diagnostics and in vivo imaging.

Decorating bacteria with self-assembled synthetic receptors

“…We hypothesized that if one of the protein targets for such synthetic protein binders would be located on the cell surface, their regulatory effect 21 could be extended from the protein level to the cellular level. We also expected that the ability to reversibly change the structure of such DNA-based protein binders [11][12][13][14][15][16][17][18][19][20][21][22] and precisely control the orientation, distance, and valency of their binding units [11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27] would enable such systems to act as artificial CSPs. Namely, as artificial receptors that respond to dynamic changes in the environment and can endow the bacteria with engineered properties.…”

“…The advantages of using ODN-small-molecule conjugates as synthetic protein binders include the ability to precisely control the orientation, distances, and valency of their binding units [11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27] , as well as the ability to dynamically change their structure, which provides a means to regulate protein functions in real time [11][12][13][14][15][16][17][18][19][20][21] . This work shows that when synthetic protein binders of this class are attached to cell surfaces, their regulatory effect can be extended from the protein level to the cellular level.…”

“…In recent years, considerable attention has been devoted to developing protein binders based on oligodeoxynucleotide (ODN)-small-molecule conjugates [11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27] that, similar to CSPs, can respond to external stimuli and undergo dynamic structural changes that enable them to reversibly interact with proteins and regulate their functions [11][12][13][14][15][16][17][18][19][20][21] . We have recently developed protein binders based on ODN-small-molecule conjugates [21][22][23] and have shown that such binders can be designed to reversibly interact with different proteins 21,22 and even mediate unnatural protein-protein communication processes 21 .…”

“…Inspired by recent successes in dynamically controlling protein functions and binding interactions with ODN-small-molecule conjugates [11][12][13][14][15][16][17][18][19][20][21] and in cell surface engineering , we set out to develop a dynamic artificial receptor system that combines principles from both research areas. Specifically, we hypothesized that by attaching DNA-based, stimuli-responsive protein binders on the surfaces of living bacteria, at a specific position, and by using solely self-assembly processes, a biomimetic system that imitates the dynamic features of natural CSPs can be obtained.…”

Specific Biosensing Using DNA Aptamers and Nanopores

“…Our two‐step assay has built a bridge between the nanopore‐based single molecule method and DNA‐based circuitry designs. Apart from the aptamer‐based conformation changes used in this work, direct binding of antibodies and other proteins can also facilitate successful signal translation into output strands . Compared to the traditional fluorescence assays, our method avoids fluorophores conjugation and spectra overlap.…”