Surface-immobilized bistable polynucleotide devices for the sensing and quantification of molecular events

Abstract

Bistable devices are constructed using a polynucleotide platform for sensing molecular events such as binding or conformational changes of target molecules. Uses include measurement of target concentration, measuring the effect of environmental condition (such as heat, light, or pH) on the target, or screening a library for molecules that bind the target or modulate its biological function. Devices comprise three regions: a top lid, bottom lid, and flexible linker or hinge between them. A device has an open configuration in which the top and bottom lid are separated, and a closed configuration they are bound close together. Binding domains or variations of the target molecule are fixed to a device so that when the molecular event occurs, the device switches from open to closed, or vice versa, which generates a signal. Optimal device design is determined by the signal modality (optical or electronic) used to measure closure of surface-immobilized devices.

1 . A structure comprising a bistable molecular sensor for optical or electronic detection of an external stimulus on a surface, the bistable molecular sensor having a polynucleotide platform, comprising:
 a first polynucleotide shape and a second polynucleotide shape with a flexible hinge or flexible linker therebetween, one of the first polynucleotide shape or the second polynucleotide shape being immobilized on the surface rendering an immobilized polynucleotide shape and a tethered polynucleotide shape; and   one or more functional molecules bound to at least one of the first polynucleotide shape and the second polynucleotide shape,   the bistable molecular sensor having one of two states, the two states being a closed state and an open state, wherein:   in the open state, the tethered polynucleotide shape moves freely with respect to the second polynucleotide shape as constrained by the flexible hinge or flexible linker; and   in the closed state, the tethered polynucleotide shape is proximally positioned to the immobilized polynucleotide shape, and   the polynucleotide platform being selected from a scaffolded deoxyribonucleic acid (DNA) origami, scaffolded ribonucleic acid (RNA) origami, scaffolded hybrid DNA:RNA origami, single-stranded DNA tiles, multi-stranded DNA tiles, single-stranded RNA origami, multi-stranded RNA tiles, or hierarchically composed DNA or RNA origami with multiple scaffolds.   
     
     
         2 - 74 . (canceled)