Behavior of Polycatalytic Assemblies in a Substrate-Displaying Matrix

Abstract

We describe polycatalytic assemblies, comprising one or two streptavidin molecules and two to six attached nucleic acid catalysts (deoxyribozymes), with phosphodiesterase activity. When exposed to a matrix covered at high densities with oligonucleotide substrates, these molecules diffuse through the matrix continuously cleaving the substrate at rates comparable to those of individual catalysts in solution. Rates of diffusion (movement), processivity, and resident times of assemblies can be controlled through the number of catalytic units and the length of substrate/product recognition regions. The assemblies were characterized at the ensemble level using surface plasmon resonance.

Active Self-Assembly of Simple Units Using an Insertion Primitive

“…Particularly notable are the rich dynamical systems constructed out of synthetic nucleic acids, whose four-base code gives rise to a means of programming specific molecular interactions. DNA has been used to build autonomous walkers [4,14,28,31,33,34,43,55,56], logic and catalytic circuits [39,50,55,58], and triggered assembly of linear [10,44] and dendritic structures [55]. Now that our once passive subunits can actively sense, walk and otherwise actively interact, how do these new "rules" change the prospects for what we can build from the bottom-up?…”

Direct observation of stepwise movement of a synthetic molecular transporter

“…This precisely controlled, long-range transport could lead to the development of systems that could be programmed and routed by instructions encoded in the nucleotide sequences of the track and motor. Such systems might be used to create molecular assembly lines modelled on the ribosome.An effective linear molecular motor must traverse its track without dissociating [1][2][3][4][5][6][7]10,12 and run unidirectionally without external intervention [4][5][6][7][8][9][10][11][12] . Directionality may be imposed by the sequential addition of DNA instructions 1-3 or, for autonomous motors, by modifying the track sites that have been visited 5,6,12 , by coupling motion to a unidirectional reaction cycle 4,9,12 or by coordinating the conformation changes of different parts of the motor 11,12 .…”

“…Controlled motion at the nanoscale can be achieved by using Watson-Crick base-pairing to direct the assembly and operation of a molecular transport system consisting of a track, a motor [1][2][3][4][5][6][7][8][9][10][11][12] and fuel [13][14][15] , all made from DNA. Here, we assemble a 100-nm-long DNA track on a two-dimensional scaffold 16 , and show that a DNA motor loaded at one end of the track moves autonomously and at a constant average speed along the full length of the track, a journey comprising 16 consecutive steps for the motor.…”

Radar Sounding of the Medusae Fossae Formation Mars: Equatorial Ice or Dry, Low-Density Deposits?

“…This may be achieved directly when the inputs and outputs are themselves nucleic acids, such as for the detection, analysis, and response to complex nucleic acid samples (9,30) or for the control of nucleic acid nanomachines (2,31). Nucleic acid circuits can also respond to and control more general chemical events: In principle, the release of an oligonucleotide could regulate covalent chemistry by controlling (deoxy)ribozyme activity (9) or reactant proximity (32).…”