DNA performs diverse functional roles in biology, nanotechnology, and biotechnology, but current methods for autonomously synthesizing arbitrary single-stranded DNA are limited. Here, we introduce the concept of Primer Exchange Reaction (PER) cascades, which grow nascent single-stranded DNA with user-specified sequences following prescribed reaction pathways. PER synthesis happens in a programmable, autonomous, in situ, and environmentally responsive fashion, providing a platform for engineering molecular circuits and devices with a wide range of sensing, monitoring, recording, signal processing, and actuation capabilities. We experimentally demonstrate a nanodevice that transduces the detection of a trigger RNA into the production of a DNAzyme that degrades an independent RNA substrate, a signal amplifier that conditionally synthesizes long fluorescent strands only in the presence of a particular RNA signal, molecular computing circuits that evaluate logic (AND, OR, NOT) combinations of RNA inputs, and a temporal molecular event recorder that records in the PER transcript the order in which distinct RNA inputs are sequentially detected.

The dendritic-nucleation/array-treadmilling model provides a conceptual framework for the generation of the actin network driving motile cells. We have incorporated it into a 2D, stochastic computer model to study lamellipodia via the self-organization of filament orientation patterns. Essential dendritic-nucleation submodels were incorporated, including discretized actin monomer diffusion, Monte-Carlo filament kinetics, and flexible filament and plasma membrane mechanics. Model parameters were estimated from the literature and simulation, providing values for the extent of the leading edge-branching/capping-protective zone (5.4 nm) and the autocatalytic branch rate (0.43/sec). For a given set of parameters, the system evolved to a steady-state filament count and velocity, at which total branching and capping rates were equal only for specific orientations; net capping eliminated others. The standard parameter set evoked a sharp preference for the ؎35 degree filaments seen in lamellipodial electron micrographs, requiring Ϸ12 generations of successive branching to adapt to a 15 degree change in protrusion direction. This pattern was robust with respect to membrane surface and bending energies and to actin concentrations but required protection from capping at the leading edge and branching angles >60 degrees. A ؉70/0/؊70 degree pattern was formed with flexible filaments Ϸ100 nm or longer and with velocities <Ϸ20% of free polymerization rates.lamellipodium ͉ cytoskeleton ͉ plasma membrane T he polymerization of soluble actin monomers between filament ''barbed ends'' and the plasma membrane (PM) generates the force of protrusion in cell motility (1, 2). Other proteins required for lamellipodial motility (3) are arp2/3, which nucleates (branches) free barbed ends at Ϸ70 degrees from existing ones (4); a PMbound activator of arp2/3 (5); ADF/cofilin, which promotes the depolymerization of pointed ends (6) and perhaps debranching reactions (7); and capping protein, a terminator of barbed end growth (8). The generation and persistence of lamellipodia from these elements is described in the ''dendritic-nucleation/arraytreadmilling'' conceptual model (2,4,9). This model can be subdivided into three main processes: the kinetics of filament (de)polymerization, branching, and capping; filament-PM interactions, which limit polymerization rates; and the diffusion of actin monomers and other soluble components. Such a system is ''complex'' in the sense that many copies of each component type interact to exhibit ''emergent'' system properties not expected from the individual rules of interaction (10). In contrast to ''complicated'' systems of many dissimilar components with precisely defined interactions, complex systems can self-organize and adapt to environmental change.An important emergent property is the self-organization of lamellipodial actin filaments into orientations at Ϯ35 degrees with respect to the direction of protrusion (11,12). Maly and Borisy (11) predicted Ϯ35 or ϩ70/0/Ϫ70 degree patterns with a 2D mathematical...

Precise fabrication of semiconducting carbon nanotubes (CNTs) into densely aligned evenly spaced arrays is required for ultrascaled technology nodes. We report the precise scaling of inter-CNT pitch using a supramolecular assembly method called spatially hindered integration of nanotube electronics. Specifically, by using DNA brick crystal-based nanotrenches to align DNA-wrapped CNTs through DNA hybridization, we constructed parallel CNT arrays with a uniform pitch as small as 10.4 nanometers, at an angular deviation <2° and an assembly yield >95%.