Computational programs for predicting RNA sequences with desired folding properties have
been extensively developed and expanded in the past several years. Given a secondary …

Small RNAs, a large class of ancient posttranscriptional regulators, have recently attracted
considerable attention. A plethora of small RNAs has been identified and characterized …

We describe a framework for designing the sequences of multiple nucleic acid strands
intended to hybridize in solution via a prescribed reaction pathway. Sequence design is …

An RNA design algorithm takes a target RNA structure and finds a sequence that folds into
that structure. This is fundamentally important for engineering therapeutics using RNA …

The asymmetric subcellular distribution of RNA molecules from their sites of transcription to
specific compartments of the cell is an important aspect of post‐transcriptional gene …

We describe an algorithm for designing the equilibrium base-pairing properties of a test tube
of interacting nucleic acid strands. A target test tube is specified as a set of desired “on …

Motivations: The design of RNA sequences folding into predefined secondary structures is a
milestone for many synthetic biology and gene therapy studies. Most of the current software …

Recent advances in experimental DNA origami have dramatically expanded the horizon of
DNA nanotechnology. Complex 3D suprastructures have been designed and developed …

In this review paper we discuss fatgraphs as a conceptual framework for RNA structures. We
discuss various notions of coarse-grained RNA structures and relate them to fatgraphs. We …

ABSTRACT RNA has become an integral building material in synthetic biology. Dominated
by their secondary structures, which can be computed efficiently, RNA molecules are …