Methods of making nucleic acid nanostructures

A method for ex-vivo production of a non-naturally occurring nucleic acid nanostructure of arbitrary 2-D or 3-D shape comprising:

• a) selecting a desired shape for the nanostructure;
• b) providing a single stranded DNA polynucleotide scaffold having a known sequence;
• c) designing a folding path for said polynucleotide scaffold to form said desired shape;
• d) designing a plurality of single stranded oligonucleotide helper/staple strands to hold said polynucleotide scaffold based on said desired shape wherein said oligonucleotide helper/staple strands are at least partially complementary to said polynucleotide scaffold such that said oligonucleotide helper/staple strands anneal with said polynucleotide scaffold into a domain comprising a B-form DNA structural unit and wherein a subset of said oligonucleotide helper/staple strands have annealing sites that constrain crossovers and contact points between helices to form desired angles and desired shape and wherein a set of said oligonucleotide helper/staple strands form a loop between parallel strands of said polynucleotide scaffold;
• e) mixing said single-stranded polynucleotide scaffold with said plurality of oligonucleotide helper/staple strands to form a mixture;
• and
• f) producing said nanostructure by allowing said polynucleotide scaffold and said plurality of oligonucleotide helper/staple strands to anneal, wherein at least a subset of said oligonucleotide helper/staple strands bind said polynucleotide scaffold in two or more separate regions and bring these separate regions of said polynucleotide scaffold together to form a desired bend or angle in the polynucleotide scaffold producing parallel helices held together by a periodic pattern of crossovers spaced so that the distance between crossovers formed by two consecutive oligonucleotide helper/staple strands is an odd number of half turns apart.