Method for organizing individual molecules on a patterned substrate and structures assembled thereby

1. A structure comprising:

a substrate having a patterned surface of one or more negatively-charged binding sites and a non-binding background; and

a molecular shape comprising polynucleotides generated by a polynucleotide platform, the molecular shape being bound to one of the one or more binding sites,

wherein the molecular shape comprises a plurality of faces comprising a binding face and one or more non-binding faces,

wherein the binding face of the molecular shape has an outline that matches the outline of the one or more binding sites,

wherein the non-binding face of the molecular shape comprises a plurality of modifications that are repellant to the binding site,

wherein the majority of the binding face of the molecular shape has an unmodified phosphate backbone, and

wherein, in the presence of a multivalent cation, the one or more binding sites have a higher binding affinity for the unmodified phosphate backbone of the binding face than for the one or more non-binding faces.

2. The structure of claim 1 , wherein the patterned surface of the substrate at the one or more binding sites comprises:

silanols;

carboxylate groups;

negatively charged functional groups;

negatively charged polymers; or

an inherent negative charge.

3. The structure of claim 1 , wherein the modifications that are repellant to the binding site comprise at least one of:

a plurality of single stranded DNA extensions;

a neutral polymer;

a zwitterionic coating; or

combinations thereof.

4. The structure of claim 1 , wherein the patterned surface of the substrate has a non-binding background comprising:

trimethyl silyl groups;

neutral functional groups;

a neutral polymer;

a zwitterionic coating; or

combinations thereof.

5. The structure of claim 1 , wherein the molecular shape has a shape corresponding to a shape of a binding site of the one or more binding sites.