Molecular computing elements: gates and flip-flops

Abstract

This invention relates to novel molecular constructs that act as various logic elements, i.e. gates and flip-flops. The constructs are useful in a wide variety of contexts including, but not limited to, computation and control systems. The basic functional unit of the construct comprises a nucleic acid having at least two protein binding sites that cannot be simultaneously occupied by their cognate binding protein. This basic unit can be assembled in number of formats providing molecular constructs that act like traditional digital logic elements (flip-flops, gates, inverters, etc.).

What is claimed is:  
     
         1 . A system comprising 
 an isolated nucleic acid having a length of at least 5 base pairs and having a nucleotide sequence that encodes a first protein binding site and a second protein binding site where said first and second protein binding sites are spaced in proximity to each other such that:    when said first protein binding site is specifically bound by a protein, said second binding site cannot be bound by a protein that otherwise specifically recognizes and binds said second binding site; and    when said second binding site is specifically bound by a protein, said first binding site cannot be bound by a protein that otherwise specifically recognizes and binds said first binding site, and    a nucleic acid binding protein that specifically binds said first protein binding site or said second protein binding site.    
     
     
         2 . The composition of  claim 1 , wherein said nucleic acid is a double-stranded nucleic acid.  
     
     
         3 . The composition of  claim 1 , wherein said nucleic acid is a deoxyribonucleic acid (DNA).  
     
     
         4 . The composition of  claim 1 , wherein said first binding site and said second binding site have the same nucleotide sequence.  
     
     
         5 . The composition of  claim 4 , wherein said first binding site and said second binding site have the nucleotide sequence of SEQ ID NO: 1.  
     
     
         6 . The composition of  claim 1 , wherein said first binding site or said second binding site is specifically recognized and bound by a protein selected from the group consisting of Fis, and Tus.  
     
     
         7 . The composition of  claim 1 , wherein said first binding site or said second binding site is bound by EF-tu.  
     
     
         8 . The composition of  claim 1 , wherein said first binding site is within 20 nucleotides of said second binding site.  
     
     
         9 . The composition of  claim 1 , wherein said first binding site is within 1 nucleotides of said second binding site  
     
     
         10 . The composition of  claim 8 , wherein said first binding site has a strength of at least 2.4 bits as determined by individual information theory.  
     
     
         11 . The composition of  claim 1 , wherein the difference in strength between said first protein binding site and said second protein binding site is at least 0 bits as determined by individual information theory.  
     
     
         12 . The composition of  claim 1 , further comprising a third protein binding site wherein said third site is in proximity to said first protein binding site or to said second protein binding site such that specific binding of said third binding site with a protein precludes specific protein binding of said first or said second protein binding sites.  
     
     
         13 . The composition of  claim 1 , wherein: 
 said first protein binding site is a Fis binding site;    said second protein binding site is a Fis binding site; and    said binding sites are separated from each other by less than 12 nucleotide base pairs.    
     
     
         14 . The composition of  claim 13 , wherein said nucleic acid is a deoxyribonucleic acid comprising the sequence of SEQ ID NO: 2 or SEQ ID NO: 3.