Multiple Word DNA Computing on Surfaces

Abstract

The enzymatic manipulation of DNA molecules immobilized on a surface that each contain linked, multiple "DNA words" is demonstrated, with applications to DNA computing. A new DESTROY operation to selectively remove unmarked DNA strands from surfaces, consisting of polymerase extension followed by restriction enzyme cleavage, has been developed for multiple-word DNA computing. DNA polymerase is used to extend DNA primers hybridized to DNA strands that are covalently attached to a chemically modified gold thin film. The efficiency of this surface polymerase extension reaction is >90%, as determined by removal of the extended DNA molecules from the surface followed by gel electrophoretic analysis. Complete extension of the DNA strands creates a Dpn II restriction enzyme site in the duplex DNA; these molecules may then be cleaved from the surface by addition of Dpn II, with an efficiency exceeding 90%. DNA molecules may be protected from such destruction by hybridization of a peptide nucleic acid (PNA) oligomer to one of the words. The hybridized PNA blocks polymerase extension, thereby preventing formation of the restriction site and consequent strand cleavage. The utility of these operations for DNA computing is demonstrated by solving a small (2-bit) Satisfiability problem in which information was encoded in two tandem words.

Two-dimensional enzyme diffusion in laterally confined DNA monolayers

“…The side-access effect reported in this study has not been hitherto described, although other investigations demonstrated enzymatic reactions on surface-bound DNA molecules 6,[21][22][23][38][39][40][41][42][43][44] . These studies used either longer dsDNA molecules 23,40 or molecules provided with significantly less-rigid surface linkers and/ or different chemical strategies for DNA self-assembly 6,23,39,41 .…”

“…Several studies involved ligation enzymes 42,43 , the reactions of which occurred on DNA-binding sites that are readily available on the topmost interface of the matrices. In contrast, Corn 39 , and Daube and co-workers 40 used restriction enzymes and dsDNA densities close to our experimental conditions, and their results Figure 4, relative to the DpnII reaction, for consensus (solid blue squares) and control (open red circles) dsDnA matrices. Data are means ± s.d.…”

“…These studies used either longer dsDNA molecules 23,40 or molecules provided with significantly less-rigid surface linkers and/ or different chemical strategies for DNA self-assembly 6,23,39,41 . Several studies involved ligation enzymes 42,43 , the reactions of which occurred on DNA-binding sites that are readily available on the topmost interface of the matrices.…”

Biomolecular computing: Is it ready to take off?

“…While Adleman's techniques were based on selecting one molecule representing a solution from the midst of many that represented non-solutions, Landweber and co-workers [59] devised methods to create all possible solutions of a problem in the form of RNA-DNA hybrids, and then exhaustively eliminate the sequences that did not satisfy the problem's constraints. This approach was used to solve a combinatorial chess problem using a 10-bit DNA memory strand [60,61]. A similar approach was developed, based on inactivating, rather than digesting the non-candidate solutions at the University of Leiden [47].…”

“…A similar approach was developed, based on inactivating, rather than digesting the non-candidate solutions at the University of Leiden [47]. Chemists at the University of Wisconsin developed a computation format and biological steps based on surface-immobilized oligodeoxynucleotides, high-affinity non-covalent hybridization with PNAs, and fluorescence readout [61]. Considerable efforts have been made to define information content and operations in DNA and other biomolecules according to concepts of mathematics, computer science, and linguistics [34,62].…”