Meta-DNA: synthetic biology via DNA nanostructures and hybridization reactions.

Journal Article (Journal Article)

Can a wide range of complex biochemical behaviour arise from repeated applications of a highly reduced class of interactions? In particular, can the range of DNA manipulations achieved by protein enzymes be simulated via simple DNA hybridization chemistry? In this work, we develop a biochemical system which we call meta-DNA (abbreviated as mDNA), based on strands of DNA as the only component molecules. Various enzymatic manipulations of these mDNA molecules are simulated via toehold-mediated DNA strand displacement reactions. We provide a formal model to describe the required properties and operations of our mDNA, and show that our proposed DNA nanostructures and hybridization reactions provide these properties and functionality. Our meta-nucleotides are designed to form flexible linear assemblies (single-stranded mDNA (ssmDNA)) analogous to single-stranded DNA. We describe various isothermal hybridization reactions that manipulate our mDNA in powerful ways analogous to DNA-DNA reactions and the action of various enzymes on DNA. These operations on mDNA include (i) hybridization of ssmDNA into a double-stranded mDNA (dsmDNA) and heat denaturation of a dsmDNA into its component ssmDNA, (ii) strand displacement of one ssmDNA by another, (iii) restriction cuts on the backbones of ssmDNA and dsmDNA, (iv) polymerization reactions that extend ssmDNA on a template to form a complete dsmDNA, (v) synthesis of mDNA sequences via mDNA polymerase chain reaction, (vi) isothermal denaturation of a dsmDNA into its component ssmDNA, and (vii) an isothermal replicator reaction that exponentially amplifies ssmDNA strands and may be modified to allow for mutations.

Full Text

Duke Authors

Cited Authors

  • Chandran, H; Gopalkrishnan, N; Yurke, B; Reif, J

Published Date

  • July 2012

Published In

Volume / Issue

  • 9 / 72

Start / End Page

  • 1637 - 1653

PubMed ID

  • 22237679

Pubmed Central ID

  • PMC3367821

Electronic International Standard Serial Number (EISSN)

  • 1742-5662

International Standard Serial Number (ISSN)

  • 1742-5689

Digital Object Identifier (DOI)

  • 10.1098/rsif.2011.0819


  • eng