The Perils of Polynucleotides Revisited
DNA computing relies on the successful implementation of physical chemistry techniques involving oligonucleotides of prescribed sequence. Our laboratory has been involved in the assembly and manipulation of designed oligonucleotides in order to pursue studies in genetic recombination and nanofabrication. We have constructed a large number of unusual branched DNA motifs used to build a variety of DNA objects, lattices, and nanomechanical devices. Our experience with these systems has uncovered a large number of experimental pitfalls that may confront individuals working with DNA-based computation. A decade ago, we presented our experience in this area in the hope that we could help investigators to anticipate experimental problems that affect DNA computing schemes. Here, we review these points from the vantage point of further experience, indicating both modifications to the original criteria and new points as well.
KeywordsMajor Groove Nucleotide Pair Branch Migration Sequence Symmetry Nanomechanical Device
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- 13.Sherman WB (2007) Disentangling kinetics and energetics in DNA nanostructure assembly: forming parallel double crossover molecules. In: Proceedings of the fourth conference on foundations of nanoscience, Snowbird, Utah, April 18–21, 2007. Science Technica Inc, pp 65–65 Google Scholar
- 22.Hsieh P, Panyutin IG (1995) DNA branch migration. In: Eckstein F, Lilley DMJ (eds) Nucleic acids and molecular biology, vol 9. Springer, Berlin, pp 42–65 Google Scholar
- 28.Wu G, Jonoska N, Seeman NC (2008) Self-assembly of a DNA nano-object demonstrates natural computation (submitted for publication) Google Scholar
- 29.Wang H, Di Gate RJ, Seeman NC (1998) The construction of an RNA knot and its role in demonstrating that E. coli DNA topoisomerase III is an RNA topoisomerase. In: Sarma RH, Sarma MH (eds) Structure, motion, interaction and expression of biological macromolecules. Adenine Press, New York, pp 103–116 Google Scholar
- 32.Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor Google Scholar