Background

Background

What are RNA and DNA oligonucleotides?
To put it simply, RNA/DNA oligonucleotides, also called “oligos”, are short strands of RNA or DNA (typically >100 bases in length). Currently oligos are useful in a wide variety of applications including: gene isolation, gene synthesis, testing for genetic diseases, so called ‘silencing RNA’ is used to prevent the expression of certain genes.[1][2] More recently, oligonucleotide microarrays haven been shown to have great potential for rapid high-throughput chemical and genetic screening .[3][4] More recently, the finding of charge transport through DNA[5][6], has opened the door for yet more applications for oligos in molecular electronics seem to be on the horizon.[7][8]

What makes a chimera a chimera?
Chimeric DNA is a DNA/RNA hybrid that contains both RNA and DNA bases on the same chain. They have emerged as useful tools for in vivo genetic engineering[9][10][11] as the addition RNA and DNA bases on the same strand increase its stability in vivo.[12] While this increase in stability seems to be a product of decreased nuclease recognition[13] , our investigation has suggested that under certain conditions Chimeras may be more unstable than either DNA or RNA.

Why Use Chimeras for mol-Comp?
There are four key properties of Chimeric DNA oligos that seem to make for a valuable material in molecular electronics:

They’re cheap, for example, 20USD can buy you over a quadrillion individual molecules. [14] Were each nucleotide to represent one bit that would be over a petabyte of data storage for 20USD.

They can likely transport electricity to the same extent as pure DNA oligonucleotides[15]

They can selectively self-assemble into large-scale structures via base pairing

There are promising methods for direct, large-scale manipulation of chimeric nucleotide structure

References:
[1] K. Itakura, et al. “Synthesis and Use of Synthetic Oligonucleotides” 1984, Annual Reviews of Biochemistry.
[2] M. Matzke “RNA: Guiding Gene Silencing” 2001, Science.
[3] M. Heller “DNA Microarray Technology: Devices, Systems, and Applications” 2002, Annual Reviews of Biomedical Engineering.
[4] B. Baker “An Electronic, Aptamer-Based Small-Molecule Sesor for the Rapid, Label-Free Detection of Cocaine in Adulterated Samples and Biological Fludis” 2005, Journal of the American Chemical Society.
[5] E. Boon & J. Barton, “Charge Transport in DNA” 2002, Current Opinion in Structural Biology.
[6] D. Porath et al. “Direct measurement of electrical transport through DNA molecules” 1999, Nature.
[7] A. Rakitin et al. “Metallic Conduction through Engineered DNA: DNA Nanoelectronic Building Blocks” 2001, Physical Review Letters.
[8] N. Tao “Electron transport in molecular junctions” 2006, Nature.
[9] B. Kren et al. “In vivo site-directed mutagenesis of the factor IX gene by Chimeric RNA/DNA oligonucleotides” 1998, Nature Medicine.
[10] T. Zhu et al. “Targeted Manipulation of maize genes in vivo using chimeric RNA/DNA oligonucleotides” 1998, Proceedings of the National Academy of Science.
[11] T. Zhu et al. “Engineering herbicide-resistant maize using chimeric RNA/DNA oligonucleotides” 2000, Nature Biotechnology.
[12] N. Taylor et al. “Chimeric DNA-RNA hammerhead ribozymes have enhanced in vitro catalytic efficiency and increased stability in vivo” 1992, Nucleic Acids Research.
[13] M. Gottikh et al. “Chimeric Antisense Oligonucleotides: Synthesis and Nuclease Resistance in Biological Media” 1994, Antisense Research and Development.
[14]http://www.idtdna.com/order/cart.aspx
[15] C. Nogues et al. “Sequence Dependence of Charge Transport Properties of DNA” 2006, Journal of Physical Chemistry.

Background
What are RNA and DNA oligonucleotides? To put it simply, RNA/DNA oligonucleotides, also called “oligos”, are short strands of RNA or DNA (typically >100 bases in length). Currently oligos are useful in a wide variety of applications including: gene isolation, gene synthesis, testing for genetic diseases, so called ‘silencing RNA’ is used to prevent the expression of certain genes.[1][2] More recently, oligonucleotide microarrays haven been shown to have great potential for rapid high-throughput chemical and genetic screening .[3][4] More recently, the finding of charge transport through DNA[5][6], has opened the door for yet more applications for oligos in molecular electronics seem to be on the horizon.[7][8] What makes a chimera a chimera? Chimeric DNA is a DNA/RNA hybrid that contains both RNA and DNA bases on the same chain. They have emerged as useful tools for in vivo genetic engineering[9][10][11] as the addition RNA and DNA bases on the same strand increase its stability in vivo.[12] While this increase in stability seems to be a product of decreased nuclease recognition[13] , our investigation has suggested that under certain conditions Chimeras may be more unstable than either DNA or RNA. Why Use Chimeras for mol-Comp? There are four key properties of Chimeric DNA oligos that seem to make for a valuable material in molecular electronics: They’re cheap, for example, 20USD can buy you over a quadrillion individual molecules. [14] Were each nucleotide to represent one bit that would be over a petabyte of data storage for 20USD. They can likely transport electricity to the same extent as pure DNA oligonucleotides[15] They can selectively self-assemble into large-scale structures via base pairing There are promising methods for direct, large-scale manipulation of chimeric nucleotide structure
References: [1] K. Itakura, et al. “Synthesis and Use of Synthetic Oligonucleotides” 1984, Annual Reviews of Biochemistry. [2] M. Matzke “RNA: Guiding Gene Silencing” 2001, Science. [3] M. Heller “DNA Microarray Technology: Devices, Systems, and Applications” 2002, Annual Reviews of Biomedical Engineering. [4] B. Baker “An Electronic, Aptamer-Based Small-Molecule Sesor for the Rapid, Label-Free Detection of Cocaine in Adulterated Samples and Biological Fludis” 2005, Journal of the American Chemical Society. [5] E. Boon & J. Barton, “Charge Transport in DNA” 2002, Current Opinion in Structural Biology. [6] D. Porath et al. “Direct measurement of electrical transport through DNA molecules” 1999, Nature. [7] A. Rakitin et al. “Metallic Conduction through Engineered DNA: DNA Nanoelectronic Building Blocks” 2001, Physical Review Letters. [8] N. Tao “Electron transport in molecular junctions” 2006, Nature. [9] B. Kren et al. “In vivo site-directed mutagenesis of the factor IX gene by Chimeric RNA/DNA oligonucleotides” 1998, Nature Medicine. [10] T. Zhu et al. “Targeted Manipulation of maize genes in vivo using chimeric RNA/DNA oligonucleotides” 1998, Proceedings of the National Academy of Science. [11] T. Zhu et al. “Engineering herbicide-resistant maize using chimeric RNA/DNA oligonucleotides” 2000, Nature Biotechnology. [12] N. Taylor et al. “Chimeric DNA-RNA hammerhead ribozymes have enhanced in vitro catalytic efficiency and increased stability in vivo” 1992, Nucleic Acids Research. [13] M. Gottikh et al. “Chimeric Antisense Oligonucleotides: Synthesis and Nuclease Resistance in Biological Media” 1994, Antisense Research and Development. [14]http://www.idtdna.com/order/cart.aspx [15] C. Nogues et al. “Sequence Dependence of Charge Transport Properties of DNA” 2006, Journal of Physical Chemistry.