DNA-RNA

Abstract

We carried out the first simulations of Ned Seeman's DNA crossover structures that laid out how to do self-assembly with DNA [#594, 651, 707, 1182]. Tod Pascal studied the branched three-way junction [#995] where he found that the stable structure is strongly affected by salt concentration and by the ratio of MgCl₂ to NaCl [995]. He also applied 2PT method to calculate the entropy and free energy changes during the rearrangement showing that the barrier is entropic. While he was a materials science graduate student, Si-Ping Han used DNA origami to self-organize carbon nanotubes (CNT) into field-effect transistors. In addition he used DNA to organize CNTs into parallel bundles. But, the major breakthrough in nucleic acid devices was Si-Ping Han's idea to develop a dual double helix of RNA we refer to a conditional siRNA (cond-siRNA). This incorporates a sensor element targeted to say HIV or AML that in turn serves as a logic device that only in the cells expressing proteins for this virus disassembles to release a 23 RNA fragment that incorporates into the dicer element of the ribosome to kill the cell by preventing expression of a protein vital to the cell. This promises to enable very selectively killing of diseased cells while not affecting adjacent cells that do not have the virus.

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