Incorporation and use of modified nucleotides in aqueous DNA computing |
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Authors: | Angela M Pagano Sammy D Pishanider Susannah Gal |
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Affiliation: | (1) Department of Biological Sciences, State University of New York at Cortland, P.O. Box 2000, Cortland, NY 13045, USA;(2) Department of Biological Sciences, Binghamton University, P.O. Box 6000, Binghamton, NY 13902, USA |
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Abstract: | The concept of aqueous computing involves the use of large numbers of initially identical molecules to serve as memory registers
in a fluid environment. Here, we test a new approach to aqueous computing where modified nucleotides are used to “write” on
double-stranded DNA molecules to establish the logical values of true or false for a set of clauses. We introduce an implementation
scenario where binding proteins specific to each modification can be used to selectively isolate DNA fragments with these
modified nucleotides. In addition, we present initial results showing successful incorporation and detection of modifications.
We have successfully labeled DNA fragments with four modifications, specifically Alexa Fluor-488, BODIPY-FL, biotin, and digoxigenin
using polymerase chain reaction. The first two produce fluorescent molecules that can be distinguished by their color. We
have confirmed that binding proteins or antibodies to these four modifications are specific and do not detect the other modifications.
We have also successfully separated the DNAs labeled with Alexa Fluor and biotin using binding proteins. We present attempts
at rebinding these modified molecules to a second binding protein; the equivalent of applying more than one clause to a set
of values. We have found some challenges with this approach that likely can be resolved with further work. As there are millions
of molecules with corresponding binding proteins, this approach has the potential to yield unlimited computing power as compared
with other aqueous computing methods. |
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Keywords: | Antibodies Binding proteins Fluorescent DNA Modified nucleotides Satisfiability problems |
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