NDLI: Incorporation and use of modified nucleotides in aqueous DNA computing

Content Provider	Springer Nature Link
Author	Paga, Angela M. Pishanider, Sammy D. Gal, Susannah
Copyright Year	2008
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.
Starting Page	423
Ending Page	438
Page Count	16
File Format	PDF
ISSN	15677818
Journal	Natural Computing
Volume Number	7
Issue Number	3
e-ISSN	15729796
Language	English
Publisher	Springer Netherlands
Publisher Date	2008-03-06
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Antibodies Binding proteins Fluorescent DNA Modified nucleotides Satisfiability problems Complexity Artificial Intelligence (incl. Robotics) Processor Architectures Evolutionary Biology Theory of Computation
Content Type	Text
Resource Type	Article
Subject	Computer Science Applications

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