Abstract
Within recent years nucleic acids have become a focus of interest for prototype implementations of molecular computing concepts. During the same period the importance of ribonucleic acids as components of the regulatory networks within living cells has increasingly been revealed. Molecular computers are attractive due to their ability to function within a biological system; an application area extraneous to the present information technology paradigm. The existence of natural information processing architectures (predominately exemplified by protein) demonstrates that computing based on physical substrates that are radically different from silicon is feasible. Two key principles underlie molecular level information processing in organisms: conformational dynamics of macromolecules and self-assembly of macromolecules. Nucleic acids support both principles, and moreover computational design of these molecules is practicable. This study demonstrates the simplicity with which one can construct a set of nucleic acid computing units using a new computational protocol. With the new protocol, diverse classes of nucleic acids imitating the complete set of boolean logical operators were constructed. These nucleic acid classes display favourable thermodynamic properties and are significantly similar to the approximation of successful candidates implemented in the laboratory. This new protocol would enable the construction of a network of interconnecting nucleic acids (as a circuit) for molecular information processing.
Highlights
Suggestions for implementing a molecular computer with nucleic acids followed the encoding principle of genetic information [1]
The results indicate, that the computational protocol (P-ER2), which aims to increase the degree of freedom in generating a diversified structure configuration for the design of molecular logic gates seems to be rather inefficient
In order to design nucleic acid computing units, a protocol that includes a multi-stable sequence design algorithm is required. The development of such protocol is discussed and using RNA logic gate as test case, we evaluate the performance of the new protocol
Summary
Suggestions for implementing a molecular computer with nucleic acids followed the encoding principle of genetic information [1]. Major progress in the application of nucleotides for information processing came about two decades later with Adleman’s insight that random oligonucleotides could be the basic tokens for information processing [2] His method employed enzymes only to stabilise (through covalent bonds) the products of a self-assembly process (hybridisation of partially complementary oligonucleotides) but not in the information processing itself, and did not require enzymes with sequence specificity. In RNA interference, a short interfering RNA molecule (siRNA) forms complementary base pairs with a target region in mRNA, allowing a protein complex called RISC (RNAinduced silencing complex) to attach and cleave the target region [9,10] Another short RNA called microRNA (miRNA), generated from an enzyme named Dicer that cleaves non-coding RNAs (i.e., RNA that do not code protein), binds imperfectly with the target region in mRNA (forming a bulge), preventing the translation machinery from accessing this target region [11]. The ability of these RNA molecules provides an interesting application scenario for molecular information technology
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