# DNA Computing: Concepts for Medical Applications
## 4 A Concept for PCR Automation by Means of Biomolecular Computers  
Biomolecular computers, specifically those with queue memory, which use type IIB restriction endonucleases may be used for automating the PCR method. The proposed new approach (called Queue-PCR) to automating the PCR method consists of the use of biomolecular computers as the hardware and the software for a wide range of PCR solutions. In comparison with the conventional PCR, this approach has the advantage of reading numerous replicated DNA fragments by the appropriately programmed biomolecular computer (Figure 7). The first step involves the replication of selected DNA fragments using the starters and the polymerase--as in the conventional PCR protocol. In the next step, the appropriately programmed biomolecular software in the form of transition molecules (see \(t_{1}\), \(t_{2}\), \(t_{3}\), Figure 8) enables cutting the respective DNA fragments. The transition molecules enable both reading the DNA fragments and writing the read-out DNA fragment at the same time (Figure 8). The key elements in this approach are the appropriately programmed transition molecules that are unique for each transition executed by the biomolecular computer--they have the unique sticky ends and the encoded queue symbols.  
Figure 7: Diagram Queue-PCR of a new PCR automation concept of the use of biomolecular computers with type queue memory based on type IIB restriction endonuclease. The first step of Queue-PCR concept is replication of selected DNA fragments and the next step is sequential cutting and ligating DNA molecules by means of molecular software and hardware. Abbreviations: \(t_{1}\), \(t_{2}\), \(t_{3}\), \(t_{4}\), \(t_{5}\)—respective transition molecules (molecular software); PCR—conventional PCR method; the numbers: 58, 114, 1047, 1087 denote positions on the genome. The blue line denotes the genome fragment multiplicated by the PCR. The green rectangle denotes the sequence recognized by type IIB restriction endonuclease (molecular hardware). The DNA fragments amplify by PCR are denoted by blue color. The restriction sites are denoted by light green color. The remaining colors schematically illustrate the queue symbols.  
After reading the DNA fragments (see Appendix A), the appropriately programmed and designed biomolecular computer will return, as the standard output, information on the result of the operation, e.g., in the form of fluorescence (see Appendix B). An important element in the new approach to designing diagnostic biochips is the use of a restriction enzyme cutting DNA in two directions (as described in the previous subsection). This enables designing transition molecules which also comprise writing the information (queue symbols) and reading multiple DNA fragments replicated by the PCR method. In the final phase of DNA reading, a chain is formed that changes the color of the solution due to  
Figure 8: Operation of the restriction enzyme _Bae_I in a system which reads the genome fragment—reading and writing information into the queue. The molecular software (\(t_{1}\), \(t_{2}\), \(t_{3}\)) allows alternating and autonomous cleavage of DNA molecules which are genome fragments obtained by the PCR method. The biomolecular computer produces the final DNA fragment, as a standard output, after the cyclic reactions of cutting and ligating the genome fragment obtained by the PCR method. The green circle denotes the factor of fluorescence. The DNA fragments that are cleaved by restriction enzyme (_Bae_I) are denoted in yellow. The restriction sites are denoted by light green color. The other colors schematically illustrate the queue symbols that are placed in the queue.  
fluorescence. This approach may additionally be supplemented with DNA sequencing using the restriction enzymes [33; 34].