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Molecular Computing - Employing Nucleic Acids as Molecular Computing Devices

With a large quantity of DNA, bio-molecular-based computers may offer the possibility that massive parallelism could be used for solving NP complete problems in polynomial time. Instances of NP complete problems, such as the maximum clique problem and the SAT problem have been solved using DNA/DNA hybridization. A key question in DNA computing is the fidelity of the basic operations employed and the scalability of the computation as a whole. When DNA/DNA hybridization is used as a basic computational operation, the accuracy of the computation will depend on the ability to discriminate between perfectly matching hybrids (the bits of the library and their complementary oligomers) and those with mismatches. In this regard, the quality of the DNA code design is playing a critical role in the fidelity of the computation. The problem of designing sets of modular RNA and DNA sequences, which hybridize in a predefined way, is fundamental not only for molecular computing but also for many applications in contemporary molecular biology and nanotechnology such as strand selection, PCR and isothermal amplification reactions, DNA-chip arrays, ribozyme design, and self-assembly of DNA. We have designed a 12-bit DNA library that encodes binary information by our own software based on thermodynamics constrains. The results show a high level of specific hybridization achieved for all library words under identical conditions (Table 1). The approach can be used for designing molecular logic gates for biosensor arrays that function in parallel.

Table 1. A 12-bit DNA library that encodes binary information.The melting points for all words are calculated thermodynamically for 50 mM NaCl and 1 uM oligomer using two different thermodynamic data. The highest and the lowest melting points are 2.9+/- oC (without taking into account the GC and AT init. w/term.) according to Breslauer et al. (1986) (Melting points-1) and Allawi and Santa Lucia (1997) (Melting points-2).

 N    Bits  5'- 3' Word
sequences 		5'- 3' Capture
sequences 		 Melting points-1    Melting points-2 
1 1.1  CCATCACTACCTTCAT   ATGAAGGTAGTGATGG  45.3 46.8
2 1.0  TCCTCTATCATCCTCA   TGAGGATGATAGAGGA  46.6 46.5
3 2.1  TCCCTATTCACTCTCT   AGAGAGTGAATAGGGA  44.6 46.7
4 2.0  CACACCTCAACTTCTT   AAGAAGTTGAGGTGTG  44.9 48.0
5 3.1  ACTTCCCTTCTACACA   TGTGTAGAAGGGAAGT  44.8 48.1
6 3.0  CACCATCCTTATCTCA   TGAGATAAGGATGGTG  46.7 46.4
7 4.1  TCTCTCAATCCACTTC   GAAGTGGATTGAGAGA  45.6 46.6
8 4.0  TACAATCCCACACTTT   AAAGTGTGGGATTGTA  45.6 46.6
9 5.1  TCTCTTCCTCTTACCA   TGGTAAGAGGAAGAGA  45.8 47.0
10 5.0  TCATACCTAACTCCCT   AGGGAGTTAGGTATGA  44.6 46.7
11 6.1  CTCATCTTAACCACCT   AGGTGGTTAAGATGAG  44.7 46.7
12 6.0  ACCATTACTTCAACCA   TGGTTGAAGTAATGGT  45.6 46.6
13 7.1  TTCTACAACCTACCCT   AGGGTAGGTTGTAGAA  44.4 47.3
14 7.0  TCCAACTTAACACTCC   GGAGTGTTAAGTTGGA  45.3 47.3
15 8.1  ACCTTTACCCTATCCT   AGGATAGGGTAAAGGT  46.2 47.1
16 8.0  ACACCCTAACAATCAA   TTGATTGTTAGGGTGT  45.6 46.6
17 9.1  CACCCATTCCTAATAC   GTATTAGGAATGGGTG  45.4 45.2
18 9.0  TCCTACACAAACATCA   TGATGTTTGTGTAGGA  43.8 46.3
19 10.1  ATTCTCACTCACAACC   GGTTGTGAGTGAGAAT  44.6 47.8
20 10.0  ACCACTCCAATAACTC   GAGTTATTGGAGTGGT  44.2 47.0
21 11.1  TCCTACTCTCCAATCA   TGATTGGAGAGTAGGA  46.4 47.1
22 11.0  TCTTTCACACATCCAT   ATGGATGTGTGAAAGA  46.3 46.7
23 12.1  ACACCATTTCACCTAA   TTAGGTGAAATGGTGT  45.6 46.6
24 12.0  ACACTAATCCTCCAAC   GTTGGAGGATTAGTGT  44.2 47.0

Molecules with attributes of AND logic function must remain inactive unless receiving two separate molecular impulses that trigger activity. Candidate RNA constructs possessing AND logic function triggered by 16-nt effector DNAs were designed using the same principles and computational procedures used to identify candidate YES RNA switches. However, additional steps were added to permit computation of four different structural states with high stability. As with the YES gate computations, one of the structural states must permit the formation of the active hammerhead core, in this case, only when presented with two effector DNA sequences. The remaining three states should not permit ribozyme function, even if either of the two effector DNAs is present independently. Our computational search efforts indicate that many thousands of ribozymes with the same AND gate properties can be generated. Many molecular logic gates with various functions can be designed to work in parallel.

Figure 1. Design and characterization of AND-1, an oligonucleotide-specific molecular switch that possesses AND logic function. (a) AND-1 is designed to form the active hammerhead structure and self-cleave only when presented simultaneously with its two corresponding effector DNAs (DNA-7 and DNA-8). The dot matrix plots for the ON state showing some character of the OFF states (stem IV) is depicted. (b) Activation of AND-1 self-cleavage requires both full-length DNA-7 and DNA-8 effectors. Maximum incubation time is 60 min. (c) Kinetics of AND-1 self-cleavage under various combinations of effector DNAs.

References:
1. Robert Penchovsky and Jorg Ackerman - DNA library design for molecular computation – 2003, J Comput Biol., 10665277, Q2 – 20 т. (Biochemistry, Genetics and Molecular Biology), IF – 1,89

2. Robert Penchovsky & Ronald R Breaker - Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes – 2005, Nature Biotechnology, 10870156, Q1(Biochemistry, Genetics and Molecular Biology), IF – 43,5

3. Robert Penchovsky - Engineering integrated digital circuits with allosteric ribozymes for scaling up molecular computation and diagnostics – 2012, ACS Synth Biol, 21615063, Q1 (Biochemistry, Genetics and Molecular Biology), IF – 5,382

4. Robert Penchovsky - An Integrated DNA Selection in Micro-flow Reactors as an Approach for Molecular Computation and Diagnostics. Ph.D. thesis, Universität zu Köln -2003.