Computing: DNA

Several attempts were made to apply nanostructures made of DNA or proteins to the development of alternative computation or computer memory. The concept of DNA computing was developed as an alternative computation approach based on information and data stored as sequenced DNA nucleotides and DNA-specific hybridization and elongation as a means to reach the answer or solution to a problem. Available tools of molecular biology were employed to identify and analyze the results [66-68]. This multistage computation is based on the assumption that solutions can be sought in parallel, thus compensating for the relatively slow processing time. 

The Scientific American website (www.sciam.com) has an interesting ask the experts section, including further information on DNA computing. 

CNTs own excellent materials properties. DNA is an excellent molecule to construct macromolecular networks because it is easy to synthesize, with a high specificity of interaction, and is conformationally flexible. The complementary base-paring properties of DNA molecules have been used to make two-dimensional crystals and prototypes of DNA computers and electronic circuits (Yan et al., 2002 Batalia et al., 2002). Therefore functionalization of CNTs with DNA molecules has great potential for applications such as developing nanodevices or nanosystems, biosensors, electronic sequencing, and gene transporters. 

Indeed solutions to several practical problems have been demonstrated, e.g., computation of Pascal s triangle modulo 2 [151], exclusive or (XOR) calculation using triple crossover [152] or string tiles [151]. Again, the annual conference Foundations of Nanoscience [143] provides a good review of the status of development of DNA computation by self assembly. Fig. 23 presents several AFM demonstrations of computation driven by DNA programmed self-assembly. 

Schulman R, Lee S, Papadakis N, Winfree E (2004) In Proceedings DNA computers 9, Madison, 2-4 Jime 2003. Lect Notes Comp Sci 2943 108-125... 

Using a bit of DNA and some commonplace biological laboratoiy techniques, researchers engineered the first DNA computer hardware ever logic made of DNA. The research was announced at the First International Conference on Computational Molecular Biology in Santa Fe, NM. 

Distance measure DnaDist DNA Compute distances to distance matrix... 

This type of problem is so complex that, with certain graphs containing less than 100 cities utilizing current algorithms it would take hundreds of years to solve [85]. Whilst electronic computers require exponentially increasing amounts of time to solve more complex problems, DNA would require a linear increase in time. However, whilst the time required to perform these calculations increases linearly, the quantity of material required for the purpose increases exponentially [87], Despite the progress achieved, practical and theoretical obstacles to creating a DNA computer remain. 

DNA computation can be built on the large array of bio-operations, as exemplified in the previous case, which could be used to write programs [88]. A program will receive a tube containing DNA strands encoding information as input and output, either yes or no or a set of tubes. A bio-computation will consist of a sequence of bio-operations performed on tubes containing DNA strands. A rela-... 

Other approaches to DNA computation have been suggested, including a method to calculate the product of Boolean matrices containing positive numbers [90]. In the case of matrices containing real numbers, the manipulation of reaction conditions allows a quantitative calculation to be performed. This use of DNA to perform an analog calculation is a new approach to computing with DNA. 

Frutos AG, Smith LM, Corn RM (1998) Enzymatic ligation reactions of DNA words on surfaces for DNA computing. J Am Chem Soc 120 10277-10282... 

A DNA computer can solve extremely difficult math problems. 

Surface ligation is also used for futuristic DNA computing on gold surfaces. The words are 16-base nucleotides T4 DNAligase is used to join the... 

Moleculai computation (DNA computing) as a massively parallel type of computing can complement rather than replace silicon computing as a computational medium in the futru e. ... 

Qinghua Liu, Liman Wang, Anthony G. Fratos, Aime E. Condon, Robert M. Com and Lloyd M. Smith, DNA computing on surfaces. Nature, 403 (2000), 175-179. 

Mitsunori Ogihara and Animesh Ray, DNA computing on a chip. Nature, 403 (2000), 143-144. Robert R Lanza, Jose B. Cibelli and Michael D. West, Human therapeutic cloning. Nature Medicine, 5 (1999), 975-977. 

It is thought that this is caused by weak preferential binding of the B-fiiranose fmm to DNA. Computer modelling studies support this theory since the pyranose form can make only two hydrogen bonds between the sugar hydroxy groups and the phosphate units, whereas three can be formed for the fiiranose structure. 

Currently, three approaches are the most popular for the identification of expressed sequences/genes in the genomic DNA computer analysis of DNA sequences for possible exons, identification of CpG islands that can be done both experimentally and using bioinformatics, and large-scale sequence analysis of transcribed sequences, like sequencing of ESTs, SAGE, and CAGE. 

---