The complexities of DNA computation

doi:10.1016/S0167-7799(99)01312-8

Trends in Biotechnology

Volume 17, Issue 4, 1 April 1999, Pages 151-154

https://doi.org/10.1016/S0167-7799(99)01312-8 Get rights and content

Abstract

Over the past few years, a handful of insightful researchers have bridged the gap between biological computing theory and actual DNA-based computation. By using ingenious encoding techniques and clever molecular-biological manipulations, simple versions of computationally complex problems have been experimentally approached or resolved. However, the technical problems revealed during the execution of these scientific set pieces make it unlikely that DNA will ever rival silicon for the solution of any real-world problem.

Section snippets

DNA computers

All DNA computations so far attempted rely on what might be called ‘hybridization logic’: the ability to encode and solve computational problems by forming correct base pairings and avoiding incorrect base pairings. Hybridization logic is not the only possiblity for DNA computation – for example, an alternative approach that we will examine below is the use of nucleic-acid enzymes as parts of nucleic-acid logic circuits; in this case, it would be catalytic transformation, rather than

Problems with DNA computations

Although the methods described above are novel and clever, their scope and power is extremely limited. Any problem that would give pause to a supercomputer can only be resolved as a DNA computation using a large number of specifically-encoded oligonucleotides. The HPP was encoded with 20 oligonucleotide strings, a maximal clique problem was encoded in 28 strings¹¹, a binary addition was carried out with seven strings³ and a method for encoding DNA words was tested with 108 strings¹⁴.

Prospects for DNA computation

Although DNA may not be a useful medium for computational problems, this does not mean that computations or logical evaluations should not be carried out with DNA. Instead, the problems that are approached using DNA should be redefined to be relevant to DNA itself. Such approaches frequently move away from the ‘hybridization logic’ inherent in DNA encoding schemes. For example, Conrad and Zauner²⁶ describe a method whereby binary integers might be encoded as B- and Z-DNA fragments, and the

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Trends in Biotechnology

FocusThe complexities of DNA computation

Abstract

Section snippets

DNA computers

Problems with DNA computations

Prospects for DNA computation

Curr. Biol.

Chem. Biol.

Biosystems

Biosystems

Chem. Biol.

Science

Science

Science

DNA Based Computers

DNA Based Computers

DNA Based Computers

Int. J. Theor. Phys.

Science

Science

Focus
The complexities of DNA computation