Circular DNA and splicing systems

Siromoney, Rani; Subramanian, K. G.; Dare, V. R.

doi:10.1007/3-540-56346-6_44

Cited by 37 publications

(42 citation statements)

References 7 publications

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“…We study properties of such recombinations. This study complements results obtained in [8,[18][19][20]23] on linear splicing, circular splicing, self-splicing and mixed splicing. The results obtained that the computational power of context-free recombination systems is very weak (which is unlikely), strengthen the conjecture that the presence of direct repeats is insufficient for accurate splicing during gene unscrambling.…”

Section: Context-free Recombinationssupporting

confidence: 87%

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DNA computing in vitro and in vivo

Kari

2001

Future Generation Computer Systems

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Section: Context-free Recombinationssupporting

confidence: 87%

“…The above operations are similar to the "splicing operation" introduced by Head [6] and "circular splicing" and "mixed splicing" [7,[18][19][20]23]. Refs.…”

Section: ) (3) •Uxv + •U XV ⇒ •Uxv U Xvmentioning

confidence: 98%

DNA computing in vitro and in vivo

Kari

2001

Future Generation Computer Systems

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“…These operations resemble the splicing operation introduced by Head (1987) as a model of DNA recombination and the splicing on circular strands studied by Siromoney et al (1992) and Pixton (1995). Paun (1995) and Csuhaj-Varju et al (1996) subsequently showed that this model has the computational power of a universal Turing Machine.…”

Section: The Formal Modelmentioning

confidence: 97%

The evolution of cellular computing: nature’s solution to a computational problem

Landweber

Kari

1999

Biosystems

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How do cells and nature 'compute'? They read and 'rewrite' DNA all the time, by processes that modify sequences at the DNA or RNA level. In 1994, Adleman's elegant solution to a seven-city directed Hamiltonian path problem using DNA launched the new field of DNA computing, which in a few years has grown to international scope. However, unknown to this field, two ciliated protozoans of the genus Oxytricha had solved a potentially harder problem using DNA several million years earlier. The solution to this problem, which occurs during the process of gene unscrambling, represents one of nature's ingenious solutions to the problem of the creation of genes. RNA editing, which can also be viewed as a computational process, offers a second algorithm for the construction of functional genes from encrypted pieces of the genome.

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“…Head [14] provided a potential biochemical example, where the formal generative capacity of the restriction enzyme BpmI in the company of a ligase is discussed. Other publications about splicing systems are written by Laun, Reddy [20] and by Siromoney, Subramanian and Dare [36], which reports splicing systems based on circular DNA strings. A new method for separation of DNA according to its substrings is developed and demonstrated in [8].…”

Section: Introductionmentioning

confidence: 99%

<title>Enzyme optimization for next level molecular computing</title>

Wasiewicz¹,

Malinowski²,

Płucienniczak

2006

SPIE Proceedings

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The main concept of molecular computing depends on DNA self-assembly abilities and on modifying DNA with the help of enzymes during genetic operations. In the typical DNA computing a sequence of operations executed on DNA strings in parallel is called an algorithm, which is also determined by a model of DNA strings. This methodology is similar to the soft hardware specialized architecture driven here by heating, cooling and enzymes, especially polymerases used for copying strings. As it is described in this paper the polymerase Taq properties are changed by modifying its DNA sequence in such a way that polymerase side activities together with peptide chains, responsible for destroying amplified strings, are cut off. Thus, it introduces the next level of molecular computing. The genetic operation execution succession and the given molecule model with designed nucleotide sequences produce computation results and additionally they modify enzymes, which directly influence on the computation process. The information flow begins to circulate. Additionally, such optimized enzymes are more suitable for nanoconstruction, because they have only desired characteristics. The experiment was proposed to confirm the possibilities of the suggested implementation.

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Circular DNA and splicing systems

Cited by 37 publications

References 7 publications

DNA computing in vitro and in vivo

DNA computing in vitro and in vivo

The evolution of cellular computing: nature’s solution to a computational problem

<title>Enzyme optimization for next level molecular computing</title>

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