A Polymerase Based Algorithm for SAT

Franco, Giuditta

doi:10.1007/11560586_20

Cited by 9 publications

(8 citation statements)

References 14 publications

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“…Recombination of two DNA strings along with a (given) common substring γ may be efficiently implemented by XPCR γ (or γ-cross-pairing PCR [6]), as well as other procedures (such as DNA extraction, combinatorial libraries generation, and mutagenesis [6,5,8,14,7]) which can be described in terms of null context splicing rules. These are rewriting rules introduced by T. Head in the context of Formal Language Theory (FLT) as particular H-systems, inspired by selective recombination induced by few (existent in nature) restriction enzymes [9]: αXγY β, αV γW β → αXγW β, αV γY β Such rule may be seen as a specific chimeras generation method, which we briefly call γ-recombination.…”

Section: Xpcr Protocolmentioning

confidence: 99%

“…Multiple XPCR or n-XPCR was designed [5] and tested in [7] as a variant of XPCR, to realize a parallel concatenation of n different types of double-stranded DNA sequences in a single step. Beside other experimental validations, starting from a pool P with seven fragments {αδ 1 γ 1 , γ i δ i+1 γ i+1 , γ 7 δ 7 β | i = 1, .., 6}, molecule αδ 1 γ 1 δ 2 γ 2 δ 3 γ 3 δ 4 γ 4 δ 5 γ 5 δ 6 γ 6 δ 7 β (long 538 bp) with seven different binary forms δ and seven different overalapping primes γ has been obtained in [7].…”

Section: Xpcr Protocolmentioning

confidence: 99%

“…In other terms, after a previous validation on relatively short synthetic sequences (150 bp long), the technique is here experimentally validated on three genes (natural sequences long 311, 518, and 1019 bp) extracted from an environmental bacterial strain, the Bulkolderia fungorum DBT1 [4], having remarkable PAH (polycyclic aromatic hydrocarbon) degradation capabilities. Moreover, some open questions about experimental implementation of XPCR technique, which were posed in [5,7], have been here answered. Importantly enough, an unexpected outcome was amplified in the experiments designed to concatenate two copies of one same gene, as reported in section 3.1.…”

Section: Introductionmentioning

confidence: 99%

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Experimental Analysis of XPCR-based protocols

Franco,

Bellamoli,

Lampis

2017

Preprint

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This paper reports some experimental results validating in a broader context a variant of PCR, called XPCR, previously introduced and tested on relatively short synthetic DNA sequences. Basic XPCR technique confirmed to work as expected, to concatenate two genes of different lengths, while a library of all permutations of three different genes (extracted from the bacterial strain Bulkolderia fungorum DBT1) has been realized in one step by multiple XPCR. Limits and potentialities of the protocols have been discussed, and tested in several experimental conditions, by aside showing that overlap concatenation of multiple copies of one only gene is not realizable by these procedures, due to strand displacement phenomena. In this case, in fact, one copy of the gene is obtained as a unique amplification product.

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Section: Xpcr Protocolmentioning

confidence: 99%

Section: Xpcr Protocolmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Experimental Analysis of XPCR-based protocols

Franco,

Bellamoli,

Lampis

2017

Preprint

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“…In the context of experimental DNA computing, overlap assembly was used in, e.g., [7,12,24,32] for the formation of combinatorial DNA or RNA libraries. Overlap assembly can also be viewed as modeling a special case of an experimental lab procedure called cross-pairing PCR, introduced in [15] and studied in, e.g., [13,14,16,27].…”

Section: Introductionmentioning

confidence: 99%

State Complexity of Overlap Assembly

Brzozowski

Kari

Bai

et al. 2018

Implementation and Application of Automata

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The state complexity of a regular language Lm is the number m of states in a minimal deterministic finite automaton (DFA) accepting Lm. The state complexity of a regularity-preserving binary operation on regular languages is defined as the maximal state complexity of the result of the operation where the two operands range over all languages of state complexities ≤ m and ≤ n, respectively. We find a tight upper bound on the state complexity of the binary operation overlap assembly on regular languages. This operation was introduced by Csuhaj-Varjú, Petre, and Vaszil to model the process of self-assembly of two linear DNA strands into a longer DNA strand, provided that their ends "overlap". We prove that the state complexity of the overlap assembly of languages Lm and Ln, where m ≥ 2 and n ≥ 1, is at most 2(m − 1)3 n−1 + 2 n . Moreover, for m ≥ 2 and n ≥ 3 there exist languages Lm and Ln over an alphabet of size n whose overlap assembly meets the upper bound and this bound cannot be met with smaller alphabets. Finally, we prove that m + n is a tight upper bound on the overlap assembly of unary languages, and that there are binary languages whose overlap assembly has exponential state complexity at least m(2 n−1 − 2) + 2. /15/B/ST6/00615.3 Informally, during a shuffle between two words with a trajectory over {0, 1, σ} + , the symbols of the trajectory are interpreted as follows: 0 (respectively 1) signifies that the corresponding letter from the first (respectively second) word is retained, and σ signifies that a letter from the first word is retained, provided it coincides with the corresponding letter in the second word.

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“…In the context of experimental DNA computing, overlap assembly was used in, e.g., [10,11,12,13] for the formation of combinatorial DNA or RNA libraries. Overlap assembly can also be viewed as modelling a special case of an experimental procedure called cross-pairing PCR, introduced in [14] and studied in, e.g., [15,16,17,18]. This paper is a continuation of the theoretical analysis of overlap assembly as a formal language operation, that was started in [1] and [2].…”

Section: Introductionmentioning

confidence: 99%

Further remarks on DNA overlap assembly

Enaganti

Ibarra

Kari

et al. 2017

Information and Computation

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The operation of overlap assembly was defined by Csuhaj-Varju, Petre, and Vaszil as a formal model of the linear self-assembly of DNA strands: The overlap assembly of two strings, xy and yz, which share an "overlap" y, results in the string xyz. This paper continues the exploration of the properties of the overlap assembly operation by investigating closure of various language classes under iterated overlap assembly, and the decidability of the completeness of a language. It also investigates the problem of deciding whether a given string is terminal with respect to a language, and the problem of deciding if a given language can be generated by an overlap assembly operation of two given others.

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A Polymerase Based Algorithm for SAT

Cited by 9 publications

References 14 publications

Experimental Analysis of XPCR-based protocols

Experimental Analysis of XPCR-based protocols

State Complexity of Overlap Assembly

Further remarks on DNA overlap assembly

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