A Conventional Strands Evaluator for DNA Computations

Abstract

The DNA sequence design is a crucial problem in DNA based computations. In the literature there is evidence that many input sets should not be used for real DNA computations. This approach might lead to high probabilities of incurring in biological faults which make computations unsafe. In this paper we present an intermediate tool between strand logical design and practical computations, that allows scientists to approach in-vitro computations reducing the probability of biological mistakes in the phase of theoretical input design for practical computations.

Fastest parallel molecular algorithms for the elliptic curve discrete logarithm problem over GF(2n)

“…A summary of the performances is shown in Table 4. In particular, using the same model but only one test tube (as in [2]), the number of bio-steps required for the addition and shifter is O(1), while for the multiplication is O(n), but we lose in number of bits that can be stored and the length of the strands increases linearly with n. This increases the probability of incurring in biological faults [8,9]. Differently from [2] and [15], our model allows to deal with and compute huge binary numbers, and to reduce to a minimum the probability of biological faults and miss-hybridizations [8,9].…”

“…Single-stranded complemenor annealing tary DNA molecules form (under appropriate conditions of temperature, pH, etc. [8,9]) double strands of DNA. This occurs through the hydrogen bonds which are formed whenever complementary base pairs are brought into proximity.…”

“…EcoRI GAAT T C), S is a [20 − 30] base-pair long DNA double strand (not containing GAAT T C), and X is a general nucleic acid subsequence repeated i-times. Such an encoding fails because it deals with very long DNA sequences which are often subjected to miss-hybridization, hairpins and shifted hybridizations [8,9]. Moreover, since a single test tube can contain at most 10 18 nucleotides, its capacity is explicitly upperbounded.…”

“…Melting is a bit of a misnomer because its effect can be equally achieved by washing the double-stranded DNA molecules in a doubly distilled water. A low salt concentration results in destabilizing any hydrogen bonds between the DNA strands [8,9] and thereby in separating the two strands. Heating can be selectively used to melt apart short double-stranded sequences while leaving longer double-stranded sequences intact.…”

“…Our model generalizes what so far described. It is unbounded in size and significantly reduces any probability of biological faults [8,9]. Its fundamental idea is to divide the binary strings into packages, each contained in a test tube, and to further split the packages into words of fixed number of bits.…”