Simulation of a DNA Renaturalization process R.Baños, P. Cordero, A.Goñi and J.Castellanos...

Simulation of a DNA Renaturalization process

R.Baños, P. Cordero, A.Goñi and J.CastellanosUniversidad Politécnica de Madrid

International Conference on Metaheuristics and Nature Inspired Computing. META’08

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Outline DNA Computing DNA Structure

Structure of Nucleic Acids DNA Renaturalization

Phisico-Chemical properties of renaturalizationComplexity of eukaryotic DNA chains

Simulation Simulation heuristicsSimulated renaturalization

Conclusions

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DNA Computing

• Leonard M. Adleman solves the “Hamiltonian Path Problem” (NP-Complete) in linear time.

• Representing the problem’s information with organic molecules.

• How to store DNA strands.

• Which biologic operations. META'08

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DNA Structure

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Structure of Nucleid Acids I

• Two types of nucleic acids (NA): DNA or deoxyribonucleic acid and RNA or ribonucleic acid.

• Nitrogenous base Adenine (A) Guanine (G) Cytosine (C) Uracil (U)

Tymine (T)

hyperphysics.phy-astr.gsu.edu

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Structure of Nucleid Acids II

• Double Helix Model

ghr.nlm.nih.gov

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genemol.org

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DNA Renaturalization

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DNA Renaturalization

• In certain conditions, a monocatenary DNA solution can return to the native form of DNA.

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ehu.es/biomoléculas/AN/an4-2.htm

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Physico-chemical properties of Renaturalization

• “Cot Equation”. Cot1/2 = 1/k ()

• One of the applications of the Cot Equation is to calculate the complexity of a DNA molecule.

Cot1/2 (DNA from any genome) Complexity of any genome -------------------- = -------------------

Cot1/2 (E. Coli DNA) 4200000 bp

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Complexity of eukaryotic DNA chains

THREE FAMILIES• Fast component or highly repetitive DNA. • Intermediate component or moderately repetitive DNA. • Slow component or no repetitive DNA.

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ucm.es/info/genetica/grupod/Estruadn/estruadn.htm

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Simulation

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Simulation heuristics

1. Annealing decision

2. Movement decision (Ramdomly)

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Simulated Renaturalization I

• The simulation is made on a board of two dimensions; each position of the board can be occupied by a simple DNA chain or be empty.

Experiment

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Simulated Renaturalization II

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Simulated Renaturalization III• One simulation cycle consists of going across every square of the

board allowing one movement for each chain.

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Simulated Renaturalization IV

• Results with a fusion temperature from 90ºC

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Simulation Restrictions

• Bidimensional simulation

• All of the different simple chains of DNA of the different groups will occupy an only square in the bidimensional board

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Conclusions

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Conclussion

• Problems: the costs, the time and the space required.

• Making these experiments easier by simplify the main bio-operations and bio-molecular processes over DNA molecules.

• Virtual laboratory

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Thank you

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