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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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UPM 2
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
META'08
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UPM 3
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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UPM 4
DNA Structure
META'08
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UPM 5
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
META'08
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UPM 6
Structure of Nucleid Acids II
• Double Helix Model
ghr.nlm.nih.gov
META'08
genemol.org
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UPM 7
DNA Renaturalization
META'08
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UPM 8
DNA Renaturalization
• In certain conditions, a monocatenary DNA solution can return to the native form of DNA.
META'08
ehu.es/biomoléculas/AN/an4-2.htm
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UPM 9
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
META'08
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UPM 10
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.
META'08
ucm.es/info/genetica/grupod/Estruadn/estruadn.htm
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UPM 11
Simulation
META'08
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UPM 12
Simulation heuristics
1. Annealing decision
2. Movement decision (Ramdomly)
META'08
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UPM 13
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
META'08
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UPM 14
Simulated Renaturalization II
META'08
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UPM 15
Simulated Renaturalization III• One simulation cycle consists of going across every square of the
board allowing one movement for each chain.
META'08
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UPM 16
Simulated Renaturalization IV
• Results with a fusion temperature from 90ºC
META'08
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UPM 17
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
META'08
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UPM 18
Conclusions
META'08
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UPM 19
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
META'08
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UPM 20
Thank you
META'08