simulation of a dna renaturalization process r.baños, p. cordero, a.goñi and j.castellanos...
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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
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
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
UPM 4
DNA Structure
META'08
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
UPM 6
Structure of Nucleid Acids II
• Double Helix Model
ghr.nlm.nih.gov
META'08
genemol.org
UPM 7
DNA Renaturalization
META'08
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
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
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
UPM 11
Simulation
META'08
UPM 12
Simulation heuristics
1. Annealing decision
2. Movement decision (Ramdomly)
META'08
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
UPM 14
Simulated Renaturalization II
META'08
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
UPM 16
Simulated Renaturalization IV
• Results with a fusion temperature from 90ºC
META'08
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
UPM 18
Conclusions
META'08
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
UPM 20
Thank you
META'08
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