Lecture4 - An Introduction to Bioinformatics Algorithms...

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www.bioalgorithms.info An Introduction to Bioinformatics Algorithms DNA Mapping and Brute Force Algorithms
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Outline Restriction Enzymes Gel Electrophoresis Partial Digest Problem Brute Force Algorithm for Partial Digest Problem Branch and Bound Algorithm for Partial Digest Problem Double Digest Problem
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Molecular Scissors Molecular Cell Biology, 4 th edition
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Discovering Restriction Enzymes Hin dII - first restriction enzyme – was discovered accidentally in 1970 while studying how the bacterium Haemophilus influenzae takes up DNA from the virus Recognizes and cuts DNA at sequences: GTGCAC GTTAAC
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Discovering Restriction Enzymes Werner Arber Daniel Nathans Hamilton Smith Werner Arber – discovered restriction enzymes Daniel Nathans - pioneered the application of restriction for the construction of genetic maps Hamilton Smith - showed that restriction enzyme cuts DNA in the middle of a specific sequence My father has discovered a servant who serves as a pair of scissors. If a foreign king invades a bacterium, this servant can cut him in small fragments, but he does not do any harm to his own king. Clever people use the servant with the scissors to find out the secrets of the kings. For this reason my father received the Nobel Prize for the discovery of the servant with the scissors". Daniel Nathans’ daughter (from Nobel lecture)
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Recognition Sites of Restriction Enzymes Molecular Cell Biology, 4 th edition
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Uses of Restriction Enzymes Recombinant DNA technology Cloning cDNA/genomic library construction DNA mapping
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Restriction Maps A map showing positions of restriction sites in a DNA sequence If DNA sequence is known then construction of restriction map is a trivial exercise In early days of molecular biology DNA sequences were often unknown Biologists had to solve the problem of constructing restriction maps without knowing DNA sequences
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Full Restriction Digest Cutting DNA at each restriction site creates multiple restriction fragments : Is it possible to reconstruct the order of the fragments from the sizes of the fragments {3,5,5,9} ?
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Full Restriction Digest: Multiple Solutions Alternative ordering of restriction fragments: vs
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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Measuring Length of Restriction Fragments Restriction enzymes break DNA into restriction fragments.
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