Bluenoise Posted May 12, 2007 Share Posted May 12, 2007 Let say you fragment genomic DNA into around 500bp fragments. Now lets say you denature these fragments by heat or whatever. How would you go about ensuring that as many fragments as possible anneal to their complementary strand. Now obviously as you'll likely have 1000s of times genomic coverage each fragment will have 1000s available that it can consider complementary but it will have about 10 000 - 100 000 times that are not considered complementary. Conventional wisdom suggest that the best solution is to just mix them together in a buffer of moderate salt concentration heat a beaker to around 95C drop the tube containing the oligos in and let it slowly cool to at least 65C. However is there a better way? I reallised that annealing oligos is a pretty simple thing. However, usually one considers small oligos and rarely more than 2-4 species. Finding the optimum match for each becomes more tricky when you have long ones and a 100 000 different species. Maybe the best thing to do it just greatly increase the time it take the temperature to drop? Link to comment Share on other sites More sharing options...
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