Last class Paper reading Data analysis Intro to Paper 1.

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Restriction Analysis of Plasmids

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Presentation transcript:

Last class Paper reading Data analysis Intro to Paper 1

Type II REs GCATGC CGTACG RE1 GC CGTA ATGC CG

The RE conundrum Why doesn’t RE cut up genomic DNA in bacteria?

Solving the RE conundrum ___________ DNA at ___________! Make ___________________________ (Why?) gDNA = Protected viral DNA = Degraded! gDNA = Protected viral DNA = Degraded! NOTE: ____________ on “__” or “__” residue

The Restriction-Methylation system GCATGC CGTACG RE1 GC CGTA ATGC CG RE1 GCATGC CGTACG CH 3

Lab 4 Methylation specificity

Analytical uses of RE DNA 1 = bp You have:Pure DNA 1 Pure DNA 2 DNA 2 = bp Unknown DNA: Maybe pure 1/2 or mixture Sequencer is broken! Need a quick answer: What is unknown?

RE Map Locations of RE sites on DNA Relative locations

RE Maps  Size + Pattern Known: Circular DNA, Uncut ~ 12Kb Known: RE2 = 6Kb DNA Known: RE1 = 6Kb DNA Known: RE1 + RE2 = 3Kb DNA RE MAP?

RE Mapping example Known: Circular DNA, Uncut ~ 12Kb Known: RE1 + RE3 = 4Kb + 8Kb DNA Known: RE1 or RE3 = 12Kb DNA Known: RE2 = 2Kb + 8Kb DNA Known: RE2 + RE3 = 2Kb + 6Kb DNA Known: RE2 + RE1 = 2Kb + 6Kb DNA RE MAP?

Paper 1 What is a miRNA? Till this paper, how many miRNAs were known? Why are miRNAs important?

Identifying new miRs How were new miRNAs identified? Were cDNA & informatics search sufficient to confirm?

Figure 1A-C What is the purpose?

Figure 1D Conclusions? Objections? Questions?

Figure 1E Conclusions? Objections? Questions?

Table 1 What is summarized? Conclusions?

Figure 2 What is shown? Unanswered questions? Objections?

Paper 1 wrap up Conclusion/s? Future experiment/s?