1. Last class Paper reading Data analysis Intro to Paper 1

2. Type II REs GCATGC CGTACG RE1 GC CGTA ATGC CG

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

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

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

6. Lab 4 Methylation specificity

7. Analytical uses of RE DNA 1 = 10000 bp You have:Pure DNA 1 Pure DNA 2 DNA 2 = 10000 bp Unknown DNA: Maybe pure 1/2 or mixture Sequencer is broken! Need a quick answer: What is unknown?

8. RE Map Locations of RE sites on DNA Relative locations

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

10. 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?

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

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

13. Figure 1A-C What is the purpose?

14. Figure 1D Conclusions? Objections? Questions?

15. Figure 1E Conclusions? Objections? Questions?

16. Table 1 What is summarized? Conclusions?

17. Figure 2 What is shown? Unanswered questions? Objections?

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