2. Welcome to Molecular Biology Through Discovery Tuesday, 17 September 2013 DNA Structure

6. DNA Structure Biology Today and Tomorrow Starr, Evers, and Starr (2010)

7. DNA Structure Biology: Understanding Life Alters (2000)

8. DNA Structure E. How can the helical structure of DNA and internucleotide distance be discerned from Franklin and Gosling's x-ray photograph?

9. DNA Structure E. How can the helical structure of DNA and internucleotide distance be discerned from Franklin and Gosling's x-ray photograph?

10. DNA Structure http://h2physics.org/?cat=48

11. DNA Structure http://h2physics.org/?cat=48

12. DNA Structure http://h2physics.org/?cat=48

13. DNA Structure http://h2physics.org/?cat=48 1 Å = 10 -8 cm 1 cm

14. DNA Structure http://h2physics.org/?cat=48 ΔxΔx a D ~D ~D + nλ Would like to be able to do the math. a = f (D, λ, Δx)= λ D / Δx

15. DNA Structure http://h2physics.org/?cat=48

16. DNA Structure SQ7. What would you expect to happen to the diffraction pattern if the helix shown in Fig. 8B-D were squashed, i.e. the helix were more tightly wound, more like a solenoid?

17. DNA Structure SQ7. What would you expect to happen to the diffraction pattern if the helix shown in Fig. 8B-D were squashed, i.e. the helix were more tightly wound, more like a solenoid? ? ? ? ?

18. DNA Structure SQ7. What would you expect to happen to the diffraction pattern if the helix shown in Fig. 8B-D were squashed, i.e. the helix were more tightly wound, more like a solenoid? ? ? angle?

19. DNA Structure SQ7. What would you expect to happen to the diffraction pattern if the helix shown in Fig. 8B-D were squashed, i.e. the helix were more tightly wound, more like a solenoid?

20. DNA Structure SQ7. What would you expect to happen to the diffraction pattern if the helix shown in Fig. 8B-D were squashed, i.e. the helix were more tightly wound, more like a solenoid? ? angle?

21. DNA Structure

22. It's necessary to be slightly underemployed if you are to do something significant. - Jim Watson

23. From the nucleotides shown above, construct a double-stranded DNA fragment with the sequence ACTG. You may: duplicate (Ctrl-d) horizontal flip (Alt-hgoh) vertical flip (Alt-hgov) and/or rotate (Alt-hgor) the nucleotides, but you may not change the relative positions of their atoms. NH 2 N N N N P O O O O - N N N O P O O O O - O N NH O P O O O O - NH 2 N N N NH O P O O O O -

24. DNA Directionality & Palindromes SQ10. If one strand of DNA had the sequence 5'-GGACT-3', what would be the sequence of the second strand?

25. DNA Directionality & Palindromes I understand what a palindrome is in English but when it comes to DNA how come 5'-AGTTGA-3' isn't a palindrome when it's anti-parallel strand is 3'-TCAACT-5' which is also a palindrome.

26. Palindromic Sequences What is it? What about with DNA? GCTATCG Backwards = forwards ROTATOR TTAATGTGAGTTAGCTCACTCATT AATTACACTCAATCGAGTGAGTAA DNA is double stranded

27. What is it? What about with DNA? GCTATCG Backwards = forwards ROTATOR DNA is redundant TTAATGTGAGTTAGCTCACTCATT AATTACACTCAATCGAGTGAGTAA DNA is double stranded Palindromic Sequences

28. What is it? What about with DNA? GCTATCG Backwards = forwards ROTATOR DNA is redundant TTAATGTGAGTTAGCTCACTCATT AATTACACTCAATCGAGTGAGTAA DNA is double stranded TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA DNA has direction (read 5’->3’) 5’- -3’ 3’- -5’ Palindromic Sequences

29. TTAATGTGAGTTAGCTCACTCATT AATTACACTCAATCGAGTGAGTAA 5’- -3’ 3’- -5’ TA T G GC AT GC TA GC TTAAT TCATT AATTA AGTAA CG TA CG AT CG G T AT DNA: cruciform RNA: stem/loop Palindromic Sequences Palindromic sequences as structural RNA

30. TTAATGTGAGTTAGCTCACTCATT AATTACACTCAATCGAGTGAGTAA 5’- -3’ 3’- -5’ tRNA UA U G GC AU GC UA GC UUAAU UCAUU DNA: cruciform RNA: stem/loop Palindromic Sequences Palindromic sequences as structural RNA

31. Palindromic Sequences Palindromic sequences as protein binding sites why palindromes are targeted by DNA-binding proteins why [are] palindromes… targeted by DNA-binding proteins

32. recognizes GTGAGTT NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA Palindromic Sequences Palindromic sequences as protein binding sites

33. NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA Palindromic Sequences Palindromic sequences as protein binding sites

34. Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

35. Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

36. Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

37. recognizes GTGAGTT Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

38. Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNN NNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

39. Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNN NNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

40. Palindromes: Serve as binding sites for dimeric protein Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNN NNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

41. GTA..(8).. TAC 5’-GTA..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN 3’-CAT..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN gene RNA Polymerase Palindromic Sequences Palindromic sequences as protein binding sites

42. GTA..(8).. TAC 5’-GTA..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN 3’-CAT..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN gene Transcription factor RNA Polymerase Palindromic Sequences Palindromic sequences as protein binding sites RNA

43. Reading articles

44. Read through (Highlight problems) Reread (Put words to problems) Plan solution to problems (What do you need to know?) Solve problems (Find what you need to know)

45. Problem Set 5

47. Goodbye from Molecular Biology Through Discovery Tuesday, 17 September 2013