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

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

DNA Structure Biology: Understanding Life Alters (2000)

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

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

DNA Structure

DNA Structure

DNA Structure

DNA Structure 1 Å = cm 1 cm

DNA Structure ΔxΔx a D ~D ~D + nλ Would like to be able to do the math. a = f (D, λ, Δx)= λ D / Δx

DNA Structure

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?

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? ? ? ? ?

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?

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?

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?

DNA Structure

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

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 -

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

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.

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

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

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

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

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

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

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

NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA Palindromic Sequences Palindromic sequences as protein binding sites

Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

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

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

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

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

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

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

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Problem Set 5

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