Lecture4CMFinalFall09 - Lecture 4 More about DNA Lecture...

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Lecture 4 More about DNA
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Lecture Outline DNA Structure (continued) Spectrophotometry of DNA DNA Denaturation DNA Hybridization Restriction Enzymes
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Chemical information in the major and minor grooves Edges of base pairs are differentiated by the pattern and presence of -H bond acceptors (A) -H bond donors (D) -Nonpolar Hydrogens (H) -Methyl groups (M) Text, Fig. 6-10
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Sequence-specific DNA binding proteins Interactions with H-bond donors and acceptors and van der Waals surfaces in the grooves allow proteins to recognize specific sequences without disrupting the double helix. The major groove contains more information. E.g., C-G and G-C look different in the major groove but not in the minor groove. See Text pp 108-110
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The Double Helix
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DNA structure is not uniform along the helix Most DNA in cells is believed to be more or less in the B form Structure can vary along the helix - different base sequences cause structural variations Intrinsic bends “Propeller twist” Binding of proteins to DNA can also induce bending DNA is a dynamic molecule
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[GCTCGAAAA] 4 Sequence Dependent Bends in DNA Runs of A-T base pairs spaced about 10 bps apart cause bending.
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Propeller twist Normal B-form base pairs Twisted base pairs Text, Fig. 6-12
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Protein binding can bend DNA Histone binding bends the double helix. Text, Fig. 7-25
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Multiple Conformations of DNA A-DNA B-DNA Z-DNA
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Text. Fig. 6-11
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A. B. C. Clicker Question: Which one is Z-DNA?
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Spectrophotometry of DNA Bases absorb UV light with a maximum at 260nm (remember they’re aromatic). Absorption is dependent on the environment of the chromophore. The environment is different in single stranded and double stranded DNA so they absorb differently.
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Schematic of a UV-Vis Spectrophotometer
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Spectrophotometry of DNA The Hyperchromic Effect Wavelength (nm) Absorbance Native Denatured 200 250 260 300 1.5 1.0 0.5 0
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This note was uploaded on 02/17/2010 for the course MCB MCB 250 taught by Professor Miller during the Fall '09 term at University of Illinois at Urbana–Champaign.

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Lecture4CMFinalFall09 - Lecture 4 More about DNA Lecture...

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