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Chapter 6 The structure of DNA and RNA
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DNA is composed of polynucleotide chain: the helical structure of DNA
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Purines and pyrimidines
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Base tautomers
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The two chains of the double helix have complementary sequences
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DNA is usually a right-handed double helix
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The major groove is rich in chemical information
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DNA strands can separate (denature) and reassociate
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Dependence of DNA denaturation on G+C content and on salt concentration
high
Low salt
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Topological states of covalently closed, circular (ccc) DNA
LK=Tw+ Wr Linking number is composed of twist and writhe
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Two forms of writhe of supercoiled DNA
interwound
toroidal writhe
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Lko is the linking Number of fully relaxed cccDNA under Physiological conditions
• Lko for such a molecule is the number of base pairs divided by 10.5.
• For a cccDNA of 10500 base pairs, Lk = +1,000 (DNA is right-handed)
• DNA in cells is negatively supercoiled• Linking difference △Lk = Lk- Lko
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Relaxing DNA with DNAse I
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Relaxed DNA
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Supertwisted DNA: DNA in cells is negatively supercoiled
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Topoisomerases can relax supercoiled DNASchematic for changing the linking number in DNA with topoisomerase II
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Schematic mechanism of action for topoisomerase I
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DNA topoisomers can be separated by electrophoresis
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Intercalation of ethidium inot DNA
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RNA contains ribose and uracil and is usually single-stranded
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Hairpin
bulge
loop
Double helical characteristics of RNA
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RNA can fold up into complex tertiary structures
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Some RNAs are enzymes, known as ribozymesThe hammerhead ribozyme cleaves RNA by the formation of a 2’, 3’ cyclic phosphate