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