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

high

Low salt

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

interwound

toroidal writhe

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 DNASchematic 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

Hairpin

bulge

loop

Double helical characteristics of RNA

RNA can fold up into complex tertiary structures

Some RNAs are enzymes, known as ribozymesThe hammerhead ribozyme cleaves RNA by the formation of a 2’, 3’ cyclic phosphate