11 September, 2006

Chapter 6

DNA Structure

Overview• The classical DNA structure is an antiparallel duplex of

polynucleotides .• The two strands of DNA have complementary sequence because of base

pairing interactions.• The major groove of a DNA duplex is carries accessible information

about the sequence.• DNA can exist in alternative structures.• DNA molecules can melt and anneal.• The linking number, composed of twist and writhe is a property of

covalently closed circles.• DNA in cells is negatively supercoiled.• Topoisomerases cleave and rejoin strands to change the supercoiling

state of DNA.• RNA is usually single stranded, and form complex seconbdary and

tertiary structures, including some that have enzymatic activity.

The DNA duplex

Bases, nucleosides,

and nucleotides

Base pairing

Bases and Alternative

Base Isoforms

Base Pairing

Major Groove Sequence Information

Alternative DNA Structures

DNA can melt and anneal.

DNA Tm Depends on %GC and [salt].

DNA renaturation kinetics depend on sequence complexity.

Linking number and DNA topology

DNA in most cells is negatively supercoiled.Nicked DNA spontaneously relaxes.

Topoisomerases enzymatically change the linking number.

Topoisomerases also disentangle DNA molecules.

Topoisomerase action

DNA topoisomers can be separated electrophoretically.

Ethidium causes DNA to underwind.

RNA Structures

Non-W/C base pairs

Some RNAs are enzymes.