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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.