DNA & RNA Structure
Fig 1.9
20 Å
Deoxyribonucleic acid (DNA)
is the genetic material
GC
AT
CG
34 Å
TA
TA
GC
AT
Major
Groove
TA
3.4 Å
Strands are
antiparallel
Minor
Groove
CG
CG
GC
AT
GC
-Stores genetic information in the
form of a code: a linear sequence of
nucleotides.
- Replicated by copying the strands
using each as a template for the
production of the complementary
strand.
3 Ways of Depicting DNA Structure
Nucleosides (of DNA) – Precursors to Nucleotides
Nucleoside = base + sugar
Sugar = deoxyribose; 5 carbons, no OH on the 2nd (or 2’)
carbon; base is attached to carbon 1
The 4 Nucleotides (precursors) of DNA
γ
β
α
RNA
Ribose replaces deoxyribose; uracil replaces thymine
Before we continue some terminology
Nucleotide Name Table
Purines
Adenine (A)
Guanine (G)
Cytosine (C)
Nucleotides in DNA
deoxyadenylate
deoxyguanylate
deoxycytidylate
Nucleotides in RNA
adenylate
guanylate
cytidylate
Pyrimidines
Thymine (T)
Uracil (U)
deoxythymidylate
or thymidylate
uridylate
Abbreviations
Nucleoside
AMP
GMP
monophos phates
Nucleoside
ADP
GDP
diphos phates
Nucleoside
ATP
GTP
triphos phates
For deoxynucleotides add 'd ' in front of the above three.
CMP
TMP
UMP
CDP
TDP
UDP
CTP
TTP
UTP
e.g., AMP is a ribonucleotide, dAMP is a deoxyribonucleotide
In DNA and RNA,
nucleotides are
held together by
phosphodiester
bonds.
Higher Order RNA Structure
Stem-loops are common elements of secondary RNA structure.
Stems are doublestranded regions of
RNA that are A-form
helices. They usually
follow Watson-Crick
base pairing rules (U
replaces T), but other
pairs occur (G – U is
common).
(DNA is typically a Bform helix).
Stem
loop
Secondary structure diagram
Cr.LSU rRNA intron
Tertiary structure diagram
Tetrahymena rRNA intron
What chemical forces hold (or drive)
the DNA strands together?
(also applies to double-stranded regions
of RNA)
1. Hydrogen bonds between bases
Also important
that the purinepyrimidine base
pairs are of
similar size.
2. DNA strands also held together by base stacking:
Van der Waals interactions between
successive (or neighbor) base-pairs
Evidence:
Compounds that interfere with Hydrogen bonds
(urea, formamide) don’t separate strands by
themselves, still requires heat
3. Double-stranded helix structure also promoted
by having phosphates on outside, interact with
H2O and counter ions (K+, Mg2+, etc.)
Double-stranded (DS) DNA statistics
(B-form)
1.
2.
3.
4.
Helix is right handed
10 base-pairs/turn
3.4 nm (34 angstroms)/turn
Helix has a major groove and a minor groove.
3 Ways of Depicting DNA Structure
10
1
0
Molecular Visualization:
www.umass.edu/microbio/chime/
DNA Structure:
www.umass.edu/molvis/tutorials/dna/
Study Helix Stability with Melting Curves
DNA melting
curve of
Streptococcus
DNA.
When DNA melts,
the 2 strands
come apart, and
its absorbance
in the UV region
increases.
Tm= temp. at which 50% of DNA is melted.
Re-Annealing or Hybridization
Works with:
• DNA - DNA
• DNA - RNA
• RNA - RNA
Basis of many techniques in molecular biology.
Base composition (G-C content) determines
melting temperature: varies among organisms
G-C content also
determines density
of DNA (g/cc)
Separation of nuclear
(nuc) and
mitochondrial (mt) DNA
on a CsCl-ethidium
bromide gradient –
visualized with longwave UV light.