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DNA & RNA Structure
Fig 1.9
34 Å
3.4 Å
20 Å
MinorGroove
MajorGroove
GC
CG
AT
TA
CG
GCAT
TA
TA
AT
GCCG
GC
Strands areantiparallel
Deoxyribonucleic acid (DNA)is the genetic material
-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.
-DNA
Major groove
Minor groove
P
O
O -
C
C
O
O
3'
5'Phosphodiester
Bond
3' hydroxyl
5' phosphate
a nucleotide
This ring isdeoxyribose
A. Organic chemistry model(single stranded DNA)
C. Space filling model (double stranded DNA)
B. Ribbon model (double stranded DNA)
P
C
3'
5'
P
C
3'
5'
N1
N
O
O
HP
C
3'
5'
N1
N
N H
H
O
P
C
3'
5'
N
1N H
NH2
ON
N
N
1N
H
NH2N
N
OH
O
O
O
O
CH 3
H
H
H
H
H
T
C
G
A
3 Ways of Depicting DNA Structure
.
O
H
H
OH
H
H
H
N
N
NH2
N
N
HOCH2
2-deoxy-ADENOSINE
O
H
H
OH
H
H
H
HOCH2
N
NHN
N
O
H2N
2-deoxy-GUANOSINE
O
H
H
OH
H
H
H
HOCH2
O N
H N
O
CH3
2-deoxy-THYMIDINE
O
H
H
OH
H
H
H
HOCH2
O N
N
NH2
2-deoxy-CYTIDINE
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
.
O
H
H
OH
H
H
H
O N
N
NH2
CH2P O
O
O -
P O
O
O -
P O- O
O
O - 1'
2'3'
4'
5'
2'-deoxycytidine 5' triphosphate
O
H
H
H
H
CH2P O
O
O -
P O
O
O -
P O- O
O
O - 1'
2'3'
4'
5'
N
N
NH2
N
N
2'-deoxyadenosine 5' triphosphate
OH H
O
H
H
OH
H
H
H
CH2P O
O
O -
P O
O
O -
P O- O
O
O - 1'
2'3'
4'
5'
N
NHN
N
O
H2N
2'-deoxyguanosine 5' triphosphate
O
H
H
OH
H
H
H
CH2P O
O
O -
P O
O
O -
P O- O
O
O - 1'
2'3'
4'
5'
O N
H N
O
CH3
thymidine 5' triphosphate
The 4 Nucleotides (precursors) of DNA
γ β α
.
RIBOSE
1
OHOCH2
H
H
OH
H
OH
H
OH23
4
5OHOCH2
H
H
OH
H
OH
H
H
1
23
4
5
2-DEOXY-RIBOSE
O N
H N
O
H
CH3
THYMINE
O N
H N
O
H
URACIL
RNA DNA
Molecular Differences between Ribonucleic Acid (RNA)& 2-deoxy-ribonucleic acid (DNA).
Ribose replaces deoxyribose; uracil replaces thymine
RNA
Before we continue some terminologyNucleotide Name Table
Purines PyrimidinesAdenine (A) Guanine (G) Cytosine (C) Thymine (T) Uracil (U)
Nucleotides in DNA deoxyadenylate deoxyguanylate deoxycytidylate deoxythymidylateor thymidylate
Nucleotides in RNA adenylate guanylate cytidylate uridylateAbbreviations
Nucleosidemonophosphates
AMP GMP CMP TMP UMP
Nucleosidediphosphates
ADP GDP CDP TDP UDP
Nucleosidetriphosphates
ATP GTP CTP TTP UTP
For deoxynucleotides add 'd' in front of the above three.
e.g., AMP is a ribonucleotide, dAMP is a deoxyribonucleotide
In DNA and RNA, nucleotides are held together by phosphodiester bonds.
Stem-loops are common elements of secondary RNA structure.
Stem loop
Stems are double-stranded 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 B-form helix).
Higher Order RNA Structure
Secondary structure diagram Tertiary structure diagram
Cr.LSU rRNA intron 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 purine-pyrimidine 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
3. Double-stranded helix structure also promoted by having phosphates on outside, interact with H2O and counter ions (K+, Mg2+, etc.)
Evidence: Compounds that interfere with Hydrogen bonds (urea, formamide) don’t separate strands by themselves, still requires heat
Double-stranded (DS) DNA statistics
(B-form)
1. Helix is right handed2. 10 base-pairs/turn3. 3.4 nm (34 angstroms)/turn4. Helix has a major groove and a minor groove.
-DNA
Major groove
Minor groove
P
O
O -
C
C
O
O
3'
5'Phosphodiester
Bond
3' hydroxyl
5' phosphate
a nucleotide
This ring isdeoxyribose
A. Organic chemistry model(single stranded DNA)
C. Space filling model (double stranded DNA)
B. Ribbon model (double stranded DNA)
P
C
3'
5'
P
C
3'
5'
N1
N
O
O
HP
C
3'
5'
N1
N
N H
H
O
P
C
3'
5'
N
1N H
NH2
ON
N
N
1N
H
NH2N
N
OH
O
O
O
O
CH 3
H
H
H
H
H
T
C
G
A
3 Ways of Depicting DNA Structure
1
0
10
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
Separation of nuclear (nuc) and mitochondrial (mt) DNA on a CsCl-ethidium bromide gradient – visualized with long-wave UV light.
G-C content also determines density of DNA (g/cc)