Nucleic Acids
•
DNA
•
Double helix
•
Stores genetic code as a linear
sequence of bases
•
≈ 20 Å in diameter
•
Human genome ≈ 3.3 x 109 bp
•
≈ 25,000 genes
DNA: organization
DNA: a style?
Life Science, UC Davis
Perth, Australia
Chambord, France
History of DNA
1865
Gregor Mendel publishes his work on plant breeding with the notion
of "genes" carrying transmissible characteristics
1869
"Nuclein" is isolated by Johann Friedrich Miescher à Tübingen
in the laboratory of Hoppe-Seyler
1892
Meischer writes to his uncle "large biological molecules composed
of small repeated chemical pieces could express a rich language in
the same way as the letters of our alphabet"
1920
Recognition of the chemical difference between DNA and RNA
Phoebus Levene proposes the "tetranucleotide hypothesis"
1938
William Astbury obtains the first diffraction patters of DNA fibres
History of DNA
1944
Oswald Avery (Rockefeller Institute) proves that DNA carries the
genetic message by transforming bacteria. DNA is the main
constituent of genes.
History of DNA
1950
Erwin Chargaff discovers A/G = T/C
History of DNA
Maurice Wilkins
Kings College London
History of DNA
Rosalind
Franklin
(in Paris)
History of DNA
X-ray fibre
diffraction pattern of
B-DNA(1950)
Linus Pauling’s DNA
History of DNA
1953
Watson and Crick propose the double helix as the structure of DNA
based on the work of Erwin Chargaff, Jerry Donohue, Rosy Franklin
and John Kendrew
Watson and Crick
It has not escaped our notice
that the specific pairing we have
postulated suggests a possible
copying mechanism for the
genetic material.
It has not escaped our notice …
1973 X-ray structure confirms double helix (Rich)
Double helix ?
1974 t-RNA structure (Kim)
Dodecamer (Oct. 1980) – Structure of first
complete turn of B DNA (Dickerson)
NA structure
OH ribose
H deoxyribose
Nucleoside
Nucleotide
In a nucleotide, e.g., adenosine monophosphate (AMP), the
base is bonded to a ribose sugar, which has a phosphate in
ester linkage to the 5' hydroxyl.
NH2
NH2
N
N
N
N
N
H
ribose
H
−2
O3P
5' CH2
O
3'
OH
H
OH
2'
adenosine
N
N
O
CH2
H 1'
H
N
N
N
N
4'
adenine
adenine
N
HO
NH2
H
O
H
H
OH
H
OH
adenosine monophosphate (AMP)
¾ Nucleotides are linked by
phosphodiester bonds
¾ Strand has a direction
(5'→3')
Base families
The nucleotides found in cells are derivatives of the heterocyclic highly basic,
compounds, purine and pyrimidine:
Purine (Pur / R)
Pyrimidine (Pyr / Y)
Bases
tymine(T)
adenine(A)
•
•
•
•
guanine(G)
Names. T ---> U in RNA
Numbering
Bonding character
Position of hydrogen. Tautomers.
cytosine (C)
uracil(U)
Tautomeric
Structures
•Keto versus enol
•Different HB patterns
Watson-Crick base pairs
DNA/RNA chemical structure
RNA : A,U,G,C + ribose
DNA : A ,T,G,C + deoxyribose
Base pair dimensions
• A:T and G:C pairs are
spatially similar
• 3 H-bonds vs 2
• Sugar groups are attached
asymmetrically on the same
side of the pair
• Leads to a major and
minor grove
• Bases are flat but the
hydrogen bonding leads to
considerable flexibility
• Base stacking is flexible
Base Stacking
Major Defining Feature of DNA Morphology.
Base Morphology – Propeller Twist
Base Morphology - Buckle
Base Morphology – Base Pair Twist
Base Morphology - Roll
A Beta-nucleoside ring
•
•
•
•
Ring is never flat – has 5
internal torsional angles
The pucker is determined by
what is bound
A variety of puckers have
been observed
Pucker has a strong
influence on the overall
conformation
The Ribose
Ring is
Never Flat
Endo/Exo
C5’
Base
ENDO
EXO
Sugar conformation
The ribose is a flexible ring
that has two preferred
conformations in polynucleotides:
-C3’-endo, found mostly in RNA
and in DNA “single strand”
-C2’-endo, found mostly in DNA
Sugar pucker
described as
pseudorotation
North : C3’-endo
East : O4’-endo
South : C3’-endo
"2 B or not 2 B ...."
W. Shakespeare 1601
Pseudorotation Equations
(ν4 - ν1) - (ν3 - ν0)
tan P = -----------------------------2ν2 (Sin 36° + Sin72°)
Amp = ν2 / cos P
ν4
ν0
ν1
ν3
ν2
Altona et al. J. Am. Chem. Soc. 94, 1972, 8205
Base
Preferred sugar puckers
Preferred Puckers
B-DNA
A-DNA, RNA
“Principles of Nucleic Acid Structure”
Saenger, (1984).
Nucleotide triphosphates
NH2
2'-deoxyadenosine 5' triphosphate
O
N
2'-deoxyguanosine 5' triphosphate
H2N
O
-O
P
O
O-
P
O
P
O
CH
5' 2
O-
O-
4'
H
N
HN
N
N
O
O
O
N
O
H
H
1'
-O
O
O-
2' H
H
3'
OH
P
O
P
N
N
O
O
O-
P
O
O-
CH
5' 2
4'
H
O
H
H
3'
OH
2'
H
1'
H
NH2
O
N
2'-deoxycytidine 5' triphosphate
O
O
N
thymidine 5' triphosphate
O
O
O
O
-O
P
O-
O
P
O-
O
P
O-
O
CH3
HN
CH
5' 2
4'
H
O
H
3'
OH
H
2'
H
-O
P
O
O
O
P
O
P
1'
H
O-
O-
N
O-
O
CH
5' 2
4'
H
O
H
H
3'
OH
2'
H
1'
H
Backbone
Conformation
I
Backbone Conformation - II
ν0
Backbone conformation - III
α:
O3’ – P – O5’ – C5’
g-
β:
P – O5’ – C5’ – C4’
t
γ:
O5’ – C5’ – C4’ – C3’
g+
δ:
C5’ – C4’ – C3’ – O3’
g+
ε:
C4’ – C3’ – O3’ – P
t
ζ:
C3’ – O3’ – P – O5’
g-
χ(Y) :
O4’ – C1’ – N1 – C2
g-
χ(R) :
O4’ – C1’ – N9 – C4
g-
Backbone torsion angles
δ:
C5’ – C4’ – C3’ – O3’
γ:
O5’ – C5’ – C4’ – C3’
β:
P – O5’ – C5’ – C4’
α:
O3’ – P – O5’ – C5’
ζ:
C3’ – O3’ – P – O5’
ε:
C4’ – C3’ – O3’ – P
Sugar pucker and P-P distance
Position of the
bases
A DNA
B DNA
syn-anti glycosidic conformations
Glycosidic bond connects ribose sugar to the base