Intro DNA

Introduction to DNA
Lecture notes edited by John Reif from PPT lectures by:
Natalia Tretyakova, College of Pharmacy, U. of Minnesota

Richard Lavery, Institut de Biologie Physico-Chimique, Paris
Image from
http://zen-haven.dkhttp://zen-haven.dk
DNA
Double helix
Stores genetic code as a linear
sequence of bases
20 in diameter
Human genome 3.3 x 109 bp
25,000 genes
Richard Lavery
Institut de Biologie Physico-Chimique, Paris
DNA Size Scale
Chemical bond
(10-10 m)
Amino acid
10
(10-9 m)
Globular protein
100
(10-8 m)
Virus
1000 (10-7 m)
Cell nucleus
1 m
(10-6 m)
Bacterial cell
5 m
(10-5 m)
Chromosome DNA
10 cm
(10-1 m)
Biological length scale

Richard Lavery
DNA BASES
The Building Blocks of DNA
OH ribose
H deoxyribose
Nucleoside
Nucleotide
Richard Lavery
Nucleotides are linked by

phosphodiester bonds
Strand has a direction
(5'3')
DNA is negatively charged
on phosphate backbone.
Richard Lavery
N7
C5
C4
C6
C8
N1
N9
C4
C2
C5
C6
N3
C2
N1
N3
Purine (Pur / R)
Pyrimidine (Pyr / Y)
Base families
Richard Lavery
DNA and RNA nucleobases

O
NH2
7
N
9N
NH
8
H
Purine
N
H
N
H
Adenine (A)
Guanine (G)
NH2
4
5
NH2
H3C
NH
NH
2
N1
H
Pyrimidine
Natalia Tretyakova
College of Pharmacy, U. of Minnesota
N
H
Cytosine (C)
N
H
N
H
Thymine (T)
Uracil (U)
(DNA only)
(RNA only)
Purine Bases
The 9 atoms that make up the fused rings (5 carbon, 4 nitrogen) are numbered 1-9.
All ring atoms lie in the same plane.
Richard B. Hallick
Introductory Course in Biology or Biochemistry
Purine Nucleotides
Natalia Tretyakova
Pyrimidine Bases
All pyrimidine ring atoms lie in the same plane.
Richard B. Hallick
Pyrimidine Nucleotides
Natalia Tretyakova

Nomenclature of nucleobases, nucleosides,
and mononucleotides
nucleobase
(Deoxy)
nucleoside
Adenine (A)
2-Deoxyadenosine
(dA)
2- Deoxyguanosine
(dG)
2- Deoxythymidine
(dT)
2- Deoxycytidine
(dC)
Uridine (U)
Guanine (G)
Thymine (T)
Cytosine (C)
Uracil (U)
Natalia Tretyakova
5-mononucleotide
Deoxyadenosine 5-monophosphate
(5-dAMP)
Deoxyguanosine 5-monophosphate
(5-dGMP)
Deoxythymidine 5-monophosphate
(5-dTMP)
Deoxycytidine 5-monophosphate
(5-dCMP)
Uridine 5-monophosphate (5-UMP)
Structural differences between DNA and RNA

DNA
RNA
O
O
H3C
NH
NH
N
O
H
Uracil (U)
N
O
H
Thymine (T)
HO
CH2
Base
CH2
2'-deoxyribose
Natalia Tretyakova
HO
Base
OH
ribose
Deoxyribose Sugar
The hydroxyl groups on the 5'- and 3'carbons link to the phosphate groups
to form the DNA backbone.
Richard B. Hallick
Nucleosides
A nucleotide is a nucleoside with one
or more phosphate groups covalently
attached to the 3'- and/or 5'-hydroxyl
group(s).
Richard B. Hallick
Preferred conformations of nucleobases and sugars in

DNA and RNA
NH2
NH2
N
N
HO
N
O
HO
OH
OH
Syn conformation
Anti conformation
Sugar puckers:
5.9 A
HO
2'
5'
7.0 A
O
3'
BASE
1'
H (OH)
HO
Natalia Tretyakova
2' endo (B-DNA)
HO HO
5'
3'
BASE
1'
H (OH)
3' endo (RNA)
Nucleosides Must Be Converted to

5-Triphosphates to be Part of DNA and RNA
HO
O
P O
HO
HO
O
Base
Kinase
ATP
OH
Base
OH
Mo no ph osphate
ATP
O
O
O
HO P O P O P O
HO
OH OH
O
OH
Triphosp ha te
Natalia Tretyakova
Base
Kinase
ATP
O
O
HO P O P O
HO
OH
Kinase
O
OH
Di phosphat e
Base
DNA BASE PAIRING
Thymine -Adenine
Cytosine -Guanine
Watson-Crick base pairs

Richard Lavery
A-T and G-C Base Pairing
Richard B. Hallick
Hydrogen bond donors and acceptors on each

edge of a base pair
Major groove
To
y
ox
e
d
os
b
ri
To
Minor groove
Natalia Tretyakova
de
ox
y
r ib
ose
Purine always binds with a Pyrimidine

Richard Lavery
Base pair dimensions

Richard Lavery
RNA : A,U,G,C + ribose
DNA : A ,T,G,C + deoxyribose
DNA/RNA chemical structure

Richard Lavery
DNA BACKBONE STRUCTURE
Helix Axis View:
Backbone structure:
Alternating backbone of deoxyribose and phosphodiester groups

Chain has a direction (known as polarity), 5'- to 3'- from top to bottom
Oxygens (red atoms) of phosphates are polar and negatively charged
Bases extend away from chain, and stack atop each other
Bases are hydrophobic
Richard B. Hallick
OnScreen DNA Model app
B-DNA STRUCTURE
Video of DNA Helix Structure:

http://www.youtube.com/watch?v=ZGHkHMoyC5I
Contains material from:

Alberts, Bray, Hopkin, Johnson, Lewis, Raff, Roberts, Walter, Essential Cell Biology, Second
Edition, Garland Science Publishing, 2004
B-DNA Structure
20
GC
AT
CG
CGCGTTGACAACTGCAGAATC
34
TA
TA
GC
AT
Major
Groove
TA
3.4
Strands are
antiparallel
Richard Lavery
Minor
Groove
CG
CG
GC
AT
GC
Features of the B-DNA Double Helix

Two DNA strands form a helical spiral, winding around a helix axis in a right-handed spiral
The two polynucleotide chains run in opposite directions
The sugar-phosphate backbones of the two DNA strands wind around the helix axis like the railing of a sprial
staircase
The bases of the individual nucleotides are on the inside of the helix, stacked on top of each other like the steps of a
spiral staircase.
Richard B. Hallick
B-DNA (axial view)

Richard Lavery
R.H. helix
B-DNA (lateral view)

Richard Lavery
Base stacking: an axial view of B-DNA
Natalia Tretyakova
PI Bonds (Mechanism of PI Base Stacking)
Forces stabilizing DNA double helix

1. Hydrogen bonding (2-3 kcal/mol per base pair)
2. Stacking (hydrophobic) interactions
(4-15 kcal/mol per base pair)
3. Electrostatic forces.
Comparison to other bonds
1. Covalent Bond Energies:
1. C-C 85 kcal/mol
2. C-O 87 kcal/mol
Natalia Tretyakova
B-DNA
right handed helix
helical axis passes through
base pairs
23.7 A
Sugars are in the 2 endo

conformation.
HO
O
3'
7.0 A
BASE
1'
H (OH)
HO
planes of bases are nearly

perpendicular to the helix axis.
2'
5'
Bases are the anti conformation.

NH2
3.4 A rise between base pairs
Wide and deep
HO
OH
Bases have a helical twist of

34.6 (10.4 bases per helix turn)
Narrow and deep
Natalia Tretyakova
Helical pitch = 34 A
DNA can deviate from the ideal Watson-Crick structure
Helical twist ranges from 28 to 42

Propeller twisting 10 to 20
Base pair roll

Natalia Tretyakova
DNA grooves
Richard Lavery
Major groove and Minor groove of DNA

Hypothetical situation: the two grooves would have similar size if dR residues
were attached at 180 to each other
To deoxyribose-C1
Base
C1 -To deoxyribose
Base
Major groove
Major groove
H2N
NH
N
N
y
ox
e
od
o
rib
C-1
e
s
Natalia Tretyakova
N
N
C-1
N
NH2
Minor groove
NH2
C-1
To
d
O
HN
O
eox
yr i
bo
se
Minor groove
N
C-1
Major and minor groove of the double

helix
Major groove
H2
N
NH
N
N
To
de
os
ib
r
y
ox
NH2
e C-1
C-1T
NH2
N
N
C-1
O
HN
O
Natalia Tretyakova
eox
Minor groove
Wide and deep
Narrow and deep
od
N
C-1
yr i
bo
se
B-type duplex is not possible for RNA

HO
CH2
Base
OH
ribose
steric clash
Natalia Tretyakova
A-DNA STRUCTURE
De-hydration
Hydration
5
3
3
5
Antiparallel
strands
A and B DNA allomorphs

Richard Lavery
A-DNA (longitudinal view)

Richard Lavery
R.H. helix
A-DNA (lateral view)

Richard Lavery
A-form helix: dehydrated DNA; RNA-DNA hybrids
Right handed helix
Sugars are in the 3 endo

conformation.
planes of bases are tilted

20 relative the helix axis.
Bases are the anti conformation.
25.5 A
11 bases per helix turn

Helical pitch = 25.3 A
Top View
Natalia Tretyakova
The sugar puckering in A-DNA is 3-endo

5.9 A
O
2'
5'
7.0 A
O
3'
BASE
1'
H (OH)
O
2' endo (3' exo) B-DNA
Natalia Tretyakova
O
5'
3'
BASE
1'
O
2'
H (OH)
3' endo (A-DNA)
A-DNA has a shallow minor

groove and a deep major groove
Major groove
O H2N
To
se N
o
ib
yr
x
o
de
NH
N
NH2
Minor groove
Major groove
N To d
eo
xy
rib
os
e
Helix axis
To
B-DNA
Natalia Tretyakova
O H2N
e
os
ir b
y
ox
e
d
NH
N
NH2
Minor groove
A-DNA
N To d
eo
xy
rib
os
e
Z-DNA STRUCTURE
Z-DNA (longitudinal view)

Richard Lavery
L.H. helix
Z-DNA (lateral view)

Richard Lavery
Base pairs are rotated in Z-DNA

Richard Lavery
Z-form double helix: polynucleotides of alternating purines

and pyrimidines (GCGCGCGC) at high salt
Left handed helix
Backbone zig-zags because sugar

puckers alternate between 2 endo
pyrimidines and 3 endo (purines)
planes of the bases are

tilted 9 relative the helix
axis.
Bases alternate between anti

(pyrimidines) and syn conformation
(purines).
12 bases per helix turn

18.4 A
Flat major groove

Narrow and deep minor groove
Natalia Tretyakova
Helical pitch = 45.6 A
Sugar and base conformations in Z-DNA alternate:

5-GCGCGCGCGCGCG
3-CGCGCGCGCGCGC
C: sugar is 2-endo, base is anti
G: sugar is 3-endo, base is syn
NH2
N
HO
2'
5'
O
3'
HO
C
Natalia Tretyakova
N
1'
HN
O
H2N
HO HO
5'
N
3'
1'
Comparing A, B and Z-DNA
Natalia Tretyakova
Biological relevance of the minor types of DNA secondary

structure
Although the majority of chromosomal DNA is in B-form,
some regions assume A- or Z-like structure
Runs of multiple Gs are A-like
The upstream sequences of some genes contain
5-methylcytosine = Z-like duplex
NH2
H3C
N
N
H
5-methylcytosine (5-Me-C)
Structural variations play a role in DNA-protein interactions

RNA-DNA hybrids and ds RNA have an A-type structure
Natalia Tretyakova
Backbone Dihedrals
Backbone dihedrals - I
Richard Lavery
+10
+60
Staggered
Eclipsed
Dihedral angle definition

Richard Lavery
gauche +
gauche -
trans
Favoured conformations
Richard Lavery
O3 P O5 C5
g-
P O5 C5 C4
O5 C5 C4 C3
g+
C5 C4 C3 O3
g+
C4 C3 O3 P
C3 O3 P O5
g-
(Y) :
O4 C1 N1 C2
(R) :
O4 C1 N9 C4
Backbone dihedrals - II
Richard Lavery
g-
syn-anti glycosidic conformations

Richard Lavery
C5
Base
ENDO
EXO
Sugar ring puckering

Richard Lavery
Sugar pucker
described as
pseudorotation
North : C3-endo
East : O4-endo
South : C3-endo
"2 B or not 2 B ...."
W. Shakespeare 1601
tan P = (4 - 1) - (3 - 0)
22 (Sin 36 + Sin72)
1
Amp = 2 / Cos P
Pseudorotation Equations
Altona et al. J. Am. Chem. Soc. 94, 1972, 8205
Base
Preferred sugar puckers

Richard Lavery
Sugar pucker and P-P distance

Richard Lavery
UNUSUAL DNA STRUCTURES
Reversed Watson-Crick
Watson-Crick
Hoogsteen
Reversed Hoogsteen
Alternative base pairs

Richard Lavery
- note C(N3) protonation
Watson-Crick + Hoogsteen = Base triplet

Richard Lavery
Richard Lavery
Triple helix DNA
Guanine Hoogsteen pairing Base tetraplex
Richard Lavery
Watson Crick vs Hoogsteen

Hydrogen Bonding.
(inset, G-C bonding also shown)
Robert E Johnson et. al

University of Texas Medical Branch
Quadruplex DNA
Richard Lavery
Inverted repeat can lead to loop formation
Richard Lavery
Holliday junction
DNA cruciform
Richard Lavery
Richard Lavery
PNA versus DNA
Achiral, peptide-like backbone

Backbone is uncharged High thermal stability
High-specificity hybridization with DNA
Resistant to enzymatic degradation
Can displace DNA strand of duplex
Pyrimidine PNA strands can form 2:1 triplexes with ssDNA
Biotechnological applications
Richard Lavery
Peptide Nucleic acid(PNA)
Richard Lavery
Parallel-stranded DNA
I-DNA: intercalated parallel-stranded duplexes

Richard Lavery
and nucleotide anomers

Richard Lavery
H OH is not the only change in passing from DNA to RNA ....

Richard Lavery
Biophysical properties of DNA
Biophysical properties of DNA
Facile denaturation (melting) and re-association of the duplex

are important for DNAs biological functions.
In the laboratory, melting can be induced by heating.
A260
Single strands
TM
duplex
70
80
90
100
T, C
Hybridization techniques are based on the affinity of complementary

DNA strands for each other.
Duplex stability is affected by DNA length, % GC base pairs, ionic strength, the
presence of organic solvents, pH
Negative charge can be separated by gel electrophoresis
Natalia Tretyakova
Separation of DNA fragments by PAGE
DNA strands are negatively charged .

Migrate towards the (+) electrode (anode)
Migration time ~ ln ( number of base pairs)
Principles of Nucleic Acid Structure, W. Saenger, 1984 Springer-Verlag

Nucleic Acid Structure, Ed. S. Neidle, 1999 Oxford University Press
DNA Structure and Function, R.R. Sinden, 1994 Academic Press
Biochemistry, D. Voet and J.G. Voet, 1998 DeBoeck
The Eighth Day of Creation, H.F. Judson, 1996 Cold Spring Harbour Press
Books on DNA
Richard Lavery
HISTORY of DNA
1865
1869
1892
1920
1938
Gregor Mendel publishes his work on plant breeding with the notion
of "genes" carrying transmissible characteristics
"Nuclein" is isolated by Johann Friedrich Miescher Tbingen
in the laboratory of Hoppe-Seyler
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"
Recognition of the chemical difference between DNA and RNA
Phoebus Levene proposes the "tetranucleotide hypothesis"
William Astbury obtains the first diffraction patters of DNA fibres
History of DNA
Richard Lavery
1944
Oswald Avery (Rockefeller Institute) proves that DNA carries the

genetic message by transforming bacteria
History of DNA
Richard Lavery
1950
Erwin Chargaff discovers A/G = T/C
History of DNA
Richard Lavery
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
History of DNA
Richard Lavery
Maurice Wilkins Kings College, London

Richard Lavery
Watson-Crick model of DNA was based on X-ray

diffraction picture of DNA fibres
(Rosalind Franklin and Maurice Wilkins)
Rosalind Franklin
Natalia Tretyakova
Rosalind Franklin (in Paris)

Richard Lavery
X-ray fibre diffraction pattern of B-DNA

Richard Lavery
Linus Paulings DNA

Richard Lavery
DNA secondary structure double helix

James Watson and Francis Crick, 1953- proposed a model for DNA
structure
Francis Crick
Jim Watson
DNA is the molecule of heredity (O.Avery, 1944)

Natalia Tretyakova
X-ray diffraction (R.Franklin and M. Wilkins)
Watson and Crick

Richard Lavery
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

Richard Lavery
Double helix ?
Richard Lavery
Nucleic Acids
DNA
RNA
(ribonucleic acids)
(deoxyribonucleic acids)
Central Dogma of Biology
replication
DNA
RNA
Proteins
transcription translation
DNA
Natalia Tretyakova
Cellular Action
Dickerson Dodecamer (Oct. 1980)

Richard Lavery

Intro DNA

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Intro DNA

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Introduction to DNA

Lecture notes edited by John Reif from PPT lectures by:

Natalia Tretyakova, College of Pharmacy, U. of Minnesota

DNA Size Scale

Biological length scale

The Building Blocks of DNA

Nucleotides are linked by

DNA and RNA nucleobases

Structural differences between DNA and RNA

Preferred conformations of nucleobases and sugars in

2' endo (B-DNA)

Nucleosides Must Be Converted to

DNA BASE PAIRING

Watson-Crick base pairs

A-T and G-C Base Pairing

Hydrogen bond donors and acceptors on each

Purine always binds with a Pyrimidine

Base pair dimensions

RNA : A,U,G,C + ribose

DNA : A ,T,G,C + deoxyribose

DNA/RNA chemical structure

DNA BACKBONE STRUCTURE

Helix Axis View:

Alternating backbone of deoxyribose and phosphodiester groups

OnScreen DNA Model app

Video of DNA Helix Structure:

Contains material from:

Features of the B-DNA Double Helix

B-DNA (axial view)

B-DNA (lateral view)

Base stacking: an axial view of B-DNA

PI Bonds (Mechanism of PI Base Stacking)

Forces stabilizing DNA double helix

Sugars are in the 2 endo

planes of bases are nearly

Bases are the anti conformation.

3.4 A rise between base pairs

Wide and deep

Bases have a helical twist of

DNA can deviate from the ideal Watson-Crick structure

Helical twist ranges from 28 to 42

Base pair roll

Major groove and Minor groove of DNA

Major and minor groove of the double

Wide and deep

Narrow and deep

B-type duplex is not possible for RNA

A and B DNA allomorphs

A-DNA (longitudinal view)

A-DNA (lateral view)

A-form helix: dehydrated DNA; RNA-DNA hybrids

Right handed helix

Sugars are in the 3 endo

planes of bases are tilted

11 bases per helix turn

The sugar puckering in A-DNA is 3-endo

A-DNA has a shallow minor

Z-DNA (longitudinal view)

Z-DNA (lateral view)

Base pairs are rotated in Z-DNA

Z-form double helix: polynucleotides of alternating purines

Left handed helix

Backbone zig-zags because sugar