Laura Carol
Elisabet Freixas
Alba Romaguera
Structural Biology - UPF
Introduction
DNA
store and transmit
genetic information
A little bit of history
• End of s. XIX, Friedrich Miescher isolates
for first time DNA in salmon sperm
• 1944 Avery, MacLeod & McCarty discovered
DNA could transfect from a pathogenic
bacteria strain to another no pathogenic.
• Experiment of transfection of E.Coli by
Bacteriophage T2. Hershey & Chase
• 1953 Watson & Crick proposed a structure
for DNA after observing a X-ray diffraction
image of DNA taken by R. Franklin (1952)
DNA
Composition
DNA (deoxyribonucleic acid):
macromolecule composed by
a repetition of:
Backbone
Phosphate group
phosphodiester bond
Sugar: 2’-deoxyribose
glycosidic bond
Nitrogenous base
Neidle S, 2008
Backbone
β-D-2-deoxyribose
Backbone
Phosphate group - Phosphodiester bond Polynucleotide with N residues
Triphosphate deoxynucleoside
Pyrophosphate
Polynucleotide with N + 1
Mathews CK, residues
2002
Backbone
Rotation
α
β
χ
γ
δ
ε
ζ
Backbone
desoxyribose angles
v0: C4'-O4'-C1'-C2'
v1: O4'-C1'-C2'-C3'
v2: C1'-C2'-C3'-C4'
υ4 υ0 v3: C2'-C3'-C4'-O4'
v4: C3'-C4'-O4'-C1'
υ1
υ3
υ2
Backbone
Deoxyribose conformations
Backbone
Ring pucker
C2’endo (B-DNA/Z-DNA C/T) – C3’endo (A-DNA/ Z-DNA A/G)
Backbone
Ring Pucker - distance between P
C2’endo (B-DNA / Z-DNA C/T) – C3’endo (A-DNA / Z-DNA A/G)
Nitrogenous bases
Four nitrogenous bases: G C T A
Pyrimidine (Y) T
Thymine (T)
Cytosine (C)
C
T C
Nitrogenous bases
Four nitrogenous bases: G C T A
Purines (R)
Adenine (A)
Guanine (G)
G
A
Nitrogenous bases
Deoxynucleoside – deoxynucleotide
dAMP
Deoxyadenosina5’
Deoxyadenosine monophosphate
Nitrogenous bases Deoxynucleotides
dTMP dCMP
dAMP dGMP
Nitrogenous bases
Properties
TT
T C
Blackburn GM, 2006
A G
Nitrogenous bases
Tautomers
Sinden RR, 1994
Nitrogenous bases
β Glycosidic bond
Purines: O4’-C1’-N9-C4 Pyrimidines O4’-C1’-N1-C2
Nitrogenous bases
Anti (B-DNA/A-DNA/Z-DNA pyrimidine) -120º > χ > 180º
C
A
χ
χ
Nitrogenous bases
Syn conformation (Z-DNA purine) 0º < χ < 90º
G
χ
PRIMARY STRUCTURE
Primary structure
Single strand
Primary structure
5’ 3’
SECONDARY STRUCTURE
Secondary structure
Watson and Crick double helix model
Secondary structure
Base Pairing Watson & Crick
A·T G·C
Secondary structure
Base Pairing Watson & Crick
G·C A·T
Secondary structure
Hoogsteen base pairing
C+*G·C
Triple helix
Secondary structure
Hoogsteen base pairing
• T·A*T
Triple helix
Secondary structure
Base pair stacking
Sinden RR, 1994
Secondary structure
Stability
Hydrogen bonds between bases
Base pair stacking
Secondary structure
Conformational Parameters
•Major/minor groove
• Helix sense
• Residues per turn
• Axial rise
• Helix pitch
• Helix diameter
•Base pair tilt
DNA FORMS
Canonical forms:
DNA duplexes:
A-DNA
B-DNA
Z-DNA
Non-canonical forms:
Triplexes
Quadruplexes
Canonical forms
Structural parameter A-DNA B-DNA Z-DNA
Helical sense Right-handed Right-handed Left-handed
Major groove Narrow and deep Wide and deep Flattened
Minor groove Wide and shallow Narrow and deep Narrow and deep
Helical diameter (Å) 23 20 18
Sugar pucker C3’-endo C2’-endo C2’-endo at C
C3’-endo at G
Glycosidic bond anti anti Anti at C, syn at G
Helical pitch (Å) 28,2 34 45
Base pairs/ turn (n) 11 10,4 12 (6 dímers)
Axial rise(Å) 2,9 3,3 3,7
Tilt (º) 19 -6 -9
Rotation per residue 33o 360 60o per dimmer
(=360o/n) 300 per residue
Repeat unit (base pairs) 1 1 2
Phosphate -88/-44 -40/-98 -146/80 at C
conformation (α/ζ)(°) 60/-58 at G
B-DNA
B-DNA
Structural parameter B-DNA
Helical sense Right-handed
Minor
Major groove Wide and deep
groove
Minor groove Narrow and deep
Helical diameter (Å) 20
Sugar pucker C2’-endo
Major
Glycosidic bond anti groove
Helical pitch (Å) 34
Base pairs/ turn (n) 10,4
Axial rise(Å) 3,3
Tilt (º) -6
PDB: 2HKB
B-DNA
Structural parameter B-DNA
Helical sense Right-handed
Major groove Wide and deep Minor
Minor groove Narrow and deep groove
Helical diameter (Å) 20
Sugar pucker C2’-endo
Glycosidic bond anti
Helical pitch (Å) 34
Major
Base pairs/ turn (n) 10,4
groove
Axial rise(Å) 3,3
Tilt (º) -6
PDB: 2HKB
B-DNA
Structural parameter B-DNA
Helical sense Right-handed
Major groove Wide and deep
Minor groove Narrow and deep
Helical diameter (Å) 20
C2’ G anti
Sugar pucker C2’-endo
endo
Glycosidic bond anti
Helical pitch (Å) 34
Base pairs/ turn (n) 10,4
Axial rise(Å) 3,3
Tilt (º) -6
PDB: 2HKB
B-DNA 1
Structural parameter B-DNA
Helical sense Right-handed 2
Major groove Wide and deep
3
Minor groove Narrow and deep
4
Helical diameter (Å) 20 5
6
Sugar pucker C2’-endo
7
Glycosidic bond anti
8
Helical pitch (Å) 34
9
Base pairs/ turn (n) 10,4
10
Axial rise(Å) 3,3
Tilt (º) -6
B-DNA
Structural parameter B-DNA
Helical sense Right-handed
Major groove Wide and deep
Minor groove Narrow and deep
Helical diameter (Å) 20
Sugar pucker C2’-endo
Glycosidic bond anti
Helical pitch (Å) 34
PDB: 2HKB
Base pairs/ turn (n) 10,4
Axial rise(Å) 3,3
Tilt (º) -6
A-DNA
PDB: 115D
A-DNA
Structural parameter A-DNA
Helical sense Right-handed
Minor
groove
Major groove Narrow and deep
Minor groove Wide and shallow
Helical diameter (Å) 23
Sugar pucker C3’-endo
Major
Glycosidic bond anti groove
Helical pitch (Å) 28,2
Base pairs/ turn (n) 11
Axial rise(Å) 2,9
Tilt (º) 19
PDB: 115D
A-DNA
Structural parameter A-DNA
Helical sense Right-handed
Major groove Narrow and deep
Minor groove Wide and shallow
Helical diameter (Å) 23
Sugar pucker C3’-endo
Glycosidic bond anti C3’
endo
Helical pitch (Å) 28,2
Base pairs/ turn (n) 11
Axial rise(Å) 2,9
Tilt (º) 19
G anti
PDB: 115D
A-DNA
Structural parameter A-DNA
Helical sense Right-handed
Major groove Narrow and deep
1
Minor groove Wide and shallow
2
Helical diameter (Å) 23
3
Sugar pucker C3’-endo 4 5
Glycosidic bond anti 6 7
89
Helical pitch (Å) 28,2
10
Base pairs/ turn (n) 11
Axial rise(Å) 2,9 11
Tilt (º) 19
PDB: 115D
A-DNA
Structural parameter A-DNA
Helical sense Right-handed
Major groove Narrow and deep
Minor groove Wide and shallow
Helical diameter (Å) 23
Sugar pucker C3’-endo
Glycosidic bond anti
Helical pitch (Å) 28,2
Base pairs/ turn (n) 11
Axial rise(Å) 2,9
Tilt (º) 19
PDB: 115D
Z-DNA
PDB: 1DCG
Z-DNA
Structural parameter Z-DNA
Minor
Helical sense Left-handed
groove
Major groove Flattened
Minor groove Narrow and deep
Helical diameter (Å) 18
Sugar pucker C2’-endo at C
C3’-endo at G Major
Glycosidic bond Anti at C, syn at G groove
Helical pitch (Å) 45
Base pairs/ turn (n) 12 (6 dímers)
Axial rise(Å) 3,7
Tilt (º) -9
PDB: 1DCG
Z-DNA
Structural parameter Z-DNA
Helical sense Left-handed
Major groove Flattened
Minor groove Narrow and deep C
c2’endo
Helical diameter (Å) 18
Sugar pucker C2’-endo at C
C3’-endo at G
Glycosidic bond Anti at C, syn at G
Helical pitch (Å) 45
Base pairs/ turn (n) 12 (6 dímers)
Axial rise(Å) 3,7
Tilt (º) -9 G
c3’endo
PDB: 1DCG
Z-DNA
Structural parameter Z-DNA
Helical sense Left-handed G syn
Major groove Flattened
Minor groove Narrow and deep
Helical diameter (Å) 18
Sugar pucker C2’-endo at C
C3’-endo at G
Glycosidic bond Anti at C, syn at G C anti
Helical pitch (Å) 45
Base pairs/ turn (n) 12 (6 dímers)
Axial rise(Å) 3,7
Tilt (º) -9
PDB: 1DCG
Z-DNA
1
Structural parameter Z-DNA
Helical sense Left-handed
2
Major groove Flattened 3
4
Minor groove Narrow and deep 5
Helical diameter (Å) 18
6
Sugar pucker C2’-endo at C
C3’-endo at G 7
Glycosidic bond Anti at C, syn at G 8
9
Helical pitch (Å) 45 10
Base pairs/ turn (n) 12 (6 dímers)
11
Axial rise(Å) 3,7
12
Tilt (º) -9
PDB: 1DCG
Z-DNA
Structural parameter Z-DNA
Helical sense Left-handed
Major groove Flattened
Minor groove Narrow and deep
Helical diameter (Å) 18
Sugar pucker C2’-endo at C
C3’-endo at G
Glycosidic bond Anti at C, syn at G
Helical pitch (Å) 45
Base pairs/ turn (n) 12 (6 dímers)
Axial rise(Å) 3,7
Tilt (º) -9
PDB: 1DCG
Canonical forms:
DNA duplexes:
A-DNA
B-DNA
Z-DNA
Non-canonical forms:
Triplexes
Quadruplexes
Non-canonical forms
Triplexes
PDB: 1D3X
Triplexes – Hoogsteen base pair
PDB: 1D3X
Classification of triplexes THYMINE
CYTOSINE
ADENINE
GUANINE
YR*Y or YR*R
Built from DNA, RNA
or both.
Intramolecular or
intermolecular.
Orientation
PDB: 1D3X
Triplexes
Axial Rise 3,4 nm
Glycosidic bond Anti
Sugar pucker C2’ endo
PDB: 1D3X
PARALLEL ANTIPARALLEL
MOTIF MOTIF
Hogsteen Homopyrimidine strand (T+C)
Watson-Crick Homopurine strand (A+G)
PARALLEL
TRIPLEX (YR*Y) Pyrimidine
Purine
PDB: 1D3X
ANTI-PARALLEL
TRIPLEX ( YR*R)
PDB: 134D
YR*Y PDB: 1D3X
C
C
C
G
G
YR*R
PDB: 134D
Quadruplexes
PDB: 1JPQ
G-QUADRUPLEX STRUCTURES
A G-quadruplex is a DNA secondary structure that
consists of multiple vertically stacked guanine tetrads.
Identified in:
Eukaryotic telomeres
Non-telomeric genomic regions
Gene promoters
Recombination sites
DNA tandem repeats
PDB: 1JPQ
G-TETRADE: H+ ACCEPTORS
- 4 guanines
- monovalent
cation
H+ DONORS
PDB: 1JPQ
G-quadruplexes classification
SYN
• Number of strands
• Orientation
• Conformation
• Loop
ANTI
PDB: 1JPQ
Unimolecular quadruplex structure
PDB: 201d
Bimolecular quadruplex structure
PDB: 1JPQ
Tetramolecular quadruplex structure
PDB: 139B
Bibliography
BOOKS
Branden C, Tooze J.Introduction to protein structure. 2nd edition. 1999. Garland Publishing,
Inc. Pg. 121-202. USA
Bourne PE, Weissig H. Structural bioinformatics. 2003. Wiley-Liss. USA. 41-60; 135-158.
Devlin TM. Biochemistry with chemical correlations. 7ª ed. EUA. John Wiley&Sons Inc; 2010.
Creighton TE. The biophysical chemistry of nucleic acids and proteins. Helvetian press. 2010. 1-
106.
Stryer L. Bioquímica. 3ªed. Ed Reverté, s.a. Vol 1. 1988 71-87
Sinden RR. DNA: structure and function. 1994. Academic press, Inc. UK. Chapter 1, 5, 6.
Neidle S. Principles of nucleic acid structure. 2008. Academic press, Inc. USA. Chapter 2,3.
Mathews CK, Van Holde KE, Ahern KG, Bioquímica. 3th edition. 2002. Pearson. Chapter 4.
Blackburn GM, Gait MJ, Loakes D, Williams DM. Nucleic acids in chemistry and biology. 3rd
edition, 2006. RSC publishing.
ARTICLES
Rich A, Nordheim A, Wang AHJ. The chemistry and biology of left-handed z-DNA. Ann. Rev.
Biochem. 1984, 53: 791-846
Frank-Kamenetskii MD. Triplex DNA structures. Annu. Rev. Biochem. 1995. 64:65-95
Burge S, Parkinson GN, Hazel P, Todd A, Neidle S. Quadruplex DNA: sequence, topology and
structure. Nucleic Acid Research, 2006;34: 5402-5415
Huppert JL. Structure, location and interactions of G-quadruplexes. FEBS Journal 277: 3452-3458
Thank you for your attention
