Principles of Nucleic Acid Structure: Springer Advanced Texts in Chemistry
Autor Wolfram Saengeren Limba Engleză Paperback – 2 oct 1988
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Specificații
ISBN-13: 9780387907611
ISBN-10: 0387907610
Pagini: 556
Dimensiuni: 155 x 235 x 30 mm
Greutate: 0.8 kg
Ediția:1st ed. 1984. Corr. 2nd printing 1988
Editura: Springer
Colecția Springer
Seria Springer Advanced Texts in Chemistry
Locul publicării:New York, NY, United States
ISBN-10: 0387907610
Pagini: 556
Dimensiuni: 155 x 235 x 30 mm
Greutate: 0.8 kg
Ediția:1st ed. 1984. Corr. 2nd printing 1988
Editura: Springer
Colecția Springer
Seria Springer Advanced Texts in Chemistry
Locul publicării:New York, NY, United States
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CHARLES
R.
CANTOR
New
York
Preface
This
monograph
is
based
on
a
review
on
polynucleotide
structures
written
for
a
book
series
in
1976.
Cuprins
1
Why
Study
Nucleotide
and
Nucleic
Acid
Structure?.-
2
Defining
Terms
for
the
Nucleic
Acids.-
2.1
Bases,
Nucleosides,
Nucleotides,
and
Nucleic
Acids—Nomenclature
and
Symbols.-
2.2
Atomic
Numbering
Scheme.-
2.3
Torsion
Angles
and
Their
Ranges.-
2.4
Definitions
of
Torsion
Angles
in
Nucleotides.-
2.5
Sugar
Pucker
Modes:
The
Pseudorotation
Cycle.-
2.6
syn/anti
Orientation
About
the
Glycosyl
Bond.-
2.7
Orientation
About
the
C4?-C5?
Bond.-
2.8
Helical
Parameters:
Hydrogen
Bonding
Between
Bases.-
Summary.-
3
Methods:
X-Ray
Crystallography,
Potential
Energy
Calculations,
and
Spectroscopy.-
3.1
Crystal
Structure
Analysis
of
Small
Molecules.-
3.2
Potential
Energy
Calculations.-
3.3
Crystallography
of
Macromolecules.-
3.4
Fiber
Structure
Determination.-
3.5
Spectroscopic
Methods.-
Summary.-
4
Structures
and
Conformational
Properties
of
Bases,
Furanose
Sugars,
and
Phosphate
Groups.-
4.1
Geometry
of
Bases.-
4.2
Preferred
Sugar
Puckering
Modes.-
4.3
Factors
Affecting
Furanose
Puckering
Modes.-
4.4
Bond
Distances
and
Angles
in
Furanoses.-
4.5
syn/anti
Conformation.-
4.6
The
high
anti
(-sc)
Conformation.-
4.7
Factors
Affecting
the
syn/anti
Conformation:
The
Exceptional
Guanosine.-
4.8
The
Orientation
About
the
C4?-C5?
Bond.-
4.9
Factors
Influencing
the
Orientation
about
the
C4?-C5?
Bond.-
4.10
The
“Rigid
Nucleotide”.-
4.11
The
Phosphate
Mono-
and
Diester
Groups
and
the
Pyrophosphate
Link:
Bonding
Characteristics
and
Geometry.-
4.12
Orientation
About
the
C-O
and
P-O
Ester
Bonds.-
4.13
Correlated
Rotations
of
Torsion
Angles
in
Nucleotides
and
in
Nucleic
Acids.-
4.14
Helical
or
Not
Helical—and
if,
What
Sense?.-
Summary.-
5
Physical
Properties
of
Nucleotides:
Charge
Densities,
pK
Values,
Spectra,
and
Tautomerism.-
5.1
Charge
Densities.-
5.2
pK
Values
of
Base,
Sugar,
and
Phosphate
Groups:
Sites
for
Nucleophilic
Attack.-
5.3
Tautomerism
of
Bases.-
Summary.-
6
Forces
Stabilizing
Associations
Between
Bases:
Hydrogen
Bonding
and
Base
Stacking.-
6.1
Characterization
of
Hydrogen
Bonds.-
6.2
Patterns
of
Base-Base
Hydrogen
Bonding:
The
Symmetry
of
a
Polynucleotide
Complex.-
6.3
Detailed
Geometries
of
Watson-Crick
and
Hoogsteen
Base
Pairs.-
6.4
The
Stability
and
Formation
of
Base
Pairs
as
Determined
by
Thermodynamic,
Kinetic,
and
Quantum
Chemical
Methods:
Electronic
Complementarity.-
6.5
Patterns
of
Vertical
Base-Base
Interactions.-
6.6
Thermodynamic
Description
of
Stacking
Interactions.-
6.7
Forces
Stabilizing
Base
Stacking:
Hydrophobic
Bonding
and
London
Dispersion.-
6.8
Formation
and
Breakdown
of
Double-Helix
Structure
Show
Cooperative
Behavior.-
6.9
Base-Pair
Tautomerism
and
Wobbling:
Structural
Aspects
of
Spontaneous
Mutation
and
the
Genetic
Code.-
Summary.-
7
Modified
Nucleosides
and
Nucleotides;
Nucleoside
Di-
and
Triphosphates;
Coenzymes
and
Antibiotics.-
7.1
Covalent
Bonds
Bridging
Base
and
Sugar
in
Fixed
Conformations:
Calipers
for
Spectroscopic
Methods.-
7.2
Cyclic
Nucleotides.-
7.3
Nucleosides
with
Modified
Sugars:
Halogeno-,
Arabino-,
and
?-Nucleosides.-
7.4
Modified
Bases:
Alkylation
of
Amino
Groups
(Cytokinins)
and
of
Ring
Nitrogen,
Thioketo
Substitution,
Dihydrouridine,
Thymine
Dimers,
Azanucleosides.-
7.5
The
Chiral
Phosphorus
in
Nucleoside
Phosphorothioates.-
7.6
The
Pyrophosphate
Group
in
Nucleoside
Di-
and
Triphosphates
and
in
Nucleotide
Coenzymes.-
7.7
Nucleoside
Antibiotics:
Puromycin
as
Example.-
Summary.-
8
Metal
Ion
Binding
to
Nucleic
Acids.-
8.1
Importance
of
Metal
Ion
Binding
for
Biological
Properties
of
Nucleic
Acids.-
8.2
Modes
of
Metal
Ion
Binding
to
Nucleotides
and
Preferred
Coordination
Sites.-
8.3
Platinum
Coordination.-
8.4
Coordination
of
Metal
Ions
to
Nucleoside
Di-
and
Triphosphates:
Nomenclature
of
Bidentate
?/?
and
of
Tridentate
?/?/endo/exo
Chelate
Geometry.-
Summary.-
9
Polymorphism
of
DNA
versus
Structural
Conservatism
of
RNA:
Classification
of
A-,
B-,
and
Z-Type
Double
Helices.-
9.1
Polymorphism
of
Polynucleotide
Double
Helices.-
9.2
The
Variety
of
Polynucleotide
Helices
with
Right-Handed
Screw
Classified
into
Two
Generically
Different
Families:
A
and
B.-
Summary.-
10
RNA
Structure.-
10.1
A-RNA
and
A?-RNA
Double
Helices
Are
Similar.-
10.2
RNA
Triple
Helices
Simultaneously
Display
Watson-Crick
and
Hoogsteen
Base-Pairing.-
10.3
A
Double
Helix
with
Parallel
Chains
and
Hoogsteen
Base-Pairs
Formed
by
Poly(U)
and
2-Substituted
Poly(A).-
10.4
Mini-Double
Helices
Formed
by
ApU
and
GpC.-
10.5
Turns
and
Bends
in
UpAH+.-
Summary.-
11
DNA
Structure.-
11.1
A-DNA,
The
Only
Member
of
the
A
Family:
Three
Crystalline
A-Type
Oligonucleotides
d(CCGG),
d(GGTATACC),
and
d(GGCCGGCC).-
11.2
B-DNA
Structures
Exhibited
by
Polymeric
DNA
and
by
the
Dodecanucleotide
d(CGCGAATTCGCG):
Introduction
to
B-Family
Duplexes.-
11.3
“Alternating
B-DNA”
and
the
Tetranucleotide
d(pATAT);
d(TpA),
Dinucleoside
Phosphate
Mimicking
Double
Helical
Arrangement.-
11.4
The
Conformationally
Stiff
Unique
Poly(dA)?Poly(dT)
Double
Helix
and
Its
Transformation
into
Triple
Helix.-
11.5
C-DNA
Double
Helix
Formed
by
Natural
and
Synthetic
DNA.-
11.6
D-DNA
Is
Only
Formed
by
Synthetic
DNA
with
Alternating
A,
T-Sequence
and
by
Phage
T2
DNA.-
11.7
DNA-RNA
Hybrids
Restricted
to
RNA-Type
Double-Helices:
A
and
A´.
Polymers
and
r(GCG)
d(TATACGC).
The
B-DNA
Form
of
Poly(A)-Poly(dT)..-
Summary.-
12
Left-Handed,
Complementary
Double
Helices
—
A
Heresy?
The
Z-DNA
Family.-
12.1
Crystal
Structures
of
Oligo(dG-dC)
Display
Left-Handed
Double
Helix.-
12.2
Extrapolation
from
Oligo-
to
Polynucleotides.
The
Z-DNA
Family:
Z-,
ZI-,
ZII,
and
Z?-DNA.-
12.3
Left-Handed
Z-DNA
Visualized
in
Fibers
of
Three
Alternating
Polydeoxynucleotides.-
12.4
Factors
Stabilizing
Z-DNA.-
12.5
Does
Z-DNA
Have
a
Biological
Significance?.-
Summary.-
13
Synthetic,
Homopolymer
Nucleic
Acids
Structures.-
13.1
Right-Handed,
Base-Stacked
Single
Helix
Revealed
for
Poly(C)
and
the
O2?-Methylated
Analog.-
13.2
Bases
Turned
“in”
and
“out”
in
Nine-
and
Twofold
Single-Stranded
Helices
of
Poly(A).-
13.3
A
Double
Helix
with
Parallel
Strands
for
Poly(AH+)?Poly(AH+)
Forms
under
Acidic
Conditions.
Helix,
Loop,
and
Base-Pair
Stacks
in
ApAH+pAH+
Dimer.-
13.4
The
Deoxydinucleotide
d(pTpT)
Suggests
Single-Stranded
Poly(dT)
Helix
with
Nonstacked
Bases
Turned
“out”.-
13.5
The
Antiparallel,
A-RNA-Type
Double
Helices
of
Poly(U),
Poly(s2U)
and
poly(X).-
13.6
Sticky
Guanosine-Gel
Structure
of
Guanosine
and
Guanylic
Acid:
Quadruple
Helix
Formed
by
Poly(G)
and
Poly(I).-
Summary.-
14
Hypotheses
and
Speculations:
Side-by-Side
Model,
Kinky
DNA,
and
?Vertical?
Double
Helix.-
14.1
Side-by-Side
Model—An
Alternative?.-
14.2
Does
DNA
Fold
by
Kinking?.-
14.3
K-
and
?-Kinked
DNA:
Breathing
with
the
Speed
of
Sound.-
14.4
Bends
in
DNA
at
Junctions
of
A-
and
B-Type
Helices.-
14.5
“Vertical”
Double
Helix
for
Polynucleotides
in
high-anti
Conformation.-
Summary.-
15
tRNA—A
Treasury
of
Stereochemical
Information.-
15.1
Primary
and
Secondary
Structure
of
tRNA:
The
Cloverleaf.-
15.2
Folding
of
the
Cloverleaf
into
Tertiary
Structure:
The
L
Shape.-
15.3
Stabilization
of
tRNA
Secondary
and
Tertiary
Structure
by
Horizontal
and
Vertical
Base-Base
Interactions.-
15.4
Change
in
Sugar
Pucker,
?
Turn,
and
Loop
with
Phosphate-Base
Stacking:
Structural
Features
of
General
Importance.-
15.5
Some
Stereochemical
Correlations
Involving
Torsion
Angles
X,?
and
?,?.-
15.6
Metal
and
Polyamine
Cation
Binding
to
tRNA.-
15.7
Anticodon
Preformed
to
Allow
Rapid
Recognition
of
Codon
via
Minihelix.-
Summary.-
16
Intercalation.-
16.1
General
Phenomena
of
Intercalation
into
DNA
and
RNA
Double
Helices.-
16.2
Stereochemistry
of
Intercalation
into
DNA-
and
RNA-Type
Dinucleoside
Phosphates.-
16.3
Improving
the
Model:
The
Daunomycin-d(CpGpTpApCpG)
Complex.-
16.4
Model
Building
Studies
Extended
to
A-
and
B-DNA.-
16.5
DNA
Saturated
with
Platinum
Drug
Unwinds
into
a
Ladder
to
Produce
L-DNA.-
16.6
Actinomycin
D:
An
Intercalator
Specific
for
the
GpC
Sequence.-
Summary.-
17
Water
and
Nucleic
Acids.-
17.1
Experimental
Evidence
for
Primary
and
Secondary
Hydration
Shells
around
DNA
Double
Helices.-
17.2
Different
Hydration
States
Associated
with
A-,
B-,
and
C-DNA.-
17.3
Solvent
Accessibilities
in
A-
and
B-DNA.-
17.4
Theoretical
Considerations.-
17.5
Hydration
Schemes
in
Crystal
Structures
of
A-DNA
Tetramer
and
B-DNA
Dodecamer
Suggest
Rationale
for
A?
B
Transition.-
17.6
Water
Pentagons
in
Crystalline
Dinucleoside
Phosphate
Intercalation
Complex:
The
Generalized
Concept
of
Circular
Hydrogen
Bonds
and
of
Flip-Flop
Dynamics.-
Summary.-
18
Protein-Nucleic
Acid
Interaction.-
18.1
General
Considerations
about
Protein-Nucleic
Acid
Interactions.-
18.2
Model
Systems
Involving
Nucleic
Acid
and
Protein
Constituents.-
18.3
Model
Systems
Combining
Nucleic
Acids
and
Synthetic
Polypeptides
or
Protamines.-
18.4
Nucleotides
and
Single-Stranded
Nucleic
Acids
Adopt
Extended
Forms
When
Binding
to
Proteins.-
18.5
Nature
of
Protein-Nucleotide
and
Nucleic
Acid
Interaction
and
Recognition.-
18.6
Proteins
Binding
to
DNA
Double
Helix
and
Single
Strands.-
18.7
Prealbumin-DNA
Interaction:
A
Hypothetical
Model.-
Summary.-
19
Higher
Organization
of
DNA.-
19.1
DNA
Condensed
into
?-Form,
Supercoils,
Beads,
Rods
and
Toroids.-
19.2
Lamellar
Microcrystals
Formed
by
Fragmented
DNA.-
19.3
DNA
in
Cells
in
Organized
in
the
Form
of
Chromosomes.-
19.4
Structure
of
the
Nucleosome
Core.-
19.5
Organization
of
Nucleosomes
into
100
Å
and
300
Å
Fibers
The
Super-Superhelix
or
Solenoid.-
19.6
Organization
of
Chromatin
in
Chromosomes:
A
Glimpse
at
Transcription.-
19.7
Topological
Problems
in
Circularly
Closed,
Supercoiled
DNA.-
Summary.-
References.