Professional Documents
Culture Documents
Introductory Remarks Vs
Introductory Remarks Vs
Colleagues:
The
provided
handouts
for
the
lecture
on
nucleic
acids
contain
much
more
material
than
I
will
be
able
to
discuss
during
75
minutes.
In
my
talk
I
will
concentrate
only
on
the
most
essential
topics.
There
is
a
number
of
excellent
reviews
where
many
more
details
can
be
found.
With
Richard
tefl
we
have
recently
summarized
essentials
of
RNA
structure
determination
in
the
chapter
of
a
book
edited
by
I.
Bertini,
K.
S.
Greevy,
and
G.
Parigi,
where
all
the
basics
are
briefly
discussed
(tefl,
R.
and
Sklen,
V.,
NMR
Studies
of
RNA,
NMR
of
Biomolecules,
Towards
Mechanistic
Systems
Biology,
eds.
Bertini,
I.,
McGreevy,
K.S.,
Parigi,
G.,
Wiley-VCH,
1st
edition,
2012,
118-
135).
My
lecture
will
elaborate
the
content
of
this
overview
with
the
extension
to
basic
structural
properties
of
nucleic
acids,
as
well
to
assignments
and
structure
determination
of
both
unlabeled
and
13C/15N
enriched
nucleic
acids.
The
full
list
of
references
to
this
Chapter
is
provided
bellow
for
your
convenience.
Two
most
important
reviews
are
marked
in
bold.
Vladimr
Sklen
References:
1.
R.
Stefl
et
al.,
The
solution
structure
of
the
ADAR2
dsRBM-RNA
complex
reveals
a
sequence-specific
readout
of
the
minor
groove.
Cell
143,
225
(Oct
15,
2010).
2.
J.
F.
Milligan,
D.
R.
Groebe,
G.
W.
Witherell,
O.
C.
Uhlenbeck,
Oligoribonucleotide
synthesis
using
T7
RNA
polymerase
and
synthetic
DNA
templates.
Nucleic
Acids
Res
15,
8783
(Nov
11,
1987).
3.
S.
R.
Price,
N.
Ito,
C.
Oubridge,
J.
M.
Avis,
K.
Nagai,
Crystallization
of
RNA-protein
complexes.
I.
Methods
for
the
large-scale
preparation
of
RNA
suitable
for
crystallographic
studies.
J
Mol
Biol
249,
398
(Jun
2,
1995).
4.
L.
Ponchon,
G.
Beauvais,
S.
Nonin-Lecomte,
F.
Dardel,
A
generic
protocol
for
the
expression
and
purification
of
recombinant
RNA
in
Escherichia
coli
using
a
tRNA
scaffold.
Nat
Protoc
4,
947
(2009).
5.
L.
Ponchon,
F.
Dardel,
Recombinant
RNA
technology:
the
tRNA
scaffold.
Nat
Methods
4,
571
(Jul,
2007).
6.
W.
S.
Marshall,
R.
J.
Kaiser,
Recent
advances
in
the
high-speed
solid
phase
synthesis
of
RNA.
Curr
Opin
Chem
Biol
8,
222
(Jun,
2004).
7.
A.
G.
Tzakos,
L.
E.
Easton,
P.
J.
Lukavsky,
Complementary
segmental
labeling
of
large
RNAs:
economic
preparation
and
simplified
NMR
spectra
for
measurement
of
more
RDCs.
J
Am
Chem
Soc
128,
13344
(Oct
18,
2006).
8.
A.
G.
Tzakos,
L.
E.
Easton,
P.
J.
Lukavsky,
Preparation
of
large
RNA
oligonucleotides
with
complementary
isotope-labeled
segments
for
NMR
structural
studies.
Nat
Protoc
2,
2139
(2007).
9.
E.
P.
Nikonowicz,
A.
Pardi,
An
efficient
procedure
for
assignment
of
the
proton,
carbon
and
nitrogen
resonances
in
13C/15N
labeled
nucleic
acids.
J
Mol
Biol
232,
1141
(Aug
20,
1993).
10.
S.
S.
Wijmenga,
B.
N.
M.
van
Buuren,
The
use
of
NMR
methods
for
conformational
studies
of
nucleic
acids.
Prog
Nucl
Mag
Res
Sp
32,
287
(Jun,
1998).
11.
A.
J.
Dingley,
S.
Grzesiek,
Direct
observation
of
hydrogen
bonds
in
nucleic
acid
base
pairs
by
internucleotide
(2)J(NN)
couplings.
J
Am
Chem
Soc
120,
8293
(Aug
26,
1998).
12.
J.
Wohnert
et
al.,
Direct
identification
of
NH
center
dot
center
dot
center
dot
N
hydrogen
bonds
in
non-canonical
base
pairs
of
RNA
by
NMR
spectroscopy.
Nucleic
Acids
Res
27,
3104
(Aug
1,
1999).
13.
A.
J.
Dingley,
J.
E.
Masse,
J.
Feigon,
S.
Grzesiek,
Characterization
of
the
hydrogen
bond
network
in
guanosine
quartets
by
internucleotide
(3h)J(NC
')
and
(2h)J(NN)
scalar
couplings.
J
Biomol
Nmr
16,
279
(Apr,
2000).
14.
A.
Z.
Liu
et
al.,
NMR
detection
of
N-H
center
dot
center
dot
center
dot
O=C
hydrogen
bonds
in
C-13,N-15-labeled
nucleic
acids.
J
Am
Chem
Soc
122,
3206
(Apr
5,
2000).
15.
J.
P.
Simorre,
G.
R.
Zimmermann,
L.
Mueller,
A.
Pardi,
Correlation
of
the
guanosine
exchangeable
and
nonexchangeable
base
protons
in
C-13-(IN)-N-15-labeled
RNA
with
an
HNC-TOCSY-CH
experiment.
J
Biomol
Nmr
7,
153
(Mar,
1996).
16.
J.
P.
Simorre,
G.
R.
Zimmermann,
A.
Pardi,
B.
T.
Farmer,
L.
Mueller,
Triple
resonance
HNCCCH
experiments
for
correlating
exchangeable
and
nonexchangeable
cytidine
and
uridine
base
protons
in
RNA.
J
Biomol
Nmr
6,
427
(Dec,
1995).
17.
V.
Sklenar,
T.
Dieckmann,
S.
E.
Butcher,
J.
Feigon,
Through-bond
correlation
of
imino
and
aromatic
resonances
in
C-13-,N-15-labeled
RNA
via
heteronuclear
TOCSY.
J
Biomol
Nmr
7,
83
(Jan,
1996).
18.
J.
P.
Marino,
J.
H.
Prestegard,
D.
M.
Crothers,
Correlation
of
Adenine
H2/H8
Resonances
in
Uniformly
C-13
Labeled
Rnas
by
2d
Hcch-Tocsy
-
a
New
Tool
for
H-1
Assignment.
J
Am
Chem
Soc
116,
2205
(Mar
9,
1994).
19.
P.
Legault,
B.
T.
Farmer,
L.
Mueller,
A.
Pardi,
Through-Bond
Correlation
of
Adenine
Protons
in
a
C-13-Labeled
Ribozyme.
J
Am
Chem
Soc
116,
2203
(Mar
9,
1994).
20.
R.
Fiala,
M.
L.
Munzarova,
V.
Sklenar,
Experiments
for
correlating
quaternary
carbons
in
RNA
bases.
J
Biomol
Nmr
29,
477
(Aug,
2004).
21.
J.
P.
Simorre,
G.
R.
Zimmermann,
L.
Mueller,
A.
Pardi,
Triple-resonance
experiments
for
assignment
of
adenine
base
resonances
in
C-13/N-15-labeled
RNA.
J
Am
Chem
Soc
118,
5316
(Jun
5,
1996).
22.
J.
Wohnert,
R.
Ramachandran,
M.
Gorlach,
L.
R.
Brown,
Triple-resonance
experiments
for
correlation
of
H5
and
exchangeable
pyrimidine
base
hydrogens
in
C-
13,
N-15-labeled
RNA.
J
Magn
Reson
139,
430
(Aug,
1999).
23.
R.
Fiala,
V.
Sklenar,
C-13-detected
NMR
experiments
for
measuring
chemical
shifts
and
coupling
constants
in
nucleic
acid
bases.
J
Biomol
Nmr
39,
153
(Oct,
2007).
24.
B.
T.
Farmer,
L.
Muller,
E.
P.
Nikonowicz,
A.
Pardi,
Unambiguous
Resonance
Assignments
in
C-15,N-15-Labeled
Nucleic-Acids
by
3d
Triple-Resonance
Nmr.
J
Am
Chem
Soc
115,
11040
(Nov
17,
1993).
25.
B.
T.
Farmer,
L.
Muller,
E.
P.
Nikonowicz,
A.
Pardi,
Unambiguous
through-Bond
Sugar-to-Base
Correlations
for
Purines
in
C-13,
N-15-Labeled
Nucleic-Acids
-
the
Hscsnb,
Hscs(N)(B)C-B,
and
Hbnbcb
Experiments.
J
Biomol
Nmr
4,
129
(Jan,
1994).
26.
V.
Sklenar,
R.
D.
Peterson,
M.
R.
Rejante,
J.
Feigon,
2-Dimensional
and
3-Dimensional
Hcn
Experiments
for
Correlating
Base
and
Sugar
Resonances
in
N-15,C-13-Labeled
Rna
Oligonucleotides.
J
Biomol
Nmr
3,
721
(Nov,
1993).
27.
V.
Sklenar,
R.
D.
Peterson,
M.
R.
Rejante,
E.
Wang,
J.
Feigon,
2-Dimensional
Triple-
Resonance
Hcnch
Experiment
for
Direct
Correlation
of
Ribose
H1'
and
Base
H8,
H6
Protons
in
C-13,
N-15
Labeled
Rna
Oligonucleotides.
J
Am
Chem
Soc
115,
12181
(Dec
15,
1993).
28.
S.
Tate,
A.
Ono,
M.
Kainosho,
An
Alternative
Triple-Resonance
Method
for
the
through-Bond
Correlation
of
Intranucleotide
H1'
and
H8
Nmr
Signals
of
Purine
Nucleotides
-
Application
to
a
DNA
Dodecamer
with
Fully
C-13/N-15-Labeled
Deoxyadenosine
Residues.
J
Am
Chem
Soc
116,
5977
(Jun
29,
1994).
29.
R.
Fiala,
J.
Czernek,
V.
Sklenar,
Transverse
relaxation
optimized
triple-resonance
NMR
experiments
for
nucleic
acids.
J
Biomol
Nmr
16,
291
(Apr,
2000).
30.
B.
Brutscher,
J.
P.
Simorre,
Transverse
relaxation
optimized
HCN
experiment
for
nucleic
acids:
Combining
the
advantages
of
TROSY
and
MQ
spin
evolution.
J
Biomol
Nmr
21,
367
(Dec,
2001).
31.
H.
Schwalbe,
J.
P.
Marino,
S.
J.
Glaser,
C.
Griesinger,
Measurement
of
H,H-Coupling
Constants
Associated
with
Nu-1,
Nu-2,
and
Nu-3
in
Uniformly
C-13-Labeled
Rna
by
Hcc-Tocsy-Cch-E.Cosy.
J
Am
Chem
Soc
117,
7251
(Jul
12,
1995).
32.
H.
A.
Heus,
S.
S.
Wijmenga,
F.
J.
M.
Vandeven,
C.
W.
Hilbers,
Sequential
Backbone
Assignment
in
C-13-Labeled
Rna
Via
through-Bond
Coherence
Transfer
Using
3-
Dimensional
Triple-Resonance
Spectroscopy
(H-1,
C-13,
P-31)
and
2-Dimensional
Hetero
Tocsy.
J
Am
Chem
Soc
116,
4983
(Jun
1,
1994).
33.
J.
P.
Marino
et
al.,
A
3-Dimensional
Triple-Resonance
H-1,C-13,P-31
Experiment
-
Sequential
through-Bond
Correlation
of
Ribose
Protons
and
Intervening
Phosphorus
Along
the
Rna
Oligonucleotide
Backbone.
J
Am
Chem
Soc
116,
6472
(Jul
13,
1994).
34.
J.
P.
Marino
et
al.,
Sequential
Correlation
of
Anomeric
Ribose
Protons
and
Intervening
Phosphorus
in
Rna
Oligonucleotides
by
a
H-1,C-13,P-31
Triple-
Resonance
Experiment
-
Hcp-Cch-Tocsy.
J
Biomol
Nmr
5,
87
(Jan,
1995).
35.
R.
Ramachandran,
C.
Sich,
M.
Grune,
V.
Soskic,
L.
R.
Brown,
Sequential
assignments
in
uniformly
C-13-
and
N-15-labelled
RNAs:
The
HC(N,P)
and
HC(N,P)-CCH-TOCSY
experiments.
J
Biomol
Nmr
7,
251
(May,
1996).
36.
M.
Ebrahimi,
P.
Rossi,
C.
Rogers,
G.
S.
Harbison,
Dependence
of
13C
NMR
chemical
shifts
on
conformations
of
rna
nucleosides
and
nucleotides.
J
Magn
Reson
150,
1
(May,
2001).
37.
L.
Trantirek,
R.
Stefl,
J.
E.
Masse,
J.
Feigon,
V.
Sklenar,
Determination
of
the
glycosidic
torsion
angles
in
uniformly
C-13-labeled
nucleic
acids
from
vicinal
coupling
constants
(3)J(C2/4-H1
')
and
(3)J(C6/8-H1
').
J
Biomol
Nmr
23,
1
(May,
2002).
38.
E.
Duchardt
et
al.,
Determination
of
the
glycosidic
bond
angle
chi
in
RNA
from
cross-
correlated
relaxation
of
CH
dipolar
coupling
and
N
chemical
shift
anisotropy.
J
Am
Chem
Soc
126,
1962
(Feb
25,
2004).
39.
B.
Furtig,
C.
Richter,
J.
Wohnert,
H.
Schwalbe,
NMR
spectroscopy
of
RNA.
Chembiochem
4,
936
(Oct
6,
2003).
40.
S.
Nozinovic
et
al.,
Quantitative
2D
and
3D
Gamma-HCP
Experiments
for
the
Determination
of
the
Angles
alpha
and
zeta
in
the
Phosphodiester
Backbone
of
Oligonucleotides.
J
Am
Chem
Soc
132,
10318
(Aug
4,
2010).
41.
L.
Zidek,
H.
H.
Wu,
J.
Feigon,
V.
Sklenar,
Measurement
of
small
scalar
and
dipolar
couplings
in
purine
and
pyrimidine
bases.
J
Biomol
Nmr
21,
153
(2001).
42.
B.
S.
Tolbert
et
al.,
Major
groove
width
variations
in
RNA
structures
determined
by
NMR
and
impact
of
C-13
residual
chemical
shift
anisotropy
and
H-1-C-13
residual
dipolar
coupling
on
refinement.
J
Biomol
Nmr
47,
205
(Jul,
2010).
43.
B.
Simon,
T.
Madl,
C.
D.
Mackereth,
M.
Nilges,
M.
Sattler,
An
efficient
protocol
for
NMR-spectroscopy-based
structure
determination
of
protein
complexes
in
solution.
Angew
Chem
Int
Ed
Engl
49,
1967
(Mar
8,
2010).
44.
P.
Guntert,
Automated
structure
determination
from
NMR
spectra.
Eur
Biophys
J
38,
129
(Feb,
2009).
45.
E.
Suzuki,
N.
Pattabiraman,
G.
Zon,
T.
L.
James,
Solution
structure
of
[d(A-T)5]2
via
complete
relaxation
matrix
analysis
of
two-dimensional
nuclear
Overhauser
effect
spectra
and
molecular
mechanics
calculations:
evidence
for
a
hydration
tunnel.
Biochemistry-Us
25,
6854
(Nov
4,
1986).
46.
R.
S.
Lipsitz,
N.
Tjandra,
Residual
dipolar
couplings
in
NMR
structure
analysis.
Annu
Rev
Bioph
Biom
33,
387
(2004).
47.
B.
S.
Tolbert
et
al.,
Major
groove
width
variations
in
RNA
structures
determined
by
NMR
and
impact
of
13C
residual
chemical
shift
anisotropy
and
1H-13C
residual
dipolar
coupling
on
refinement.
J
Biomol
Nmr
47,
205
(Jul,
2010).
48.
R.
W.
W.
Hooft,
C.
Sander,
G.
Vriend,
Objectively
judging
the
quality
of
a
protein
structure
from
a
Ramachandran
plot.
Computer
Applications
in
the
Biosciences
13,
425
(Aug,
1997).
49.
C.
A.
E.
M.
Spronk,
S.
B.
Nabuurs,
E.
Krieger,
G.
Vriend,
G.
W.
Vuister,
Validation
of
protein
structures
derived
by
NMR
spectroscopy.
Prog
Nucl
Mag
Res
Sp
45,
315
(Dec
17,
2004).
50.
G.
Vriend,
WHAT
IF:
a
molecular
modeling
and
drug
design
program.
J
Mol
Graph
8,
52
(Mar,
1990).
51.
M.
S.
Babcock,
E.
P.
Pednault,
W.
K.
Olson,
Nucleic
acid
structure
analysis.
Mathematics
for
local
Cartesian
and
helical
structure
parameters
that
are
truly
comparable
between
structures.
J
Mol
Biol
237,
125
(Mar
18,
1994).
52.
I.
W.
Davis
et
al.,
MolProbity:
all-atom
contacts
and
structure
validation
for
proteins
and
nucleic
acids.
Nucleic
Acids
Res
35,
W375
(Jul,
2007).
53.
S.
S.
Wijmenga,
M.
Kruithof,
C.
W.
Hilbers,
Analysis
of
(1)H
chemical
shifts
in
DNA:
Assessment
of
the
reliability
of
(1)H
chemical
shift
calculations
for
use
in
structure
refinement.
J
Biomol
Nmr
10,
337
(Dec,
1997).
54.
P.
Davanloo,
A.
H.
Rosenberg,
J.
J.
Dunn,
F.
W.
Studier,
Cloning
and
expression
of
the
gene
for
bacteriophage
T7
RNA
polymerase.
Proc
Natl
Acad
Sci
U
S
A
81,
2035
(Apr,
1984).
55.
G.
A.
Diaz,
M.
Rong,
W.
T.
McAllister,
R.
K.
Durbin,
The
stability
of
abortively
cycling
T7
RNA
polymerase
complexes
depends
upon
template
conformation.
Biochemistry-
Us
35,
10837
(Aug
20,
1996).
56.
L.
E.
Easton,
Y.
Shibata,
P.
J.
Lukavsky,
Rapid,
nondenaturing
RNA
purification
using
weak
anion-exchange
fast
performance
liquid
chromatography.
RNA
16,
647
(Mar,
2010).
57.
I.
E.
Ichetovkin,
N.
V.
Symbatyan,
G.
Bagherzaden,
G.
A.
Korshunova,
Synthesis
of
peptide
analogue
of
oligoribonucleotide.
Vestn
Mosk
U
Khim+
38,
120
(Mar-Apr,
1997).