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Nuclear properties of selected isotopes



Spin systems in ribose and deoxyribose



Spin systems in nucleic acid bases



1H chemical shift ranges in DNA and RNA



1H chemical shift ranges in DNA and RNA



1H NMR spectrum of d(CGCGAATTCGCG)
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1H NMR spectra in H2O
Watson-Crick
d(CGCGAATTCGCG)2
B-helix
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Hoogsteen
d(AAT GGG T GGG TTT GGG T GGG TAA)
G-quadruplex

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1H COSY spectrum of DNA
d(CGCGAATTCGCG)2

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1H TOCSY spectrum of DNA
d(CGCGAATTCGCG)2

1H NOESY spectrum of DNA in D2O
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1H NOESY spectrum of DNA in H2O
d(CGCGAATTCGCG)2

Structure Determination Procedure



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Resonance Assignment


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Sequential connectivities
with exchangeable protons
Dickerson’s dodecamer
d(CGCGAATTCGCG)2‏
imino-imino
imino-amino
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Sequential resonance assignments
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d(CGCGAATTCGCG)2
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H6/8-H2’,2’’/Me
H6/8-H1’

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Assignment based on H6/8-H1’ connectivities
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Assignment based on H6/8-H1’ connectivities
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Assignment based on H6/8-H1’ connectivities


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Assignment based on H6/8-H1’ connectivities


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Assignment based on H6/8-H1’ connectivities
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Assignment based on H6/8-H1’ connectivities
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Assignment based on H6/8-H1’ connectivities


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Assignment based on H6/8-H2’2’’ connectivities
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d(CGCGAATTCGCG)2

31P spectrum of DNA
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d(CGCGAATTCGCG)2
Phosphate buffer

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Assignment of Sugar-Phosphate Backbone
HP-COSY
HP-TOCSY

1H - 31P correlation spectrum
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31P
1H
3’
4’, 5’, 5’’
d(CGCGAATTCGCG)2







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J-couplings from COSY spectra


P determination from J-couplings
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1’2’
2’3’
1’2’’
3’4’
2’’3’

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Equilibrium of N and S conformations
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3’-endo
2’-endo







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Heteronuclear NMR of Nucleic Acids
In most cases, requires samples isotopicaly enriched
by 13C and 15N (except for HSQC, HMQC)
Assignment uses NOE or through-bond experiments
Traditional constraints (NOEs, J-couplings)
Novel constraints (RDCs, residual CSA)
Studies of intramolecular dynamics

Correlation of exchangeable protons with 15N
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Gradient sensitivity-enhanced HSQC
Kay, Keifer, Saarinen, JACS 1992.
A
U
C
G
G
C
G
C
C
G
U
U
C
G
1
5
10

Identification of hydrogen and carbon atoms in bases and sugars
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(Constant-time) 1H-13C HSQC experiment
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base
sugar