Characterising RNA Dynamics using NMR Residual Dipolar Couplings - Recent Developments in Biomolecular NMR - page 194

Table 9.2 Pulse sequences for the measurement of RDCs in nucleic acids.

Pulse sequence Type of RDCs Comments

1 D C2H2 , 1 D C5H5 ,
1 D C6H6 ,

HC[C](C)
hd-TROSY-
E.COSY 96

Pseudo-3D experiments for
homonuclear decoupling employing
TROSY and E.COSY elements.

1 D C8H8 ,

1 D C4C5 , 1 D C5C6 ,

2 D C5H6 , 2 D C6H5 and

2 D C4H5

CH 2 -S 3 E HSQC 108

1 D (C5 9 H59+C59H599) and
2 D (H59H599) (in DNA
only

2D experiments with spin-state
selection for detection of up- or
downfield carbon components of
CH 2 spin states.

1 D (C29H29+C29H299)

2 D (H29H299) )

and

3D S 3 CT E.COSY 102

1 D C49H49 , 2 D C59H49 ,
1 D (C59H59+C59H599) ,
( 1 D C59H59[9] - 2 D H59H599 ),
2 D C49H59+C49H599 , and
3 D H49H59[9]

3D experiments for measuring RDCs
in methine-methylene C-H pairs.
One experiment yields eight
splittings.

1 D C19H19 , 1 D C29H29 ,
2 D C19H29,

H1C1C2
E.COSY 101,168

3D experiment utilising E.COSY for
measuring five splittings in one
experiment.

2 D C29H19 ,

3 D H19H29

and

1 D N1H1 , 1 D N3H3 ,
2 D H1C2 , 2 D H1C6 ,
2 D H3C2 , and

IPAP HN-HSQC,
IPAP H(N)C-
HSQC 88

2D experiments yielding 1-2
couplings per experiment.

2 D H3C4

1 D C29H29 and 1 D C39H39

3D IPAP-HCcH-
COSY 3D relay-
HCcH-COSY 104,168

Uses C19H19 to alleviate spectral
overcrowding in the C29H29 and
C39H39 region.

MQ-HCN 100

1 D C19H19 , 1 D C19N1/N9 ,
1 D C19C29 , 2 D H19N1/9 ,
2 D H19C29 , 2 D H19N1/9 ,
1 D C6H6 , 1 D C6N1 ,
1 D C6C5 , 1 D C8H8 ,
1 D C8N9 , 2 D H8N9 ,
2 D H6N1 , and

Suite of six MQ-based 3D
experiments yielding 1-2 splittings
per experiment.

2 D H6C5

S 3 E IS[T] 89

1 D and 2 D

2D experiments for measuring most
of the one- and two-bond
splittings.

13 C- 1 H TROSY 92 1 D C2H2 , 1 D C5H5 ,

1 D C6H6 , and

Sensitivity enhanced using TROSY
and native

1 D C8H8 13 C magnetisation.

1 D C19N9 , 1 D C8N9 ,
1 D C4N9 , 1 D C19N1 ,
1 D C6N1 , and

3D MQ/TROSY-
HCN-QJ 103

3D quantitative J-modulated
experiments for measuring one
bond C-N splittings.

1 D C2N1

ARTSY 97

1 D N1H1 , 1 D N3H3 ,
1 D C2H2 ,

Sensitivity enhanced TROSY-based
2D experiments for measuring one-
bond N-H and C-H splittings

1 D C5H5 ,

1 D C6H6 , 1 D C8H8

C-H and N-H splittings can be measured using 2D HSQC-type experiments
that employ inphase-antiphase (IPAP) 88 or spin-selective excitation meth-
ods 89-91 to encode individual components of the doublet along the 13 Cor 15 N
dimension. For larger RNA molecules (typically .40 nt), it can be
advantageous to target the slowly relaxing TROSY 13 Cor 15 N component
of the doublet for resonances in the nucleobase that have sizeable CSAs. 92-97