Limits...
Conserved nucleotides in an RNA essential for hepatitis B virus replication show distinct mobility patterns.

Petzold K, Duchardt E, Flodell S, Larsson G, Kidd-Ljunggren K, Wijmenga S, Schleucher J - Nucleic Acids Res. (2007)

Bottom Line: Motions in non-canonical structure elements were found primarily on the sub-nanosecond timescale.Different patterns of mobility were observed among several mobile nucleotides.The most mobile nucleotides are highly conserved among different HBV strains, suggesting that their mobility patterns may be necessary for the RNA's biological function.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden.

ABSTRACT
The number of regulatory RNAs with identified non-canonical structures is increasing, and structural transitions often play a role in their biological function. This stimulates interest in internal motions of RNA, which can underlie structural transitions. Heteronuclear NMR relaxation measurements, which are commonly used to study internal motion, only report on local motions of few sites within the molecule. Here we have studied a 27-nt segment of the human hepatitis B virus (HBV) pregenomic RNA, which is essential for viral replication. We combined heteronuclear relaxation with the new off-resonance ROESY technique, which reports on internal motions of H,H contacts. Using off-resonance ROESY, we could for the first time detect motion of through-space H,H contacts, such as in intra-residue base-ribose contacts or inter-nucleotide contacts, both essential for NMR structure determination. Motions in non-canonical structure elements were found primarily on the sub-nanosecond timescale. Different patterns of mobility were observed among several mobile nucleotides. The most mobile nucleotides are highly conserved among different HBV strains, suggesting that their mobility patterns may be necessary for the RNA's biological function.

Show MeSH

Related in: MedlinePlus

Representative 13C T1 decay curves for C1′ of C16, C7 and G13 (for data, see Table S1).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2175316&req=5

Figure 2: Representative 13C T1 decay curves for C1′ of C16, C7 and G13 (for data, see Table S1).

Mentions: 13C relaxation parameters T1, T1ρ and 13C-{H} NOE were measured for the C5–H and C6–H groups of the bases and all ribose carbons of the 13C-labeled C, G and U nucleotides (Table S1). Representative T1 relaxation data are shown in Figure 2. The relaxation data were analyzed by plotting and according to the Lipari-Szabo (36) approach using the program ‘ModelFree’ (28). This analysis resulted in a rotational diffusion anisotropy of 1.73 and an averaged rotational correlation time of 5.9 ns, in reasonable agreement with the anisotropy of 2.3 and averaged correlation time of 5.9 ns, estimated from hydrodynamic calculations using HydroNMR (32). The ModelFree results are also in good qualitative agreement with an analysis of the relaxation data by inspection, and mobility can in the present case be unequivocally detected by ModelFree analysis or by direct inspection of relaxation data. This indicates that the ModelFree analysis of the relaxation data neglecting the asymmetry of the base carbon CSA tensors and their non-colinearity with the C–H bond is permissible in our case, although the molecule is at the upper end of the molecular weight range for this approximation. In higher molecular weight systems, it has been demonstrated that mobility can still be detected by direct comparison of relaxation data (37).Figure 2.


Conserved nucleotides in an RNA essential for hepatitis B virus replication show distinct mobility patterns.

Petzold K, Duchardt E, Flodell S, Larsson G, Kidd-Ljunggren K, Wijmenga S, Schleucher J - Nucleic Acids Res. (2007)

Representative 13C T1 decay curves for C1′ of C16, C7 and G13 (for data, see Table S1).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2175316&req=5

Figure 2: Representative 13C T1 decay curves for C1′ of C16, C7 and G13 (for data, see Table S1).
Mentions: 13C relaxation parameters T1, T1ρ and 13C-{H} NOE were measured for the C5–H and C6–H groups of the bases and all ribose carbons of the 13C-labeled C, G and U nucleotides (Table S1). Representative T1 relaxation data are shown in Figure 2. The relaxation data were analyzed by plotting and according to the Lipari-Szabo (36) approach using the program ‘ModelFree’ (28). This analysis resulted in a rotational diffusion anisotropy of 1.73 and an averaged rotational correlation time of 5.9 ns, in reasonable agreement with the anisotropy of 2.3 and averaged correlation time of 5.9 ns, estimated from hydrodynamic calculations using HydroNMR (32). The ModelFree results are also in good qualitative agreement with an analysis of the relaxation data by inspection, and mobility can in the present case be unequivocally detected by ModelFree analysis or by direct inspection of relaxation data. This indicates that the ModelFree analysis of the relaxation data neglecting the asymmetry of the base carbon CSA tensors and their non-colinearity with the C–H bond is permissible in our case, although the molecule is at the upper end of the molecular weight range for this approximation. In higher molecular weight systems, it has been demonstrated that mobility can still be detected by direct comparison of relaxation data (37).Figure 2.

Bottom Line: Motions in non-canonical structure elements were found primarily on the sub-nanosecond timescale.Different patterns of mobility were observed among several mobile nucleotides.The most mobile nucleotides are highly conserved among different HBV strains, suggesting that their mobility patterns may be necessary for the RNA's biological function.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden.

ABSTRACT
The number of regulatory RNAs with identified non-canonical structures is increasing, and structural transitions often play a role in their biological function. This stimulates interest in internal motions of RNA, which can underlie structural transitions. Heteronuclear NMR relaxation measurements, which are commonly used to study internal motion, only report on local motions of few sites within the molecule. Here we have studied a 27-nt segment of the human hepatitis B virus (HBV) pregenomic RNA, which is essential for viral replication. We combined heteronuclear relaxation with the new off-resonance ROESY technique, which reports on internal motions of H,H contacts. Using off-resonance ROESY, we could for the first time detect motion of through-space H,H contacts, such as in intra-residue base-ribose contacts or inter-nucleotide contacts, both essential for NMR structure determination. Motions in non-canonical structure elements were found primarily on the sub-nanosecond timescale. Different patterns of mobility were observed among several mobile nucleotides. The most mobile nucleotides are highly conserved among different HBV strains, suggesting that their mobility patterns may be necessary for the RNA's biological function.

Show MeSH
Related in: MedlinePlus