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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.

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Correlation of  and Δθ0 for C–H groups and H,H contacts. Circles: C5–H or C6–H bonds and H5,H6 contacts; diamonds: C–H bonds and H,H contacts in riboses; triangles: base–ribose H,H contacts and C–H bonds involved. Filled symbols indicate H,H contacts for which  is available for both C–H bonds. A theoretical dependence of Δθ0 on  is shown as a dashed line. This correlation is based on the assumption that motion of a H,H contact is caused exclusively by motion of one C–H bond, and that  equals . Assuming that the motion has a τe at the sensitivity maximum of off-resonance ROESY, Δθ0 values corresponding to S2 values were derived from Figure S3. Data points where  and  are available and which are discussed in text were connected by horizontal lines. These data points illustrate how correlation of H,H and C–H motion can cause deviations from the theoretical dependence.
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Figure 4: Correlation of and Δθ0 for C–H groups and H,H contacts. Circles: C5–H or C6–H bonds and H5,H6 contacts; diamonds: C–H bonds and H,H contacts in riboses; triangles: base–ribose H,H contacts and C–H bonds involved. Filled symbols indicate H,H contacts for which is available for both C–H bonds. A theoretical dependence of Δθ0 on is shown as a dashed line. This correlation is based on the assumption that motion of a H,H contact is caused exclusively by motion of one C–H bond, and that equals . Assuming that the motion has a τe at the sensitivity maximum of off-resonance ROESY, Δθ0 values corresponding to S2 values were derived from Figure S3. Data points where and are available and which are discussed in text were connected by horizontal lines. These data points illustrate how correlation of H,H and C–H motion can cause deviations from the theoretical dependence.

Mentions: Results from 13C relaxation and off-resonance ROESY are compared in Figure 4. The correlation between observed and Δθ0 for all atom groups is highly significant (P < 0.001), and the same holds for separate correlations for base, ribose or base-ribose contacts. The correlation is also in agreement with a theoretical correlation (dashed line), but there are also strong differences in motion as detected by both techniques. These differences are not surprising, given that 13C relaxation and off-resonance ROESY are sensitive to motion on different timescales and around different axes. Furthermore, a larger amplitude of motion of H,H contacts compared to C–H bonds is to be expected, because more degrees of freedom can contribute to H,H motion.Figure 4.


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)

Correlation of  and Δθ0 for C–H groups and H,H contacts. Circles: C5–H or C6–H bonds and H5,H6 contacts; diamonds: C–H bonds and H,H contacts in riboses; triangles: base–ribose H,H contacts and C–H bonds involved. Filled symbols indicate H,H contacts for which  is available for both C–H bonds. A theoretical dependence of Δθ0 on  is shown as a dashed line. This correlation is based on the assumption that motion of a H,H contact is caused exclusively by motion of one C–H bond, and that  equals . Assuming that the motion has a τe at the sensitivity maximum of off-resonance ROESY, Δθ0 values corresponding to S2 values were derived from Figure S3. Data points where  and  are available and which are discussed in text were connected by horizontal lines. These data points illustrate how correlation of H,H and C–H motion can cause deviations from the theoretical dependence.
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Related In: Results  -  Collection

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Show All Figures
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Figure 4: Correlation of and Δθ0 for C–H groups and H,H contacts. Circles: C5–H or C6–H bonds and H5,H6 contacts; diamonds: C–H bonds and H,H contacts in riboses; triangles: base–ribose H,H contacts and C–H bonds involved. Filled symbols indicate H,H contacts for which is available for both C–H bonds. A theoretical dependence of Δθ0 on is shown as a dashed line. This correlation is based on the assumption that motion of a H,H contact is caused exclusively by motion of one C–H bond, and that equals . Assuming that the motion has a τe at the sensitivity maximum of off-resonance ROESY, Δθ0 values corresponding to S2 values were derived from Figure S3. Data points where and are available and which are discussed in text were connected by horizontal lines. These data points illustrate how correlation of H,H and C–H motion can cause deviations from the theoretical dependence.
Mentions: Results from 13C relaxation and off-resonance ROESY are compared in Figure 4. The correlation between observed and Δθ0 for all atom groups is highly significant (P < 0.001), and the same holds for separate correlations for base, ribose or base-ribose contacts. The correlation is also in agreement with a theoretical correlation (dashed line), but there are also strong differences in motion as detected by both techniques. These differences are not surprising, given that 13C relaxation and off-resonance ROESY are sensitive to motion on different timescales and around different axes. Furthermore, a larger amplitude of motion of H,H contacts compared to C–H bonds is to be expected, because more degrees of freedom can contribute to H,H motion.Figure 4.

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