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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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Related in: MedlinePlus

Intra-nucleotide mobility of four nucleotides in the apical stem-loop.  values are indicated as blue cones, with the opening angle derived from a ‘wobbling-in-a-cone’ model (data in Table S1). Δθ0 values are indicated as diameter of the green cylinders representing H,H contacts. U19 is included as a rigid stem nucleotide. U14, C16 and U23 show different distributions of mobility within the nucleotide. The graphic was created using VMD (46).
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Figure 6: Intra-nucleotide mobility of four nucleotides in the apical stem-loop. values are indicated as blue cones, with the opening angle derived from a ‘wobbling-in-a-cone’ model (data in Table S1). Δθ0 values are indicated as diameter of the green cylinders representing H,H contacts. U19 is included as a rigid stem nucleotide. U14, C16 and U23 show different distributions of mobility within the nucleotide. The graphic was created using VMD (46).

Mentions: To examine the motions of the mobile nucleotides, their relaxation data are displayed in the nucleotide structures (Figure 6). Using the ‘wobbling-in-a-cone’ model (34), we translated into opening angles, α, of the motions of C–H bonds. The cones are displayed in Figure 6 and the angles α are given in Table S1. For each H,H contact, the motional amplitude is displayed as a cylinder, where the diameter is proportional to the Δθ0 value. The rigid stem nucleotide U19 is shown for reference. In U14, C16 and U12, the H5,H6 contact is more rigid than the base C–H bonds, and the C1′–H bond is also more rigid than the base C–H bonds (see also Figure 5). This pattern of mobility suggests that a rotation around χ is a strong component of the motion affecting the base C–H bonds, because this rotation changes the orientation of the base C–H bonds, but not of the H5,H6 vectors. However, within this pattern there is variation. In U14, the H5,H6 contact is rigid in spite of strong mobility of C5–H and C6–H. As intermediate case, C16 and U12 show strong mobility in their H5,H6 contacts, but not as strong as their base C–H vectors. In C16, the mobility of the H5,H6 and H6,H1′ contacts instead closely matches the mobility of the C1′–H bond (Figure 5), suggesting that their motions might be correlated. Finally, in U23, base C–H bonds, the H5,H6 and an intranucleotide base-ribose contact all show similar, high mobility (Figure 6).Figure 6.


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)

Intra-nucleotide mobility of four nucleotides in the apical stem-loop.  values are indicated as blue cones, with the opening angle derived from a ‘wobbling-in-a-cone’ model (data in Table S1). Δθ0 values are indicated as diameter of the green cylinders representing H,H contacts. U19 is included as a rigid stem nucleotide. U14, C16 and U23 show different distributions of mobility within the nucleotide. The graphic was created using VMD (46).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 6: Intra-nucleotide mobility of four nucleotides in the apical stem-loop. values are indicated as blue cones, with the opening angle derived from a ‘wobbling-in-a-cone’ model (data in Table S1). Δθ0 values are indicated as diameter of the green cylinders representing H,H contacts. U19 is included as a rigid stem nucleotide. U14, C16 and U23 show different distributions of mobility within the nucleotide. The graphic was created using VMD (46).
Mentions: To examine the motions of the mobile nucleotides, their relaxation data are displayed in the nucleotide structures (Figure 6). Using the ‘wobbling-in-a-cone’ model (34), we translated into opening angles, α, of the motions of C–H bonds. The cones are displayed in Figure 6 and the angles α are given in Table S1. For each H,H contact, the motional amplitude is displayed as a cylinder, where the diameter is proportional to the Δθ0 value. The rigid stem nucleotide U19 is shown for reference. In U14, C16 and U12, the H5,H6 contact is more rigid than the base C–H bonds, and the C1′–H bond is also more rigid than the base C–H bonds (see also Figure 5). This pattern of mobility suggests that a rotation around χ is a strong component of the motion affecting the base C–H bonds, because this rotation changes the orientation of the base C–H bonds, but not of the H5,H6 vectors. However, within this pattern there is variation. In U14, the H5,H6 contact is rigid in spite of strong mobility of C5–H and C6–H. As intermediate case, C16 and U12 show strong mobility in their H5,H6 contacts, but not as strong as their base C–H vectors. In C16, the mobility of the H5,H6 and H6,H1′ contacts instead closely matches the mobility of the C1′–H bond (Figure 5), suggesting that their motions might be correlated. Finally, in U23, base C–H bonds, the H5,H6 and an intranucleotide base-ribose contact all show similar, high mobility (Figure 6).Figure 6.

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