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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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13C order parameter () as function of nucleotide sequence. Circles represent C6, crosses C5 and triangles C1′ atoms, respectively. The dashed line represents the rigid average  of base C–H groups of stem nucleotides. Gray shading marks the loop region C11–C16 and the bulged U23.
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Figure 3: 13C order parameter () as function of nucleotide sequence. Circles represent C6, crosses C5 and triangles C1′ atoms, respectively. The dashed line represents the rigid average of base C–H groups of stem nucleotides. Gray shading marks the loop region C11–C16 and the bulged U23.

Mentions: Complete ‘ModelFree’ results are given in Table S1, and order parameters , describing mobility of C–H bonds, are plotted as function of nucleotide sequence in Figure 3. According to this analysis, the stem nucleotides are rigid in the base and in the ribose moieties, with values of 0.97 ± 0.07 and 0.87 ± 0.07, respectively. The loop nucleotides U12, U14, C16 and the bulged U23 show strong motion, which is less pronounced in C1′ , compared to the bases . G13 is highly mobile at C1′ . The closing base pair C11:G15 of the pseudo-triloop is as rigid as the stem nucleotides, with of 0.85 or higher. For the majority of mobile C–H bonds, the internal motion was described by a model with a correlation time (τe) of the order of 400 ps (Table S1).Figure 3.


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)

13C order parameter () as function of nucleotide sequence. Circles represent C6, crosses C5 and triangles C1′ atoms, respectively. The dashed line represents the rigid average  of base C–H groups of stem nucleotides. Gray shading marks the loop region C11–C16 and the bulged U23.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 3: 13C order parameter () as function of nucleotide sequence. Circles represent C6, crosses C5 and triangles C1′ atoms, respectively. The dashed line represents the rigid average of base C–H groups of stem nucleotides. Gray shading marks the loop region C11–C16 and the bulged U23.
Mentions: Complete ‘ModelFree’ results are given in Table S1, and order parameters , describing mobility of C–H bonds, are plotted as function of nucleotide sequence in Figure 3. According to this analysis, the stem nucleotides are rigid in the base and in the ribose moieties, with values of 0.97 ± 0.07 and 0.87 ± 0.07, respectively. The loop nucleotides U12, U14, C16 and the bulged U23 show strong motion, which is less pronounced in C1′ , compared to the bases . G13 is highly mobile at C1′ . The closing base pair C11:G15 of the pseudo-triloop is as rigid as the stem nucleotides, with of 0.85 or higher. For the majority of mobile C–H bonds, the internal motion was described by a model with a correlation time (τe) of the order of 400 ps (Table S1).Figure 3.

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