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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

Summary and comparison of internal motions in the apical loop, derived from 13C relaxation and off-resonance ROESY. 13C-derived order parameters (from Table S1) are displayed with open symbols. Order parameters from off-resonance ROESY (derived as in Figure 4 from θ0 values listed in Table S2) are displayed as filled symbols. Bars to the left represent the average and spread of order parameters of nucleotides in helical stems, open and filled bars denote 13C and off-resonance ROESY data, respectively. The bar for intra-nucleotide contacts represents  of contacts between base and H1′ or H2′ atoms. On the right side, order parameters of individual nucleotides are presented, the nucleotides are color-coded as in Figure 1. Circles, diamonds and triangles represent contacts in the bases, riboses and ribose–base contacts, respectively.
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Figure 5: Summary and comparison of internal motions in the apical loop, derived from 13C relaxation and off-resonance ROESY. 13C-derived order parameters (from Table S1) are displayed with open symbols. Order parameters from off-resonance ROESY (derived as in Figure 4 from θ0 values listed in Table S2) are displayed as filled symbols. Bars to the left represent the average and spread of order parameters of nucleotides in helical stems, open and filled bars denote 13C and off-resonance ROESY data, respectively. The bar for intra-nucleotide contacts represents of contacts between base and H1′ or H2′ atoms. On the right side, order parameters of individual nucleotides are presented, the nucleotides are color-coded as in Figure 1. Circles, diamonds and triangles represent contacts in the bases, riboses and ribose–base contacts, respectively.

Mentions: General patterns of motion can be derived from the combination of 13C relaxation and off-resonance ROESY measurements (Figure 5). For the stem nucleotides, and Δθ0 agree not only for the H5–H6 vectors that were used for calibration, but also for the ribose moieties (see Materials and Methods section and Figure 5). The nucleotides found to be mobile according to 13C relaxation, U12, G13, U14, C16 and U23, showed an overall strong decrease in (Figure 5), and the ranges of and were similar. Note that base–ribose contacts can show the full range of behavior, from rigid (C11) to very mobile (U23 and G13). This underlines the need for motional information at many sites, which was here provided by off-resonance ROESY.Figure 5.


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)

Summary and comparison of internal motions in the apical loop, derived from 13C relaxation and off-resonance ROESY. 13C-derived order parameters (from Table S1) are displayed with open symbols. Order parameters from off-resonance ROESY (derived as in Figure 4 from θ0 values listed in Table S2) are displayed as filled symbols. Bars to the left represent the average and spread of order parameters of nucleotides in helical stems, open and filled bars denote 13C and off-resonance ROESY data, respectively. The bar for intra-nucleotide contacts represents  of contacts between base and H1′ or H2′ atoms. On the right side, order parameters of individual nucleotides are presented, the nucleotides are color-coded as in Figure 1. Circles, diamonds and triangles represent contacts in the bases, riboses and ribose–base contacts, respectively.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 5: Summary and comparison of internal motions in the apical loop, derived from 13C relaxation and off-resonance ROESY. 13C-derived order parameters (from Table S1) are displayed with open symbols. Order parameters from off-resonance ROESY (derived as in Figure 4 from θ0 values listed in Table S2) are displayed as filled symbols. Bars to the left represent the average and spread of order parameters of nucleotides in helical stems, open and filled bars denote 13C and off-resonance ROESY data, respectively. The bar for intra-nucleotide contacts represents of contacts between base and H1′ or H2′ atoms. On the right side, order parameters of individual nucleotides are presented, the nucleotides are color-coded as in Figure 1. Circles, diamonds and triangles represent contacts in the bases, riboses and ribose–base contacts, respectively.
Mentions: General patterns of motion can be derived from the combination of 13C relaxation and off-resonance ROESY measurements (Figure 5). For the stem nucleotides, and Δθ0 agree not only for the H5–H6 vectors that were used for calibration, but also for the ribose moieties (see Materials and Methods section and Figure 5). The nucleotides found to be mobile according to 13C relaxation, U12, G13, U14, C16 and U23, showed an overall strong decrease in (Figure 5), and the ranges of and were similar. Note that base–ribose contacts can show the full range of behavior, from rigid (C11) to very mobile (U23 and G13). This underlines the need for motional information at many sites, which was here provided by off-resonance ROESY.Figure 5.

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