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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

Secondary structure of the apical loop of epsilon of human HBV. The 27-nt loop contains a pseudo-triloop with the sequence C11U12G13U14G15C16 with a C11 : G15 closing base pair and with C16 being bulged out. Between the two helical stems, U23 is not base paired and forms a bulge.
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Figure 1: Secondary structure of the apical loop of epsilon of human HBV. The 27-nt loop contains a pseudo-triloop with the sequence C11U12G13U14G15C16 with a C11 : G15 closing base pair and with C16 being bulged out. Between the two helical stems, U23 is not base paired and forms a bulge.

Mentions: We have previously determined the secondary structure (10) of the apical stem-loop of epsilon by NMR, and its 3D structure (11). The structure contains two helical stems separated by the bulged U23, and is capped by a pseudo-triloop (Figure 1). In vivo, the apical loop is essential for viral replication, although its exact role has not been established yet. In agreement with its vital function for the virus, many nucleotides of the apical stem-loop (for example G13, U14, C16 and U23) are completely conserved among 1200 sequenced strains of human HBV (10). The apical stem-loop of the epsilon structure of duck HBV opens upon forming a priming-competent complex with the RT (8), but it is not known if the apical stem-loop of human HBV undergoes a similar structural change during viral replication. During the structure determination of the apical loop of human HBV, we observed that several nucleotides in the pseudo-triloop (Figure 1) of the apical stem-loop showed few NOE contacts and systematically reduced C–H residual dipolar couplings compared to the stem nucleotides. This suggested that the nucleotides in the pseudo-triloop might show internal motions in the vicinity of their respective average positions in the molecular structure. Conservation of nucleotides in the stem and the pseudo-triloop together with the suspected internal motions raised the question of whether these motions might play a role in the biological function (12) of this RNA structure.Figure 1.


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)

Secondary structure of the apical loop of epsilon of human HBV. The 27-nt loop contains a pseudo-triloop with the sequence C11U12G13U14G15C16 with a C11 : G15 closing base pair and with C16 being bulged out. Between the two helical stems, U23 is not base paired and forms a bulge.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: Secondary structure of the apical loop of epsilon of human HBV. The 27-nt loop contains a pseudo-triloop with the sequence C11U12G13U14G15C16 with a C11 : G15 closing base pair and with C16 being bulged out. Between the two helical stems, U23 is not base paired and forms a bulge.
Mentions: We have previously determined the secondary structure (10) of the apical stem-loop of epsilon by NMR, and its 3D structure (11). The structure contains two helical stems separated by the bulged U23, and is capped by a pseudo-triloop (Figure 1). In vivo, the apical loop is essential for viral replication, although its exact role has not been established yet. In agreement with its vital function for the virus, many nucleotides of the apical stem-loop (for example G13, U14, C16 and U23) are completely conserved among 1200 sequenced strains of human HBV (10). The apical stem-loop of the epsilon structure of duck HBV opens upon forming a priming-competent complex with the RT (8), but it is not known if the apical stem-loop of human HBV undergoes a similar structural change during viral replication. During the structure determination of the apical loop of human HBV, we observed that several nucleotides in the pseudo-triloop (Figure 1) of the apical stem-loop showed few NOE contacts and systematically reduced C–H residual dipolar couplings compared to the stem nucleotides. This suggested that the nucleotides in the pseudo-triloop might show internal motions in the vicinity of their respective average positions in the molecular structure. Conservation of nucleotides in the stem and the pseudo-triloop together with the suspected internal motions raised the question of whether these motions might play a role in the biological function (12) of this RNA structure.Figure 1.

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