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Structure elucidation of the hepatitis B virus encapsidation signal by NMR on selectively labeled RNAs.

Flodell, S; Cromsigt, J; Schleucher, J; Kidd-Ljunggren, Karin LU and Wijmenga, S (2002) In Journal of Biomolecular Structure and Dynamics 19(4). p.627-636
Abstract
Hepatitis B virus (HBV) HBV is DNA virus with a unique replication strategy, which involves reverse transcription of its pregenomic RNA. Essential for this reverse transcription are the 5'- and 3'-ends of its pregenomic RNA (5'-RT-RNA and 3'-RT-RNA, respectively) which form conserved bulged stem-loop structures. The 5'-RT-RNA consists of a 67 nucleotide bulged stein-loop structure, epsilon, which constitutes the signal for encapsidation of the pregenomic RNA and subsequent reverse transcription. The reverse transcriptase (RT) initially binds to the completely conserved apical loop of epsilon and a 4-nucleotide primer is synthesized from the adjacent 6-nucleotide bulge. Structural studies of epsilon can provide important parameters required... (More)
Hepatitis B virus (HBV) HBV is DNA virus with a unique replication strategy, which involves reverse transcription of its pregenomic RNA. Essential for this reverse transcription are the 5'- and 3'-ends of its pregenomic RNA (5'-RT-RNA and 3'-RT-RNA, respectively) which form conserved bulged stem-loop structures. The 5'-RT-RNA consists of a 67 nucleotide bulged stein-loop structure, epsilon, which constitutes the signal for encapsidation of the pregenomic RNA and subsequent reverse transcription. The reverse transcriptase (RT) initially binds to the completely conserved apical loop of epsilon and a 4-nucleotide primer is synthesized from the adjacent 6-nucleotide bulge. Structural studies of epsilon can provide important parameters required for the design of RNA targeted anti-viral drugs directed against Hepatitis B virus. NMR studies of large RNA systems (> ca. 50 nucleotides) require novel approaches. e.g. different labeling schemes and reduction of the system into separate structural building blocks. Recently, a new method of synthesizing C-13/N-15/H-2 labeled nucleotides has been developed based on converting specifically labeled glucose and bases into nucleotides by using enzymes from the pentose phosphate pathway and nucleotide and salvage pathways. These NTPs give a large freedom in designing different labeling patterns in in vitro synthesized RNAs under study for NMR. This opens up the way for NMR studies of RNAs that are considerably above the present size limit (up to 150 nucleotides). Here this new technique is applied for structural studies on 27, 36 and 61 nucleotides long RNA fragments, mimicking different regions of epsilon. (Less)
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Contribution to journal
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published
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in
Journal of Biomolecular Structure and Dynamics
volume
19
issue
4
pages
627 - 636
publisher
Adenine Press
external identifiers
  • wos:000174614000006
  • pmid:11843624
  • scopus:0036130616
ISSN
1538-0254
language
English
LU publication?
yes
id
b1d1b0ab-3eb3-4940-b635-34cc971c1f66 (old id 341860)
alternative location
http://www.jbsdonline.com/index.cfm?d=3011&c=4042&p=10732&do=detail
date added to LUP
2007-08-17 13:05:27
date last changed
2017-08-06 03:49:38
@article{b1d1b0ab-3eb3-4940-b635-34cc971c1f66,
  abstract     = {Hepatitis B virus (HBV) HBV is DNA virus with a unique replication strategy, which involves reverse transcription of its pregenomic RNA. Essential for this reverse transcription are the 5'- and 3'-ends of its pregenomic RNA (5'-RT-RNA and 3'-RT-RNA, respectively) which form conserved bulged stem-loop structures. The 5'-RT-RNA consists of a 67 nucleotide bulged stein-loop structure, epsilon, which constitutes the signal for encapsidation of the pregenomic RNA and subsequent reverse transcription. The reverse transcriptase (RT) initially binds to the completely conserved apical loop of epsilon and a 4-nucleotide primer is synthesized from the adjacent 6-nucleotide bulge. Structural studies of epsilon can provide important parameters required for the design of RNA targeted anti-viral drugs directed against Hepatitis B virus. NMR studies of large RNA systems (> ca. 50 nucleotides) require novel approaches. e.g. different labeling schemes and reduction of the system into separate structural building blocks. Recently, a new method of synthesizing C-13/N-15/H-2 labeled nucleotides has been developed based on converting specifically labeled glucose and bases into nucleotides by using enzymes from the pentose phosphate pathway and nucleotide and salvage pathways. These NTPs give a large freedom in designing different labeling patterns in in vitro synthesized RNAs under study for NMR. This opens up the way for NMR studies of RNAs that are considerably above the present size limit (up to 150 nucleotides). Here this new technique is applied for structural studies on 27, 36 and 61 nucleotides long RNA fragments, mimicking different regions of epsilon.},
  author       = {Flodell, S and Cromsigt, J and Schleucher, J and Kidd-Ljunggren, Karin and Wijmenga, S},
  issn         = {1538-0254},
  language     = {eng},
  number       = {4},
  pages        = {627--636},
  publisher    = {Adenine Press},
  series       = {Journal of Biomolecular Structure and Dynamics},
  title        = {Structure elucidation of the hepatitis B virus encapsidation signal by NMR on selectively labeled RNAs.},
  volume       = {19},
  year         = {2002},
}