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The effect of loop size in antisense and target RNAs on the efficiency of antisense RNA control

Hjalt, Tord LU and Wagner, E.G.H. (1992) In Nucleic Acids Research 20(24). p.6723-6732
Abstract
Most natural antisense RNAs display a high degree of
secondary structure with stem-loops as their most
prominent feature. Mutations affecting the Inhibitory
activity of these RNAs most often map in or close to
loop regions in both the antisense and target RNAs.
The primary recognition loops often contain 5- 7
unpaired nucleotldes. Nucleotide changes in the loops
affect the binding rate and, hence, the inhibitory effect
on the activity of the target RNA. Here we address the
question whether loop sizes affect binding rates
between antisense and target RNAs, using the
replication control system of plasmid R1 as a model
system. By creating a series of loop size mutants we
show that loop size... (More)
Most natural antisense RNAs display a high degree of
secondary structure with stem-loops as their most
prominent feature. Mutations affecting the Inhibitory
activity of these RNAs most often map in or close to
loop regions in both the antisense and target RNAs.
The primary recognition loops often contain 5- 7
unpaired nucleotldes. Nucleotide changes in the loops
affect the binding rate and, hence, the inhibitory effect
on the activity of the target RNA. Here we address the
question whether loop sizes affect binding rates
between antisense and target RNAs, using the
replication control system of plasmid R1 as a model
system. By creating a series of loop size mutants we
show that loop size alterations have strong effects on
the binding rates between the two reactant RNAs In
vitro, and that most of the mutations analyzed display
corresponding effects on antisense RNA control In
vivo. Our data suggest that the three-dimensional
structures of antisense and target RNA stem-loops are
crucial for determining binding rates. The Implications
of these results for the design of efficient artificial
antisense RNA control systems are discussed. (Less)
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publishing date
type
Contribution to journal
publication status
published
subject
in
Nucleic Acids Research
volume
20
issue
24
pages
10 pages
publisher
Oxford University Press
external identifiers
  • scopus:0027058934
ISSN
1362-4962
DOI
10.1093/nar/20.24.6723
language
English
LU publication?
no
id
c81e5fd1-9583-4dc8-9311-e5f3e5ccc7d7
date added to LUP
2022-08-24 12:13:59
date last changed
2023-11-21 12:05:12
@article{c81e5fd1-9583-4dc8-9311-e5f3e5ccc7d7,
  abstract     = {{Most natural antisense RNAs display a high degree of<br/>secondary structure with stem-loops as their most<br/>prominent feature. Mutations affecting the Inhibitory<br/>activity of these RNAs most often map in or close to<br/>loop regions in both the antisense and target RNAs.<br/>The primary recognition loops often contain 5- 7<br/>unpaired nucleotldes. Nucleotide changes in the loops<br/>affect the binding rate and, hence, the inhibitory effect<br/>on the activity of the target RNA. Here we address the<br/>question whether loop sizes affect binding rates<br/>between antisense and target RNAs, using the<br/>replication control system of plasmid R1 as a model<br/>system. By creating a series of loop size mutants we<br/>show that loop size alterations have strong effects on<br/>the binding rates between the two reactant RNAs In<br/>vitro, and that most of the mutations analyzed display<br/>corresponding effects on antisense RNA control In<br/>vivo. Our data suggest that the three-dimensional<br/>structures of antisense and target RNA stem-loops are<br/>crucial for determining binding rates. The Implications<br/>of these results for the design of efficient artificial<br/>antisense RNA control systems are discussed.}},
  author       = {{Hjalt, Tord and Wagner, E.G.H.}},
  issn         = {{1362-4962}},
  language     = {{eng}},
  month        = {{01}},
  number       = {{24}},
  pages        = {{6723--6732}},
  publisher    = {{Oxford University Press}},
  series       = {{Nucleic Acids Research}},
  title        = {{The effect of loop size in antisense and target RNAs on the efficiency of antisense RNA control}},
  url          = {{http://dx.doi.org/10.1093/nar/20.24.6723}},
  doi          = {{10.1093/nar/20.24.6723}},
  volume       = {{20}},
  year         = {{1992}},
}