PMID- 16445294
OWN - NLM
STAT- MEDLINE
DCOM- 20060510
LR  - 20081121
IS  - 0006-2960 (Print)
IS  - 0006-2960 (Linking)
VI  - 45
IP  - 5
DP  - 2006 Feb 7
TI  - Bimodal loop-loop interactions increase the affinity of RNA aptamers for HIV-1 
      RNA structures.
PG  - 1518-24
AB  - Multiple loop-loop interactions between adjacent RNA hairpins regulate gene 
      expression in different organisms. To demonstrate that such natural interactions 
      could be mimicked for generating RNA ligands that are able to recognize 
      simultaneously at least two structured RNA targets, a double kissing complex 
      model was designed. The target consisted of two HIV-1 transactivating responsive 
      (TAR) RNA variants, BRU and MAL, connected by a non-nucleotidic linker. The 
      double ligand was generated by combining the corresponding hairpin aptamers, 
      R06BRU and R06MAL, identified previously by in vitro selection [Duconge, F., and 
      Toulme, J. J (1999) RNA 5, 1605-1614]. The resulting interaction was analyzed by 
      thermal denaturation monitored by UV spectroscopy, electrophoretic mobility shift 
      assays (EMSAs), and surface plasmon resonance (SPR) experiments. The bimodal 
      complex was characterized by a binding equilibrium constant increased by at least 
      1 order of magnitude compared to that of the complexes between the individual 
      parent hairpins. This resulted from a slower dissociation rate. We then made use 
      of such a strategy for targeting two structured functional motifs of the folded 
      5' untranslated region (5'UTR) of HIV-1. Two bivalent RNA ligands were designed 
      that targeted simultaneously the TAR and dimerization initiation site (DIS) 
      hairpins or the TAR and poly(A) ones. The results show that these ligands also 
      displayed enhanced affinity for their target compared to the individual 
      molecules. The work reported here suggests that bimodal structured RNA ligands 
      might provide a way of increasing the affinity of aptamers for folded RNA 
      targets.
FAU - Boucard, David
AU  - Boucard D
AD  - Universite Victor Segalen, Bordeaux, F-33076, France, INSERM U386, Bordeaux, 
      F-33076, France, and Institut Europeen de Chimie et Biologie, Pessac, F-33607, 
      France.
FAU - Toulme, Jean-Jacques
AU  - Toulme JJ
FAU - Di Primo, Carmelo
AU  - Di Primo C
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Biochemistry
JT  - Biochemistry
JID - 0370623
RN  - 0 (Ligands)
RN  - 0 (RNA, Viral)
SB  - IM
MH  - Base Pairing
MH  - Electrophoresis, Polyacrylamide Gel/methods
MH  - Genetic Variation
MH  - HIV Long Terminal Repeat/genetics
MH  - HIV-1/*genetics
MH  - Kinetics
MH  - Ligands
MH  - Models, Chemical
MH  - Nucleic Acid Conformation
MH  - RNA Stability
MH  - RNA, Viral/*chemistry
MH  - Spectrophotometry, Ultraviolet/methods
MH  - Surface Plasmon Resonance/methods
MH  - Temperature
MH  - Time Factors
MH  - Transcription, Genetic
EDAT- 2006/02/01 09:00
MHDA- 2006/05/11 09:00
CRDT- 2006/02/01 09:00
PHST- 2006/02/01 09:00 [pubmed]
PHST- 2006/05/11 09:00 [medline]
PHST- 2006/02/01 09:00 [entrez]
AID - 10.1021/bi051187f [doi]
PST - ppublish
SO  - Biochemistry. 2006 Feb 7;45(5):1518-24. doi: 10.1021/bi051187f.