PMID- 20863807
OWN - NLM
STAT- MEDLINE
DCOM- 20110301
LR  - 20240406
IS  - 1096-0309 (Electronic)
IS  - 0003-2697 (Print)
IS  - 0003-2697 (Linking)
VI  - 408
IP  - 2
DP  - 2011 Jan 15
TI  - A modified fluorescent intercalator displacement assay for RNA ligand discovery.
PG  - 269-76
LID - 10.1016/j.ab.2010.09.020 [doi]
AB  - Fluorescent intercalator displacement (FID) is a convenient and practical tool 
      for identifying new nucleic acid-binding ligands. The success of FID is based on 
      the fact that it can be fashioned into a versatile screening assay for assessing 
      the relative binding affinities of compounds to nucleic acids. FID is a tagless 
      approach; the target RNAs and the ligands or small molecules under investigation 
      do not need to be modified in order to be examined. In this study, a modified FID 
      assay for screening RNA-binding ligands was established using 
      3-methyl-2-((1-(3-(trimethylammonio)propyl)-4-quinolinylidene)methyl)benzothiazolium 
      (TO-PRO) as the fluorescent indicator. Electrospray ionization mass spectrometry 
      (ESI-MS) results provide direct evidence that correlates the reduction in 
      fluorescence intensity observed in the FID assay with displacement of the dye 
      molecule from RNA. The assay was successfully applied to screen a variety of 
      RNA-binding ligands with a set of small hairpin RNAs. Ligands that bind with 
      moderate affinity to the chosen RNA constructs (A-site, TAR [transactivation 
      response element], h31 [helix 31], and H69 [helix 69] were identified.
CI  - Copyright (c) 2010 Elsevier Inc. All rights reserved.
FAU - Asare-Okai, Papa Nii
AU  - Asare-Okai PN
AD  - Department of Chemistry, Wayne State University, Detroit, MI 48202, USA.
FAU - Chow, Christine S
AU  - Chow CS
LA  - eng
GR  - R01 GM087596/GM/NIGMS NIH HHS/United States
GR  - GM087596/GM/NIGMS NIH HHS/United States
GR  - R01 GM087596-03/GM/NIGMS NIH HHS/United States
GR  - R01 AI055496-06/AI/NIAID NIH HHS/United States
GR  - R01 AI055496/AI/NIAID NIH HHS/United States
GR  - AI055496/AI/NIAID NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
DEP - 20100921
PL  - United States
TA  - Anal Biochem
JT  - Analytical biochemistry
JID - 0370535
RN  - 0 (Benzothiazoles)
RN  - 0 (Fluorescent Dyes)
RN  - 0 (Intercalating Agents)
RN  - 0 (Ligands)
RN  - 0 (tat Gene Products, Human Immunodeficiency Virus)
RN  - 61JJC8N5ZK (Paromomycin)
RN  - 63231-63-0 (RNA)
RN  - 66974FR9Q1 (Chloramphenicol)
RN  - 9014-25-9 (RNA, Transfer)
SB  - IM
MH  - Benzothiazoles/chemistry
MH  - Chloramphenicol/chemistry
MH  - Fluorescent Dyes/*chemistry
MH  - HIV Long Terminal Repeat
MH  - Intercalating Agents/*chemistry
MH  - *Ligands
MH  - Paromomycin/chemistry
MH  - RNA/*chemistry
MH  - RNA, Transfer/chemistry
MH  - Spectrometry, Mass, Electrospray Ionization/*methods
MH  - tat Gene Products, Human Immunodeficiency Virus/chemistry
PMC - PMC2980581
MID - NIHMS238864
EDAT- 2010/09/25 06:00
MHDA- 2011/03/02 06:00
PMCR- 2012/01/15
CRDT- 2010/09/25 06:00
PHST- 2010/06/30 00:00 [received]
PHST- 2010/09/13 00:00 [accepted]
PHST- 2010/09/25 06:00 [entrez]
PHST- 2010/09/25 06:00 [pubmed]
PHST- 2011/03/02 06:00 [medline]
PHST- 2012/01/15 00:00 [pmc-release]
AID - S0003-2697(10)00592-0 [pii]
AID - 10.1016/j.ab.2010.09.020 [doi]
PST - ppublish
SO  - Anal Biochem. 2011 Jan 15;408(2):269-76. doi: 10.1016/j.ab.2010.09.020. Epub 2010 
      Sep 21.