ArticleNucleic acids research2013
Thermodynamic studies of a series of homologous HIV-1 TAR RNA ligands reveal that loose binders are stronger Tat competitors than tight ones.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Electrostatic Anchoring in RNA-Ligand Design─Dissecting the Effects of Positive Charges on Affinity, Selectivity, Binding Kinetics, and Thermodynamics.Journal of medicinal chemistry · 2025Article
- Targeting structural features of viral genomes with a nano-sized supramolecular drug.Chemical science · 2021Article
- Triplex-Forming Peptide Nucleic Acids with Extended Backbones.Chembiochem : a European journal of chemical biology · 2020Article
- Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA-Small Molecule Interactions.ACS chemical biology · 2019Review
- Insights into the development of chemical probes for RNA.Nucleic acids research · 2018Article
- Development of Small Molecules with a Noncanonical Binding Mode to HIV-1 Trans Activation Response (TAR) RNA.Journal of medicinal chemistry · 2016Article
- On the Applicability of Elastic Network Models for the Study of RNA CUG Trinucleotide Repeat Overexpansion.PloS one · 2016Article
- Tetracycline determines the conformation of its aptamer at physiological magnesium concentrations.Biophysical journal · 2014Article
- Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore.Nucleic acids research · 2014Article
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Authors and funding
7 authors.
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Abstract
RNA is a major drug target, but the design of small molecules that modulate RNA function remains a great challenge. In this context, a series of structurally homologous 'polyamide amino acids' (PAA) was studied as HIV-1 trans-activating response (TAR) RNA ligands. An extensive thermodynamic study revealed the occurence of an enthalpy-entropy compensation phenomenon resulting in very close TAR affinities for all PAA. However, their binding modes and their ability to compete with the Tat fragment strongly differ according to their structure. Surprisingly, PAA that form loose complexes with TAR were shown to be stronger Tat competitors than those forming tight ones, and thermal denaturation studies demonstrated that loose complexes are more stable than tight ones. This could be correlated to the fact that loose and tight ligands induce distinct RNA conformational changes as revealed by circular dichroism experiments, although nuclear magnetic resonance (NMR) experiments showed that the TAR binding site is the same in all cases. Finally, some loose PAA also display promising inhibitory activities on HIV-infected cells. Altogether, these results lead to a better understanding of RNA interaction modes that could be very useful for devising new ligands of relevant RNA targets.
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