Multivalency in the recognition and antagonism of a HIV TAR RNA–TAT assembly using an aminoglycoside benzimidazole scaffold

Kumar, Sunil; Ranjan, Nihar; Kellish, Patrick; Gong, Changjun; Watkins, Davita L.; Arya, Dev P.

doi:10.1039/c5ob02016f

Cited by 36 publications

(27 citation statements)

References 42 publications

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“…Syntheses of compounds 1 , 2 , 3 , and 7 were previously reported (46). Compounds 4 – 6 (68), 11 (69), and 12 (70) were synthesized according to literature procedures.…”

Section: Methodsmentioning

confidence: 99%

Surface ligands in the imprinting and binding of molecularly imprinted cross-linked micelles

Arifuzzaman

Zhao

2018

Supramolecular Chemistry

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Molecular recognition in water is challenging but water-soluble molecularly imprinted nanoparticle (MINP) receptors were produced readily by double cross-linking of surfactant micelles in the presence of suitable template molecules. When the micellar surface was decorated with different polyhydroxylated ligands, significant interactions could be introduced between the surface ligands and the template. Flexible surface ligands worked better than rigid ones to interact with the polar moiety of the template, especially for those template molecules whose water-exposed surface is not properly solvated by water. The importance of these hydrophilic interactions was examined in the context of different substrates, density of the surface ligands, and surface-cross-linking density of the MINP. Together with the hydrophobic interactions in the core, the surface hydrophilic interactions can be used to enhance the binding of guest molecules in water.

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“…Syntheses of compounds 1 , 2 , 3 , and 7 were previously reported (46). Compounds 4 – 6 (68), 11 (69), and 12 (70) were synthesized according to literature procedures.…”

Section: Methodsmentioning

confidence: 99%

Surface ligands in the imprinting and binding of molecularly imprinted cross-linked micelles

Arifuzzaman

Zhao

2018

Supramolecular Chemistry

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“…AGs also interact with a number of other RNA targets. These include secondary rRNA sites [3], natural riboswitches [4], group I introns [5], and several retroviral RNA elements [6][7][8][9]. Binding stems from the ability of these positively-charged amino-rich AGs to form electrostatic interactions with the negatively-charged phosphate groups of the RNA [10], and to a lesser extent from hydrogen bonding involving the amino and hydroxyl groups of AGs [11].…”

Section: Introductionmentioning

confidence: 99%

Modified Aminoglycosides Bind Nucleic Acids in High-Molecular-Weight Complexes

et al. 2020

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Aminoglycosides represent a large group of antibiotics well known for their ability to target the bacterial ribosome. In studying 6”-substituted variants of the aminoglycoside tobramycin, we serendipitously found that compounds with C12 or C14 linear alkyl substituents potently inhibit reverse transcription in vitro. Initial observations suggested specific inhibition of reverse transcriptase. However, further analysis showed that these and related compounds bind nucleic acids with high affinity, forming high-molecular weight complexes. Stable complex formation is observed with DNA or RNA in single- or double-stranded form. Given the amphiphilic nature of these aminoglycoside derivatives, they likely form micelles and/or vesicles with surface-bound nucleic acids. Hence, these compounds may be useful tools to localize nucleic acids to surfaces or deliver nucleic acids to cells or organelles.

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“…The binding of neomycin, and other aminoglycosides drugs, to bacterial RNA affects the production of proteins through miscoding in translation, ultimately leading to bacterial death. 2–5 In addition to binding to ribosomal RNA, aminoglycosides have been shown to bind numerous other RNA, 6–10 DNA, 11–17 hybrid duplex, 18,19 triplex 20–23 and quadruplex 24–26 structures of therapeutic interest. 27 …”

Section: Introductionmentioning

confidence: 99%

Utilization of chromic polydiacetylene assemblies as a platform to probe specific binding between drug and RNA

et al. 2017

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Recognition of nucleic acids remains an important endeavor in biology. Nucleic acids adopt shapes ranging from A-form (RNA and GC rich DNA) to B-form (AT rich DNA). We show, in this contribution, shape-specific recognition of A-U rich RNA duplex by a neomycin (Neo)-polydiacetylene (PDA) complex. PDA assemblies are fabricated by using a well-known diacetylene (DA) monomer, 10,12-pentacosadiynoic acid (PCDA). The response of poly(PCDA) assemblies is generated by mixing with a modified neomycin-PCDA monomer (Neo-PCDA). The functionalization by neomycin moiety provides specific binding with homopolyribonucleotide poly (rA) - poly (rU) stimulus. Various types of alcohols are utilized as additives to enhance the sensitivity of poly(PCDA)/Neo-PCDA assemblies. A change of absorption spectra is clearly observed when a relatively low concentration of poly (rA)-poly (rU) is added into the system. Furthermore, poly(PCDA)/Neo-PCDA shows a clear specificity for poly (rA)-poly (rU) over the corresponding DNA duplex. The variation of linker between neomycin moiety and conjugated PDA backbone is found to significantly affect its sensitivity. We also investigate other parameters including the concentration of Neo-PCDA and the DA monomer structure. Our results provide here preliminary data for an alternative approach to improve the sensitivity of PDA utilized in biosensing and diagnostic applications.

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Multivalency in the recognition and antagonism of a HIV TAR RNA–TAT assembly using an aminoglycoside benzimidazole scaffold

Cited by 36 publications

References 42 publications

Surface ligands in the imprinting and binding of molecularly imprinted cross-linked micelles

Surface ligands in the imprinting and binding of molecularly imprinted cross-linked micelles

Modified Aminoglycosides Bind Nucleic Acids in High-Molecular-Weight Complexes

Utilization of chromic polydiacetylene assemblies as a platform to probe specific binding between drug and RNA

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