Dynamics of an anti-VEGF DNA aptamer: A single-molecule study

Taylor, Joshua P.; Darugar, Qusai; Kourentzi, Katerina; Willson, Richard C.; Landes, Christy F.

doi:10.1016/j.bbrc.2008.05.191

Cited by 38 publications

(55 citation statements)

References 33 publications

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“…The sites tagged with the donor and acceptor fluorophores are T394C and S652C, similar to those used in our previous smFRET investigations (30). The smFRET data from a number of such traces (170 -210 traces) for each willardiine were then processed for background and cross-talk correction (35,36) and denoised using wavelet decomposition as described previously (37). The data were then plotted as histograms of fraction of occurrence versus the FRET efficiency to determine the spread of states that the protein explores (Fig.…”

Section: Resultsmentioning

confidence: 99%

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Role of Conformational Dynamics in α-Amino-3-hydroxy-5-methylisoxazole-4-propionic Acid (AMPA) Receptor Partial Agonism

Ramaswamy¹,

Cooper

Poddar

et al. 2012

Journal of Biological Chemistry

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Section: Resultsmentioning

confidence: 99%

“…Experimental Setup for smFRET-All single-molecule fluorescence measurements were performed using a custom built confocal microscope (35,36). A 532-nm diode-pumped solid state laser (Coherent, Compass 315M-100 SL) was used for sample excitation.…”

Section: Purification and Labeling Of The Agonist-binding Domain Of Gmentioning

confidence: 99%

Role of Conformational Dynamics in α-Amino-3-hydroxy-5-methylisoxazole-4-propionic Acid (AMPA) Receptor Partial Agonism

Ramaswamy¹,

Cooper

Poddar

et al. 2012

Journal of Biological Chemistry

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“…Additionally, the above concentrations of the specific agonistbinding domain ligand, depending on the experimental conditions, was included in the buffer solution. The custom-built confocal microscope (Zeiss Axiovert 200 M) described previously was used for all smFRET measurements (27,28). A 532-nm diode-pumped solid-state laser (Coherent, Compass 315M-100 SL) focused through a FLUAR 100 ϫ 1.3 NA oil immersion microscope objective lens (Carl Zeiss, GmbH) to a power density of 50 watts/cm 2 at the sample was used to excite the sample.…”

Section: Methodsmentioning

confidence: 99%

“…4, a-e). Donor and acceptor photon counts of excited proteins were measured with millisecond resolution, collected into 10-ms bins for efficiency determination, denoised using wavelet decomposition, and then plotted as separate histograms as described previously (16,17,28).…”

Section: Cysteine Labeling Versus Unnatural Amino Acid Labeling-mentioning

confidence: 99%

Structural Dynamics of the Glycine-binding Domain of the N-Methyl-d-Aspartate Receptor

Dolino¹,

Cooper

Ramaswamy³

et al. 2015

Journal of Biological Chemistry

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Background:The agonist glycine binds to a cleft in the bilobed extracellular domain of NMDA receptors. Results: The full agonist-bound forms of the agonist-binding domain populate more of the higher efficiency closed-cleft states of the receptor. Conclusion: Cleft closure dynamics differ for the full and partial agonist-bound forms. Significance: Dynamics and the extent of cleft closure control agonist efficacy.

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“…Nucleic acids, especially RNAs, have diverse functions in living organisms that frequently involve conformational rearrangements during ligand binding and signaling, cotranscriptional folding, catalysis in ribozymes, and the assembly of ribonucleoproteins (Al-Hashimi and Walter 2008;Nick Taylor et al 2008;Forster et al 2012). Molecules that interfere with the activity of any of these RNAs are potential drugs, particularly if they can distinguish between eukaryotic and prokaryotic RNAs.…”

Section: Introductionmentioning

confidence: 99%

An adaptable pentaloop defines a robust neomycin-B RNA aptamer with conditional ligand-bound structures

İlgü

Fulton²,

Yennamalli

et al. 2014

RNA

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Aptamers can be highly specific for their targets, which implies precise molecular recognition between aptamer and target. However, as small polymers, their structures are more subject to environmental conditions than the more constrained longer RNAs such as those that constitute the ribosome. To understand the balance between structural and environmental factors in establishing ligand specificity of aptamers, we examined the RNA aptamer (NEO1A) previously reported as specific for neomycin-B. We show that NEO1A can recognize other aminoglycosides with similar affinities as for neomycin-B and its aminoglycoside specificity is strongly influenced by ionic strength and buffer composition. NMR and 2-aminopurine (2AP) fluorescence studies of the aptamer identified a flexible pentaloop and a stable binding pocket. Consistent with a wellstructured binding pocket, docking analysis results correlated with experimental measures of the binding energy for most ligands. Steady state fluorescence studies of 2AP-substituted aptamers confirmed that A16 moves to a more solvent accessible position upon ligand binding while A14 moves to a less solvent accessible position, which is most likely a base stack. Analysis of binding affinities of NEO1A sequence variants showed that the base in position 16 interacts differently with each ligand and the interaction is a function of the buffer constituents. Our results show that the pentaloop provides NEO1A with the ability to adapt to external influences on its structure, with the critical base at position 16 adjusting to incorporate each ligand into a stable pocket by hydrophobic interactions and/or hydrogen bonds depending on the ligand and the ionic environment.

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Dynamics of an anti-VEGF DNA aptamer: A single-molecule study

Cited by 38 publications

References 33 publications

Role of Conformational Dynamics in α-Amino-3-hydroxy-5-methylisoxazole-4-propionic Acid (AMPA) Receptor Partial Agonism

Role of Conformational Dynamics in α-Amino-3-hydroxy-5-methylisoxazole-4-propionic Acid (AMPA) Receptor Partial Agonism

Structural Dynamics of the Glycine-binding Domain of the N-Methyl-d-Aspartate Receptor

An adaptable pentaloop defines a robust neomycin-B RNA aptamer with conditional ligand-bound structures

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