Modified-RNA Aptamer-Based Sensor for Competitive Impedimetric Assay of Neomycin B

de‐los‐Santos‐Álvarez, Noemí; Lobo-Castañón, Marı́a Jesús; Miranda-Ordieres, and Arturo J.; Tuñón‐Blanco, Paulino

doi:10.1021/ja0689482

Cited by 112 publications

(84 citation statements)

References 18 publications

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“…RNA aptamers that specifically bound to neomycin-B over paromomycin were identified by in vitro selection (Wallis et al 1995) and this aptamer-ligand interaction has been studied intensively (Wallis and Schroeder 1997;Cowan et al 2000;de-los-Santos-Alvarez et al 2007Stampfl et al 2007). With the intent to use NEO1A in synthetic biology applications that would require that the aptamer be functional in the cell cytoplasm, we examined the interaction of NEO1A with its ligands in Buffer A that emulates the free ion concentrations of the mammalian cell cytoplasm.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

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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Section: Discussionmentioning

confidence: 99%

“…The complex is stabilized by electrostatic and Hbonding interactions (Wallis and Schroeder 1997;Cowan et al 2000;de-los-Santos-Alvarez et al 2007Stampfl et al 2007). Our NMR results (performed in a similar buffer as the original study) are consistent with the reported structure of the neomycin-B-NEO1A complex.…”

Section: Discussionmentioning

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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“…Wang & Rando, 1995) Tobramycin 2'-OMe-RNA Electrochemical (Impedence) 0.7 µM (González-Fernández et al, 2011) RNA 180 -- (Kwon et al, 2001) Kanamycin RNA 10-30 -- (Goertz, Colin Cox Ellington, 2004b) RNA Low nM -- (Goertz, Colin Cox Ellington, 2004b) RNA 1800 -- (Cowan et al, 2000) Electrochemical (Impedence) "sub µM" (de-los-Santos-Alvarez et al, 2007) Neomycin 2'-OMe-RNA Surface Plasmon Resonance (SPR) 10 nM (de-los-Santos-Álvarez et al, 2009) - (Cruz-Aguado & Penner, 2008a) Fluorescence Polarization 5 nM (Cruz-Aguado & Penner, 2008b) Electrochemical 30 pg/mL (Kuang et al, 2010) Electrochemiluminescent 0.007 ng/mL (Z. Wang et al, 2010) Mycotoxins Ochratoxin A DNA 200…”

Section: Aminoglycosidesmentioning

confidence: 99%

Advances in Aptamer-Based Biosensors for Food Safety

McKeague¹,

Giamberardino²,

DeRosa³

2011

Environmental Biosensors

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“…FIS transduction is especially well suited to detect changes that occur in the solution-electrode interface without the need of labels. This technique was one of the first used for electrochemical transduction of the aptamer-ligand recognition event for small molecules [27], where the associated conformational change can be too small to cause a significant variation in a physical property of appropriate labels such as the case of antibiotics [28,29]. But it can also be used for the detection of large molecules [30][31][32] or whole cells [33].…”

Section: Introductionmentioning

confidence: 99%

A label-free DNA aptamer-based impedance biosensor for the detection of E. coli outer membrane proteins

Queirós

de‐los‐Santos‐Álvarez

Noronha

et al. 2013

Sensors and Actuators B: Chemical

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a b s t r a c tA label-free DNA aptamer-based impedance biosensor for the detection of E. coli outer membrane proteins (OMPs) was developed. Two single stranded DNA sequences were tested as recognition elements and compared. The aptamer capture probes were immobilized, with and without 6-mercapto-1-hexanol (MCH) on a gold electrode. Each step of the modification process was characterized by Faradaic impedance spectroscopy (FIS). A linear relationship between the electron-transfer resistance (R et ) and E. coli OMPs concentration was demonstrated in a dynamic detection range of 1 × 10 −7 -2 × 10 −6 M. Moreover, the aptasensor showed selectivity despite the presence of other possible water contaminates and could be regenerated under low pH condition. The developed biosensor shows great potential to be incorporated in a biochip and used for in situ detection of E. coli OMPs in water samples.

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Modified-RNA Aptamer-Based Sensor for Competitive Impedimetric Assay of Neomycin B

Cited by 112 publications

References 18 publications

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

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

Advances in Aptamer-Based Biosensors for Food Safety

A label-free DNA aptamer-based impedance biosensor for the detection of E. coli outer membrane proteins

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