A Rational Approach to Minimal High-Resolution Cross-Reactive Arrays

Green, Eric; Olah, Mark J.; Abramova, Tatyana V.; Williams, Lance R.; Stefanović, Darko; Worgall, Tilla S.; Stojanović, Milan N.

doi:10.1021/ja0642663

Cited by 41 publications

(42 citation statements)

References 25 publications

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“…Substrate binding selectivity is critical to many applications of aptamers, and previous studies have explored approaches to modulating selectivity through sequence mutation, the incorporation of unnatural bases, or the addition of hydrophobic groups near the binding pocket of the aptamer. 14–17 Due to the nature of these chemical modifications, they typically increase the binding affinity for hydrophobic targets. Thus, the use of surfactants offers a complementary approach to modulating the substrate binding selectivity of aptamers.…”

Section: Introductionmentioning

confidence: 99%

Modulating the Substrate Selectivity of DNA Aptamers Using Surfactants

Peterson

Jahnke²,

Heemstra

2015

Langmuir

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Nucleic acid aptamers have a number of advantages compared to antibodies, including greater ease of production and increased thermal stability. We hypothesized that aptamers may also be capable of functioning in the presence of high concentrations of surfactants, which readily denature antibodies and other protein-based affinity reagents. Here we report the first systematic investigation into the compatibility of DNA aptamers with surfactants. We find that neutral and anionic surfactants have only a minor impact on the ability of aptamers to fold and bind hydrophilic target molecules. Additionally, we demonstrate that surfactants can be utilized to modulate the substrate binding preferences of aptamers, likely due to the sequestration of hydrophobic target molecules within micelles. The compatibility of aptamers with commonly used surfactants is anticipated to expand their scope of potential applications, and the ability to modulate the substrate binding preferences of aptamers using a simple additive provides a novel route to increasing their selectivity in analytical applications.

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Section: Introductionmentioning

confidence: 99%

Modulating the Substrate Selectivity of DNA Aptamers Using Surfactants

Peterson

Jahnke²,

Heemstra

2015

Langmuir

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“…4 The use of DNA (or RNA)-derived aptamers in a multiplexed fashion, although attractive because of the large number of new sequences and structures that are potentially synthesizable, has to date only been foreshadowed. Green et al 5 describe the use of a cross-reactive array of oligonucleotide aptamer to maximize the differential response of the sensors to closely allied molecules.…”

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confidence: 99%

Aptamer-Mediated Surface-Enhanced Raman Spectroscopy Intensity Amplification

2010

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A bifunctional adenosine-sensitive double-stranded DNA aptamer was used to create and control a surface-enhanced Raman spectroscopy (SERS) hot spot between a bulk Au surface and a gold nanoparticle (Au NP) attached to the aptamer via a biotin-avidin linkage. The Au NP was decorated with 4-aminobenzenethiol (4-ABT), a Raman reporter molecule. In the presence of adenosine, the target molecule, the SERS spectrum of 4-ABT increased in intensity by (concentration-dependent) factors as large as ∼4; in situ, atomic force microscopy imaging showed the mean height of the Au NP-bearing aptamer to decrease by ∼5 nm consistent with the observed SERS intensity change. Because the aptamer's geometrical change is induced by one or two molecules, while the resulting SERS intensity changes involve many reporter molecules residing in the modified hot spot, the aptamer amplifies the SERS effect.

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“…Finally, another method based on an iterative algorithm has also been proposed in the literature [87] Figure 17.11 Flowchart of the procedure for the sensor array size optimization. In this case, the algorithm will yield a sensor array with accuracy greater than 95%, but the accuracy threshold can be adjusted to any desired level.…”

Section: Principal Component Analysismentioning

confidence: 99%