Characterizing Aptamers with Reconfigurable Chiral Plasmonic Assemblies

Huang, Yike; Nguyen, Minh‐Kha; Nguyen, Vu; Loo, Jacky Fong‐Chuen; Lehtonen, Arttu J.; Kuzyk, Anton

doi:10.1021/acs.langmuir.1c03434

Cited by 6 publications

(18 citation statements)

References 48 publications

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“…We estimated the K D2 as 0.139 μM using the system parameter described in the previous study. 25 The absolute value of the K D4 was calculated as 5.1 mM, similar to the values reported in the literature. 25,44 Then, the RNA ATP aptamer was investigated with the same workflow.…”

Section: Incorporation Of Oligonucleotides Of Interest (Oni)supporting

confidence: 77%

“…For thermodynamic experiments, the samples of ONI-DNA origami-AuNRs were incubated in 70 μL reaction buffer containing different ■ RESULTS AND DISCUSSION Incorporation of Oligonucleotides of Interest. Previously, ONI-like sequences were often incorporated during the DNA origami assembly (one-step method), 31,3,25 followed by the AuNRs attachment (SI, Figure S1A). Here, we altered the fabrication process by inserting the ONI directly into the assembled DNA origami-AuNRs reporters (two-step method; SI, Figure S1B).…”

Section: Incorporation Of Oligonucleotides Of Interest (Oni)mentioning

confidence: 99%

“…The probes generate strong circular dichroism (CD) signals at the chiral state and weak CD signals at the relaxed state. The high CD signal and the high signal-to-noise ratio of the probe allows for the reliable characterization of the equilibrium populations of the hybridized and separated states of the aptamer and the complementary strand . Moreover, to maximize the yield and to minimize the possible denaturation of RNA during high temperature annealing in a high salt condition, we incorporated the oligonucleotides of interest (ONI), which are comprised of a pair of aptamer and complementary strand, into the assembled DNA origami-AuNR reporter (Figure D).…”

Section: Introductionmentioning

confidence: 99%

“…24 The essential domain can be further divided into Previously, we developed a competitive hybridization-based approach for characterizing DNA aptamers and provided a thermodynamic model, in which the Gibbs free energies of the hybridization between partial complementary strands and the aptamer were varied to generate various equilibrium states, and the coefficient of determination was used to gain insights into the aptamer domain and to validate the obtained K D values. 25 This method, however, relies on the accurate estimation of the Gibbs free energy of the aptamer−complementary strand hybridization. For DNA−DNA hybridization, the Gibbs free energy can be obtained by the computational tools, such as mfold 26 or NUPACK.…”

Section: ■ Introductionmentioning

confidence: 99%

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Measuring the Affinities of RNA and DNA Aptamers with DNA Origami-Based Chiral Plasmonic Probes

et al. 2022

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Reliable characterization of binding affinities is crucial for selected aptamers. However, the limited repertoire of universal approaches to obtain the dissociation constant (K D) values often hinders the further development of aptamer-based applications. Herein, we present a competitive hybridization-based strategy to characterize aptamers using DNA origami-based chiral plasmonic assemblies as optical reporters. We incorporated aptamers and partial complementary strands blocking different regions of the aptamers into the reporters and measured the kinetic behaviors of the target binding to gain insights on aptamers’ functional domains. We introduced a reference analyte and developed a thermodynamic model to obtain a relative dissociation constant of an aptamer–target pair. With this approach, we characterized RNA and DNA aptamers binding to small molecules with low and high affinities.

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Section: Incorporation Of Oligonucleotides Of Interest (Oni)supporting

confidence: 77%

Section: Incorporation Of Oligonucleotides Of Interest (Oni)mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

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Measuring the Affinities of RNA and DNA Aptamers with DNA Origami-Based Chiral Plasmonic Probes

et al. 2022

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“…Affimers have unlimited possibilities either in diagnosis or antiviral, antibacterial and antifungal treatment. Diverse modifications, including conjugations can increase a short half-life time of aptamers ( Huang et al, 2022 ).…”

Section: Landscape Of Opportunities: Topical Insightsmentioning

confidence: 99%

Smart therapies against global pandemics: A potential of short peptides

et al. 2022

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BackgroundAs we entered the third year of this pandemic, since the World Health Organisation (WHO) declared in March 2020 the novel coronavirus severe acute respiratory syndrome (SARS-CoV2) outbreak as a global pandemic COVID-19 (COronaVIrus Disease 19), we are still fighting with newer and newer viral mutations. The pandemic has passed the grim milestone of over 6.4 million COVID19 deaths, from more than 550 million reported cases thus far. In fact, more than 15 million people can die by the end of this year. It is highly likely that this pandemic will become endemic, while the full evolutionary potential of coronaviruses has yet to be revealed. The next pandemic is coming. A microbe with features of SARS-Middle East respiratory syndrome (MERS) and SARS-CoV-2 could lead to significantly more catastrophic loss of life. The co-evolution with other viruses should not be neglected. According to the WHO, we should expect diverse zoonotic, outbreakprone microbes, including highly pathogenic strains of influenza, Nipah, Ebola, Zika, or hemorrhagic fever viruses. 'It's an evolutionary certainty that there will be another virus with the potential to be more transmittable and deadly than this one', said Tedros Adhanom Ghebreyesus, director-general of the WHO. On the other hand, in both poor countries and regions of armed conflict, where vaccination is hampered, historic diseases are re-emerging, with migration and displacement influencing transmission risk and limiting control, and raising potential for additional outbreaks. Furthermore, there are other looming terrible threats to humanity as damaging as the bubonic plagues, such as bioterrorism or antibiotic resistant microorganisms. In most cases, both effective prevention and treatment options are limited.

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Rational design enabling aptamer‐based sensors for surface‐enhanced Raman detection of small molecules

Kissell,

Sheokand,

Strobbia

2023

J Raman Spectroscopy

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Homogeneous surface‐enhanced Raman scattering (SERS) sensors could have a significant impact in environmental analysis. The reagentless mechanism of these sensors makes them capable for in situ analysis and continuous monitoring of environmental pollutants, without having to collect environmental samples for laboratory analysis. Homogeneous SERS sensors take advantage of functional DNA strands on the surface of a SERS‐active particle. These sensors are commonly used for the detection of genomic targets. A clear path to adapt these homogeneous sensors to detect small molecules is to employ aptamer sequences. In particular, the use of duplex aptamer can make these sensors highly adaptable to different target molecules. Although there have been examples of SERS duplex aptamer sensors to detect small molecules, the design rules for this type of sensors have not been elucidated. Without design rules or a design protocol, we would not be able to fully take advantage of the adaptability of this approach to focus on new targets and applications (e.g., environmental analysis). Herein, we aim to define a protocol for the design of aptamer‐based homogeneous SERS sensors. First, we demonstrate their nonequilibrium character and the necessary length for the complementary element for the sensors to work. We demonstrate the design protocol on a well‐characterized aptamer sequence for ATP binding and then transfer the knowledge gained on an aptamer for estradiol, a common water contaminant. In this work, we establish the design protocol for a short aptamer (i.e., ATP) and analyze the issues and remedies associated with extending this protocol to longer aptamer sequences (e.g., E2).

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Characterizing Aptamers with Reconfigurable Chiral Plasmonic Assemblies

Cited by 6 publications

References 48 publications

Measuring the Affinities of RNA and DNA Aptamers with DNA Origami-Based Chiral Plasmonic Probes

Measuring the Affinities of RNA and DNA Aptamers with DNA Origami-Based Chiral Plasmonic Probes

Smart therapies against global pandemics: A potential of short peptides

Rational design enabling aptamer‐based sensors for surface‐enhanced Raman detection of small molecules

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