Structural Changes of Mercaptohexanol Self-Assembled Monolayers on Gold and Their Influence on Impedimetric Aptamer Sensors

Xu, Xingxing; Makaraviciute, Asta; Kumar, Shalen; Wen, Chenyu; Sjödin, Martin; Abdurakhmanov, Eldar; Danielson, U. Helena; Nyholm, Leif; Zhang, Zhen

doi:10.1021/acs.analchem.9b03946

Cited by 59 publications

(63 citation statements)

References 35 publications

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“…221,234,239 In our case, using catalysts is not suitable for the desired final system, indeed, they are molecules that may interact with DNA strands, and they must be removed from the system. As discussed previously in Xu et al 120 , the increase of the reaction temperature is not appropriate for the production of a highly ordered SAM. By deduction, the initial thiolated aptamer concentration incubated parameter will be explored for trying to optimize the kinetics of fixation of the DNA strands on the gold surface.…”

Section: The Sam Affords a Better Stability Upon Higher Thiolated Aptamer Concentration Incubatedmentioning

confidence: 96%

“…While its high sensitivity, its large amount of data acquired on the system, and its steady-state measurement, a signal drift related to buffer incubation occur with a self-assembled monolayer (SAM) composed of thiolated aptamer and backfiller molecules such as MCH. 120 A lack of understanding of the signal drift source is observed. The mechanism of SAM creation is a complex mechanism that involves different steps.…”

Section: Limited Stability and Aptamer Density On Gold Electrode With Current Sam Protocolsmentioning

confidence: 99%

“…84,88,208 The signal drift related to the buffer incubation, in the specific system used, has already been observed and studied. 120,121,215,228,229 Vogt et al 229 and Lazar et al 228 assigned the instability observed to the etching of the gold electrode surface because of the adsorption of the cyanide molecules coming from the redox couple potassium ferri/ferrocyanide (ferri/ferro) used as an electrolyte for the EIS experiments. In their studies, a long incubation time of the gold electrode in the ferri/ferro electrolyte has been used.…”

Section: The Separated Fixation Of 1 µM Thiolated Aptamer and 1 MM Mch Produces An Important Signal Drift Related To The Buffer Incubatiomentioning

confidence: 99%

“…By contrast here, the duration of incubation in the ferri/ferro electrolyte is approximately 2 min (one EIS measurement), thus the effect of cyanide adsorption resulting in the etching of the gold electrode surface is minimized and consequently negligible. Xu et al 120 showed the influence of the temperature on the organization of the SAM and proved that the use of high-temperature induces a re-organization of the SAM formed, resulting in an EIS signal drift measured. Here, the temperature is kept constant at 20 °C (+-5 °C), thus, the SAM re-organization due to the temperature is avoided.…”

Section: The Separated Fixation Of 1 µM Thiolated Aptamer and 1 MM Mch Produces An Important Signal Drift Related To The Buffer Incubatiomentioning

confidence: 99%

“…Numerous drawbacks appear related to the two-step protocol such as the disorganization of the SAM formed resulting in a signal drift related to the buffer incubation. 120,121,215,228,229 Long thiolated aptamers afford two adsorption interactions with the gold surface: chemisorption between the sulfur and the gold, and physisorption between the nitrogen-rich DNA strand and the gold surface. 84,121,221 The latter interaction creates a "lying-down" structure (striped phase).…”

Section: Introductionmentioning

confidence: 99%

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Electrochemical aptasensors: unravelling the critical interactions between aptamers, ligands, and electrodes

Sester¹

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Aptamers are synthetic nucleic acid single-stranded oligonucleotides that bind to a wide range of ligands, including cells, proteins, DNA strands, metal ions, and small molecules, with high specificity and affinity. Aptamers have also proven to be highly stable, readily adaptable to chemical modifications, and exhibit reversible binding. As a result, aptamer-based biosensors (aptasensors) are promising replacements for antibody-based biosensors in many applications, particularly for small molecule ligands. This thesis explores an aptamer that binds the drug methamphetamine, and its prospects when incorporated in an electrochemical (e-chem) signal transduction platform. Specifically, we examine the range of interactions between the aptamer and ligand, and with electrodes, and identify a number of challenges in generating robust e-chem aptasensors. Due to their size and limited number of functional groups, further understanding of the aptamer-small molecule ligand interactions is required for the design of future aptasensors – particularly the thermodynamics and structural information about the aptamer-ligand interaction. In fact, detecting small molecules with aptasensors can become challenging because target addition may induce little structural change, and therefore numerous nonspecific interactions may emerge as transduced signals from the biosensor. In this thesis, the combination of spectroscopic and calorimetric analytical techniques reveals a conformational selection binding model, in which binding is entropically driven, and the meth binds via hydrophobic and electrostatic interactions and only induces a modest structural change. This first-of-its-kind study is important for the selection and the design of the aptasensor transduction system. Electrochemical (e-chem) aptasensors offer high inherent sensitivity and practicality as a signal transduction platform. Indeed, different e-chem aptasensor formats have been published before, including labelled and label-free sensors. In screening the viability of three commonly used methods – including labelled and label-free, as well voltammetric and impedance-based methods – we find that each of them suffers from instability of the aptamer-functionalised electrode. This instability compromises our ability to resolve real signals and prompted us to develop ways to understand – and suppress – this baseline drift. The functionalization of the electrode is the critical step in terms of self-assembled monolayer (SAM) stability and SAM aptamer density. Consequently, different protocols of SAMformation were explored and evaluated with respect to stability. We find that instability arises from the uncontrolled arrangement of thiolated aptamers on gold electrodes (including aptamers lying down on the electrode), which is in turn affected by the density of aptamers that can be coupled to the surface. As a consequence, a new protocol is developed using disulfide aptamer pairs to increase the density of correctly tethered aptamers, and generate a stable SAM. Because of the high sensitivity of electrochemical platforms, numerous spurious electrochemical signals may be produced, and controlled for in order to confirm a positive ligand-binding signal. The specificity of the aptamer-target interaction can be checked by testing the response with an interferent molecule, or by substituting the aptamer with a non-binding nucleotide sequence. In this work, these control experiments reveal that target and interferent molecules interact directly (and in different ways) with the bare gold surface, as well as perturbing signals from the aptamer in ways that cannot be linked to a specific aptamer-ligand complex formation. Ultimately, these spurious signals compromise our ability to confirm a real binding signal. The results from this work provide the first clear picture of how an aptamer binds to its small molecule target – which we find is entropically driven, and with only minor structural change induced in the aptamer stem. In addition, the label-free EIS measurements on aptamer SAM electrodes reveal the nature of instabilities, and reveal spurious signals that cannot be sufficiently suppressed at this stage. This knowledge highlights the difficulty in fabricating e-chem aptasensors, and will assist in overcoming challenges faced during research and commercialization of aptasensors area, as well as contributing new insights into troubleshooting, data acquisition, and data validation.

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Section: The Sam Affords a Better Stability Upon Higher Thiolated Aptamer Concentration Incubatedmentioning

confidence: 96%

Section: Limited Stability and Aptamer Density On Gold Electrode With Current Sam Protocolsmentioning

confidence: 99%

Section: The Separated Fixation Of 1 µM Thiolated Aptamer and 1 MM Mch Produces An Important Signal Drift Related To The Buffer Incubatiomentioning

confidence: 99%

Section: The Separated Fixation Of 1 µM Thiolated Aptamer and 1 MM Mch Produces An Important Signal Drift Related To The Buffer Incubatiomentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Electrochemical aptasensors: unravelling the critical interactions between aptamers, ligands, and electrodes

Sester¹

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Role of Nanoscale Roughness and Polarity in Odd–Even Effect of Self‐Assembled Monolayers

Wang

Martin

et al. 2022

Angewandte Chemie

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The dependency of substrate roughness on wetting properties of self‐assembled monolayers (SAMs) has been studied extensively, but most previous studies used limited selection of probing liquid and range of surface roughness. These studies disregarded the limit to observation of sub‐nanometer odd–even parity effect, hence are inconclusive. In this work we report the role of solvent polarity on the roughness‐dependency of wetting behavior of SAMs by studying static con‐tact angle of a variety of probing liquids, with different polarities, on SAMs formed on Ag‐based substrate with different surface morphology. By overlapping the roughness ranges with previous studies on Au, the limitation of surface roughness (RMS=1 nm) to observation of the odd–even effect using water as probing liquid was confirmed, but other probing liquid yielded different roughness‐dependent behaviors, with more polar solvent showing more roughness‐dependent behavior. Based on these observations, we concluded that there exists a phase‐transition like behavior in SAMs due to substrate roughness and molecule chain length, but whose determination is dependent on the probing liquid.

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Highly Uniform DNA Monolayers Generated by Freezing‐Directed Assembly on Gold Surfaces Enable Robust Electrochemical Sensing in Whole Blood

Li,

Lv,

Duan

et al. 2023

Angewandte Chemie

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Assembling DNA on solid surfaces is fundamental to surface‐based DNA technology. However, precise control over DNA conformation and organization at solid–liquid interfaces remains a challenge, resulting in limited stability and sensitivity in biosensing applications. We herein communicate a simple and robust method for creating highly uniform DNA monolayers on gold surfaces by a freeze‐thawing process. Using Raman spectroscopy, fluorescent imaging, and square wave voltammetry, we demonstrate that thiolated DNA is concentrated and immobilized on gold surfaces with an upright conformation. Moreover, our results reveal that the freezing‐induced DNA surfaces are more uniform, leading to improved DNA stability and target recognition. Lastly, we demonstrate the successful detection of a model drug in undiluted whole blood while mitigating the effects of biofouling. Our work not only provides a simple approach to tailor the DNA‐gold surface for biosensors but also sheds light on the unique behavior of DNA oligonucleotides upon freezing on the liquid‐solid interface.

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Structural Changes of Mercaptohexanol Self-Assembled Monolayers on Gold and Their Influence on Impedimetric Aptamer Sensors

Cited by 59 publications

References 35 publications

Electrochemical aptasensors: unravelling the critical interactions between aptamers, ligands, and electrodes

Electrochemical aptasensors: unravelling the critical interactions between aptamers, ligands, and electrodes

Role of Nanoscale Roughness and Polarity in Odd–Even Effect of Self‐Assembled Monolayers

Highly Uniform DNA Monolayers Generated by Freezing‐Directed Assembly on Gold Surfaces Enable Robust Electrochemical Sensing in Whole Blood

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