Structural characterization of the saxitoxin-targeting APTSTX1 aptamer using optical tweezers and molecular dynamics simulations

Casanova-Morales, Nathalie; Figueroa, Nataniel L.; Alfaro, Karol; Montenegro, Felipe; Barrera, Nelson P.; Maze, J. R.; Wilson, Christian A.M.; Conejeros, Pablo

doi:10.1371/journal.pone.0222468

Cited by 5 publications

(3 citation statements)

References 47 publications

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“…Another possibility to attach the protein of interest to polystyrene beads is using DNA handles (Ramírez et al ., 2017). This approach can be used for studying interactions between proteins (Ramírez et al ., 2017) and non-protein molecules like aptamers (Casanova-Morales et al ., 2019). DNA handles are constructs between 500 and 1500 bp (Cecconi et al ., 2008; Kaiser et al ., 2011) that act as linkers between the protein and the bead (Halvorsen et al ., 2011).…”

Section: Detailed Description Of Intermolecular Interaction Force Exp...mentioning

confidence: 99%

“…Naturally, this assay can be used to study the binding between other kinds of molecules. For example, a refolding and unfolding experiment was used to study the dynamics of APTSTX1–aptamer, a single-stranded DNA molecule with a high affinity for saxitoxin (STX), a lethal neurotoxin (Casanova-Morales et al ., 2019).…”

Section: Detailed Description Of Intermolecular Interaction Force Exp...mentioning

confidence: 99%

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Determination of protein–protein interactions at the single-molecule level using optical tweezers

Sanchez

Robeson

Carrasco

et al. 2022

Quart. Rev. Biophys.

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Biomolecular interactions are at the base of all physical processes within living organisms; the study of these interactions has led to the development of a plethora of different methods. Among these, single-molecule (in singulo) experiments have become relevant in recent years because these studies can give insight into mechanisms and interactions that are hidden for ensemble-based (in multiplo) methods. The focus of this review is on optical tweezer (OT) experiments, which can be used to apply and measure mechanical forces in molecular systems. OTs are based on optical trapping, where a laser is used to exert a force on a dielectric bead; and optically trap the bead at a controllable position in all three dimensions. Different experimental approaches have been developed to study protein–protein interactions using OTs, such as: (1) refolding and unfolding in trans interaction where one protein is tethered between the beads and the other protein is in the solution; (2) constant force in cis interaction where each protein is bound to a bead, and the tension is suddenly increased. The interaction may break after some time, giving information about the lifetime of the binding at that tension. And (3) force ramp in cis interaction where each protein is attached to a bead and a ramp force is applied until the interaction breaks. With these experiments, parameters such as kinetic constants (koff, kon), affinity values (KD), energy to the transition state ΔG≠, distance to the transition state Δx≠ can be obtained. These parameters characterize the energy landscape of the interaction. Some parameters such as distance to the transition state can only be obtained from force spectroscopy experiments such as those described here.

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Section: Detailed Description Of Intermolecular Interaction Force Exp...mentioning

confidence: 99%

Section: Detailed Description Of Intermolecular Interaction Force Exp...mentioning

confidence: 99%

Determination of protein–protein interactions at the single-molecule level using optical tweezers

Sanchez

Robeson

Carrasco

et al. 2022

Quart. Rev. Biophys.

Self Cite

View full text Add to dashboard Cite

show abstract

“…In recent years, the main methods used to study the interaction between aptamers and small molecules has included isothermal titration calorimetry [12], surface plasmon resonance (SPR) [13], microscale thermophoresis (MST) [14], biolayer interferometry (BLI) [15], nuclear magnetic resonance (NMR) [16], circular dichroism (CD) [17], and molecular dynamics (MD) [18]. These methods provide reliable kinetic or thermodynamic information about the interaction between aptamers and small-molecule ligands.…”

Section: Introductionmentioning

confidence: 99%

Optimization of Surface-Enhanced Raman Spectroscopy Detection Conditions for Interaction between Gonyautoxin and Its Aptamer

Liu¹,

Zhao

et al. 2022

Toxins

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This study aimed to optimize the detection conditions for surface-enhanced Raman spectroscopy (SERS) of single-stranded DNA (ssDNA) in four different buffers and explore the interaction between gonyautoxin (GTX1/4) and its aptamer, GO18. The influence of the silver colloid solution and MgSO4 concentration (0.01 M) added under four different buffered conditions on DNA SERS detection was studied to determine the optimum detection conditions. We explored the interaction between GTX1/4 and GO18 under the same conditions as those in the systematic evolution of ligands by exponential enrichment technique, using Tris-HCl as the buffer. The characteristic peaks of GO18 and its G-quadruplex were detected in four different buffer solutions. The change in peak intensity at 1656 cm−1 confirmed that the binding site between GTX1/4 and GO18 was in the G-quadruplex plane. The relative intensity of the peak at 1656 cm−1 was selected for the GTX1/4–GO18 complex (I1656/I1099) to plot the ratio of GTX1/4 in the Tris-HCl buffer condition (including 30 μL of silver colloid solution and 2 μL of MgSO4), and a linear relationship was obtained as follows: Y = 0.1867X + 1.2205 (R2 = 0.9239). This study provides a basis for subsequent application of SERS in the detection of ssDNA, as well as the binding of small toxins and aptamers.

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Analyzing aptamer structure and interactions: in silico modelling and instrumental methods

Malysheva,

Dymova,

Richter

2024

Biophys Rev

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Structural characterization of the saxitoxin-targeting APTSTX1 aptamer using optical tweezers and molecular dynamics simulations

Cited by 5 publications

References 47 publications

Determination of protein–protein interactions at the single-molecule level using optical tweezers

Determination of protein–protein interactions at the single-molecule level using optical tweezers

Optimization of Surface-Enhanced Raman Spectroscopy Detection Conditions for Interaction between Gonyautoxin and Its Aptamer

Analyzing aptamer structure and interactions: in silico modelling and instrumental methods

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