Single-Molecule Force Spectroscopic Studies on Intra- and Intermolecular Interactions of G-Quadruplex Aptamer with Target Shp2 Protein

Zhao, Xueqin; Wu, Jie; Liang, Jing-Hong; Yan, Jiawei; Zhu, Zhi; Yang, Chaoyong; Mao, Bing‐Wei

doi:10.1021/jp303518b

Cited by 13 publications

(15 citation statements)

References 51 publications

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“…For instance, the aptamer domain of several riboswitches was studied using single-molecule force spectroscopy with optical tweezers (18)(19)(20) or single-molecule Förster resonance energy transfer (21,22). In other studies, the well-known thrombin aptamer was investigated using optical tweezers (23) and atomic force microscopy (24,25).…”

Section: Introductionmentioning

confidence: 99%

Nanopore Force Spectroscopy of Aptamer–Ligand Complexes

Arnaut

Langecker

Simmel

2013

Biophysical Journal

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The stability of aptamer-ligand complexes is probed in nanopore-based dynamic force spectroscopy experiments. Specifically, the ATP-binding aptamer is investigated using a backward translocation technique, in which the molecules are initially pulled through an α-hemolysin nanopore from the cis to the trans side of a lipid bilayer membrane, allowed to refold and interact with their target, and then translocated back in the trans-cis direction. From these experiments, the distribution of bound and unbound complexes is determined, which in turn allows determination of the dissociation constant Kd ≈ 0.1 mM of the aptamer and of voltage-dependent unfolding rates. The experiments also reveal differences in binding of the aptamer to AMP, ADP, or ATP ligands. Investigation of an aptamer variant with a stabilized ATP-binding site indicates fast conformational switching of the original aptamer before ATP binding. Nanopore force spectroscopy is also used to study binding of the thrombin-binding aptamer to its target. To detect aptamer-target interactions in this case, the stability of the ligand-free aptamer-containing G-quadruplexes-is tuned via the potassium content of the buffer. Although the presence of thrombin was detected, limitations of the method for aptamers with strong secondary structures and complexes with nanomolar Kd were identified.

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Section: Introductionmentioning

confidence: 99%

Nanopore Force Spectroscopy of Aptamer–Ligand Complexes

Arnaut

Langecker

Simmel

2013

Biophysical Journal

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“…As shown in Figure 10C,D, the stability of the secondary structure of a HJ24 G-quadruplex aptamer (HJ24, the aptamer sequences used was 5′-CAGGGGGTTTTGGTGGGGGGGGC-TGGGTTGTCTTGG GGGTGGGCT-3′) can be evaluated by measuring the force curve and studying the melting force. [133]…”

Section: G Quadruplex and Internal Molecular Interactionsmentioning

confidence: 99%

“…The gold-labeled AFM probe is modified with double-labeled G-quadruplex DNA and the self-assembled monolayer is labeled with DNA that had been modified at the thiolated 3′ end (also known as the T20 sequence) and diluted at a 1:5 molar ratio, reprinted with permission from Ref. [133] Copyright 2012, American Chemical Society Prior to the follow-up measurement, the cells are starved in RPMI-1640 medium without glucose for 1 hour. The 1mercapto-β-D-glucose molecule formed a covalent bond with the end of the AFM probe through heterobifunctional polyethylene glycol-hydroxysuccinimide (PEG-NHS, see Figure 11A).…”

Section: Characterization Of Proteins and Carbohydrate Molecules On The Surfaces Of Living Cellsmentioning

confidence: 99%

Research progress of single molecule force spectroscopy technology based on atomic force microscopy in polymer materials: Structure, design strategy and probe modification

Wang

et al. 2021

Nano Select

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With the rapid development of polymer materials, the simultaneous acquisition of micro‐nano structure and mesoscopic mechanical properties from the material surface with the transverse resolution of nanoscale has become a hot spot in the research of polymer materials. Atomic force microscopy‐based high‐resolution imaging and single‐molecule force spectroscopy techniques have been widely used in various related fields. This review introduces the basic design and working principles of atomic force microscopy as well as single‐molecule force microscopy and their applications in the characterization of polymer surface morphologies, polymer film phase separation, polymer crystallization behavior, polymer chain stretching, protein folding/unfolding, G quadruplex intermolecular and intramolecular interactions, living cell surface proteins, and sugars. The research status of AFM probe modification strategies such as nanomaterial processing, single molecule manipulation and biomolecule etching is reviewed, finally, the limitations and improvement potential of single molecule force spectroscopy based on atomic force microscopy (AFM‐ SMFS) are summarized and discussed, and the new research practice in the field of polymer materials is prospected.

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“…SELEX methods allowed identifying the DNA aptamer HJ24, selectively recognizing Shp2: it binds Shp2 phosphatase with affinity in the nanomolar range and strongly inhibits its activity (IC 50 = 29 nM) [89]. HJ24 adopts a G4 structure, which is a prerequisite for stable binding to Shp2 [90].…”

Section: Diseasementioning

confidence: 99%

G-quadruplex-based aptamers against protein targets in therapy and diagnostics

Platella

Riccardi

Montesarchio

et al. 2017

Biochimica et Biophysica Acta (BBA) - General Subjects

144

116

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Nucleic acid aptamers are single-stranded DNA or RNA molecules identified to recognize with high affinity specific targets including proteins, small molecules, ions, whole cells and even entire organisms, such as viruses or bacteria. They can be identified from combinatorial libraries of DNA or RNA oligonucleotides by SELEX technology, an in vitro iterative selection procedure consisting of binding (capture), partitioning and amplification steps. Remarkably, many of the aptamers selected against biologically relevant protein targets are G-rich sequences that can fold into stable G-quadruplex (G4) structures. Aiming at disseminating novel inspiring ideas within the scientific community in the field of G4-structures, the emphasis of this review is placed on: 1) recent advancements in SELEX technology for the efficient and rapid identification of new candidate aptamers (introduction of microfluidic systems and next generation sequencing); 2) recurrence of G4 structures in aptamers selected by SELEX against biologically relevant protein targets; 3) discovery of several G4-forming motifs in important regulatory regions of the human or viral genome bound by endogenous proteins, which per se can result into potential aptamers; 4) an updated overview of G4-based aptamers with therapeutic potential and 5) a discussion on the most attractive G4-based aptamers for diagnostic applications. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.

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Single-Molecule Force Spectroscopic Studies on Intra- and Intermolecular Interactions of G-Quadruplex Aptamer with Target Shp2 Protein

Cited by 13 publications

References 51 publications

Nanopore Force Spectroscopy of Aptamer–Ligand Complexes

Nanopore Force Spectroscopy of Aptamer–Ligand Complexes

Research progress of single molecule force spectroscopy technology based on atomic force microscopy in polymer materials: Structure, design strategy and probe modification

G-quadruplex-based aptamers against protein targets in therapy and diagnostics

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