Advantages of aptamers as ligands upon protein detection by AFM-based fishing

Pleshakova, Tatyana O.; Kaysheva, Anna L.; Bayzyanova, J. M.; Anashkina, A. S.; Учайкин, В. Ф.; Shumov, Ivan D.; Ziborov, Vadim S.; Konev, V. A.; Archakov, Alexander I.; Ivanov, Yu. D.

doi:10.1039/c7ay01216k

Cited by 12 publications

(26 citation statements)

References 17 publications

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“…Afterwards, the substrate surface was washed in 1 mL of deionized water at room temperature and then dried. Both efficiency of aptamer immobilization onto the silanized mica surface and the retention of their affine properties were demonstrated in our previous studies [30,31]. Consistent with the findings reported by Pleshakova et al, an insignificant number of objects (maximum of 200 per 400 μm 2 ) with heights of up to 2 nm were obtained after immobilization [30].…”

Section: Methodssupporting

confidence: 90%

Detection of Hepatitis C Virus Core Protein in Serum Using Aptamer-Functionalized AFM Chips

et al. 2019

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In the present study, we demonstrate atomic force microscopy (AFM)-based detection of hepatitis C virus (HCV) particles in serum samples using a chip with aptamer-functionalized surface (apta-based AFM chip). The target particles, containing core antigen of HCV (HCVcoreAg protein), were biospecifically captured onto the chip surface from 1 mL of test solution containing 10 µL of serum collected from a hepatitis C patient. The registration of aptamer/antigen complexes on the chip surface was performed by AFM. The aptamers used in the present study were initially developed for therapeutic purposes; herein, these aptamers have been successfully utilized as probe molecules for HCVcoreAg detection in the presence of a complex protein matrix (human serum). The results obtained herein can be used for the development of detection systems that employ affine enrichment for protein detection.

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Section: Methodssupporting

confidence: 90%

Detection of Hepatitis C Virus Core Protein in Serum Using Aptamer-Functionalized AFM Chips

et al. 2019

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“…Figure 3 presents the scheme of AFM-based fishing technique. Chip surface is functionalized by antibodies or aptamers in the case of biospecific analysis [ 122 , 123 , 127 , 129 ] ( Figure 3 , first step).…”

Section: Afm-based Molecular Detector Of Low-abundance Proteinsmentioning

confidence: 99%

“…AFM chips functionalized by aptamers (aptamer-based approach) have been applied to carry out AFM-based fishing of envelope glycoprotein gp120 of human immunodeficiency virus (HIV-1) used as biomarker in diagnosis [ 118 ]. In aptamer-based approach, the increase of AFM image contrast was observed compared to antibody-based approach when antibodies have been used as bait molecules [ 118 , 129 , 134 ]. MS analysis allowed to identify the target protein from the chip surface after biospecific fishing that proved aptamer-protein complex formation.…”

Section: Afm-based Molecular Detector Of Low-abundance Proteinsmentioning

confidence: 99%

Atomic Force Microscopy for Protein Detection and Their Physicoсhemical Characterization

Pleshakova

Bukharina

Archakov

et al. 2018

IJMS

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This review is focused on the atomic force microscopy (AFM) capabilities to study the properties of protein biomolecules and to detect the proteins in solution. The possibilities of application of a wide range of measuring techniques and modes for visualization of proteins, determination of their stoichiometric characteristics and physicochemical properties, are analyzed. Particular attention is paid to the use of AFM as a molecular detector for detection of proteins in solutions at low concentrations, and also for determination of functional properties of single biomolecules, including the activity of individual molecules of enzymes. Prospects for the development of AFM in combination with other methods for studying biomacromolecules are discussed.

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“…Subsequently, the AFM-chip was washed thrice with deonized water for 30 minutes at 37 °C and dried in presence of nitrogen flow. Emulgen 913 solution at a concentration of 0.01% that has been used in our previous study [3], [4] was used as the wash buffer.…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

Immuno-MALDI MS dataset for improved detection of HCVcoreAg in sera

Kaysheva¹,

Pleshakova²,

Stepanov³

et al. 2019

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Complicated and large-scale challenge the contemporary biomedical community faces are development of highly-sensitive analytical methods for detection of protein markers associated with development of pathogenic mechanisms [2]. The atomic force microscopy (AFM) method in combination with specific fishing is unique among other analytical protein detection approaches; it allows visualization and counting of single protein molecules [3–6]. The present dataset focus on mass spectrometry method for detection of human hepatitis C virus core antigen (HCV core Ag) taking into account the potential modification with cations in blood serum samples, using mica chips for the atomic force microscopy (AFM-chips). To conduct specific protein fishing, we used flat AFM-chips preliminary sensibilized with molecular probes – aptamers, which are single-stranded DNA sequences. In our study we used four types of aptamers up to 85 nucleotides specific against the target protein – HCVcoreAg [3,4]. Working (n = 19) and control (n = 11) AFM-chips with aptamers were preliminarily immobilized on the surface in four zones and incubated in blood serum samples (See Supplementary fig. 1). Analysis of MS data regarding modification of marker protein peptides with Na+, K+, K2Cl+, and Na2Cl + ions enables to enhance the reliability of target proteins detection in the serum thereby demonstrating a high diagnostic potential.

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Advantages of aptamers as ligands upon protein detection by AFM-based fishing

Abstract: AFM chip with immobilized aptamers can be used for HCVcoreAg detection in solution.

Cited by 12 publications

References 17 publications

Detection of Hepatitis C Virus Core Protein in Serum Using Aptamer-Functionalized AFM Chips

Detection of Hepatitis C Virus Core Protein in Serum Using Aptamer-Functionalized AFM Chips

Atomic Force Microscopy for Protein Detection and Their Physicoсhemical Characterization

Immuno-MALDI MS dataset for improved detection of HCVcoreAg in sera

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