scholarly journals A ssDNA Aptamer That Blocks the Function of the Anti-FLAG M2 Antibody

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
Amanda S. Lakamp ◽  
Michel M. Ouellette
Keyword(s):  
Lupus Erythematosus ◽  
Binding Pocket ◽  
Dna Aptamer ◽  
Commercial Application ◽  
Antigen Binding ◽  
Systemic Lupus ◽  
Therapeutic Modalities ◽  
Ssdna Aptamer ◽  
Systematic Evolution ◽  
Exponential Enrichment

Using SELEX (systematic evolution of ligands by exponential enrichment), we serendipitously discovered a ssDNA aptamer that binds selectively to the anti-FLAG M2 antibody. The aptamer consisted of two motifs (CCTTA and TGTCTWCC) separated by 2-3 bases, and the elimination of one or the other motif abrogated binding. The DNA aptamer and FLAG peptide competed for binding to the antigen-binding pocket of the M2 antibody. In addition, the aptamer eluted FLAG-tagged proteins from the antibody, suggesting a commercial application in protein purification. These findings demonstrate the feasibility of using SELEX to develop ssDNA aptamers that block the function of a specific antibody, a capability that could lead to the development of novel therapeutic modalities for patients with systemic lupus erythematosus, rheumatoid arthritis, and other autoimmune diseases.

Differentiating breast cancer molecular subtypes using a DNA aptamer selected against MCF-7 cells

2018 ◽  
Vol 6 (12) ◽  
pp. 3152-3159 ◽  
Author(s):  
Mei Liu ◽  
Tong Yang ◽  
Zhongsi Chen ◽  
Zhifei Wang ◽  
Nongyue He
Keyword(s):  
Breast Cancer ◽  
Molecular Subtypes ◽  
Personalized Therapy ◽  
Dna Aptamer ◽  
Single Stranded Dna ◽  
Systematic Evolution ◽  
Exponential Enrichment ◽  
Mcf 7

Aptamers are single-stranded DNA or RNA oligonucleotides selected by systematic evolution of ligands by exponential enrichment (SELEX), which show great potential in the diagnosis and personalized therapy of cancers, due to their specific advantages over antibodies.

scholarly journals Hydroxyl Radical Modification of Immunoglobulin G Generated Cross-Reactive Antibodies: Its Potential Role in Systemic Lupus Erythematosus

2011 ◽  
Vol 4 ◽  
pp. CMAMD.S6793 ◽  
Author(s):  
Hani A. Al-Shobaili ◽  
Ahmad A. Al Robaee ◽  
Abdullateef Alzolibani ◽  
Muhammad Ismail Khan ◽  
Zafar Rasheed
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Nucleic Acid ◽  
Immunoglobulin G ◽  
Lupus Erythematosus ◽  
Competitive Inhibition ◽  
Antigen Binding ◽  
Blood Proteins ◽  
Systemic Lupus ◽  
Human Igg ◽  
Binding Characteristics

Objective Role of reactive oxygen species (ROS) modified human Immunoglobulin G (IgG) in systemic lupus erythematosus (SLE) has been investigated. Methods Human IgG was modified by hydroxyl-radicals. Immunogenicity of native and modified human IgG was probed by inducing polyclonal antibodies in rabbits. Cross-reactions of induced antibodies with nucleic acid, chromatin, different blood proteins and their ROS modified conformers were determined by competitive inhibition ELISA. The binding characteristics of circulating autoantibodies in SLE patients (n = 72) against native and modified IgG were screened by direct binding and competition ELISA and the results were compared with healthy age-matched controls (n = 39). Results Induced antibodies against ROS-modified human IgG exhibited diverse antigen binding characteristics. Native DNA, native chromatin and their ROS-modified conformers were found to be effective inhibitors of induced antibody-immunogen interaction. Induced antibodies against native human IgG showed negligible binding to the above mentioned nucleic acid antigens. SLE sera (48.6%) showed strong binding to ROS-human IgG in comparison with its native analogue ( P < 0.01). Normal human sera (NHS) showed negligible binding with either antigen ( P > 0.05). Conclusion ROS-induced modifications in human IgG present neo-epitopes, and make it a potential immunogen. The induced antibodies against ROS-modified human IgG resembled the diverse antigen-binding characteristics of naturally occurring SLE anti-DNA autoantibodies. ROS-modified IgG may be one of the factors for the induction of circulating SLE autoantibodies.

scholarly journals In Silico Selection of Gp120 ssDNA Aptamer to HIV-1

2020 ◽  
Vol 25 (9) ◽  
pp. 1087-1093
Author(s):  
Hamideh Sepehri Zarandi ◽  
Mandana Behbahani ◽  
Hassan Mohabatkar
Keyword(s):  
In Silico ◽  
Dna Aptamer ◽  
Surface Glycoprotein ◽  
Aptamer Selection ◽  
Glycoprotein Gp120 ◽  
Systematic Evolution ◽  
Exponential Enrichment ◽  
Hiv 1 ◽  
Aptamer Sequence ◽  
Selection Of

Nucleic acid aptamers that specifically bind to other molecules are mostly obtained through the systematic evolution of ligands by exponential enrichment (SELEX). Because SELEX is a time-consuming procedure, the in silico design of specific aptamers has recently become a progressive approach. HIV-1 surface glycoprotein gp120, which is involved in the early stages of HIV-1 infection, is an attractive target for RNA and DNA aptamer selection. In this study, four single-stranded DNA aptamers, referred to as HD2, HD3, HD4, and HD5, that had the ability of HIV-1 inhibition were designed in silico. In a proposed non-SELEX approach, some parts of the B40 aptamer sequence, which interacted with gp120, were isolated and considered as a separate aptamer sequence. Then, to obtain the best docking scores of the HDOCK server and Hex software, some modifications, insertions, and deletions were applied to each selected sequence. Finally, the cytotoxicity and HIV inhibition of the selected aptamers were evaluated experimentally. Results demonstrated that the selected aptamers could inhibit HIV-1 infection by up to 80%, without any cytotoxicity. Therefore, this new non-SELEX approach could be considered a simple, fast, and efficient method for aptamer selection.

scholarly journals Preparation of a Specific ssDNA Aptamer for Brevetoxin-2 Using SELEX

2016 ◽  
Vol 2016 ◽  
pp. 1-8 ◽  
Author(s):  
Rui-Yun Tian ◽  
Chao Lin ◽  
Shi-Yu Yu ◽  
Sheng Gong ◽  
Pan Hu ◽  
...  
Keyword(s):  
Research Direction ◽  
High Affinity ◽  
Complex Processes ◽  
Ssdna Aptamer ◽  
Coefficient Corrélation ◽  
Recognition Probe ◽  
Detection Probe ◽  
Systematic Evolution ◽  
Alternative Detection ◽  
Exponential Enrichment

The existing assays for detecting brevetoxin (BTX) depend on expensive equipment with a professional operator or on an antibody with limited stability, which requires complex processes, a high cost, and a considerable amount of time. The development of an alternative detection probe is another promising research direction. This paper reports the use of aptamers binding to BTX-2 in an analytical assay using the systematic evolution of ligands by exponential enrichment (SELEX). After 12 rounds of selection, the secondary structures of 25 sequences were predicted. Compared to other aptamers, Bap5 has relatively high affinity with the lowest dissociation constant of 4.83 μM, and IC50is 73.81 ng mL−1. A good linear regression formula ofy=30.688x-7.329with a coefficient correlation ofR2= 0.9798 was obtained using a biotin-avidin ELISA. Moreover, there is no cross-reaction with the detected marine toxins, except for BTX-2. Thus, Bap5 has potential to detect BTX-2 in shellfish in the future as a substitute for the recognition probe.

scholarly journals Selection, Characterization, and Application of ssDNA Aptamer against Furaneol

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3159 ◽  
Author(s):  
Natalia Komarova ◽  
Mariia Andrianova ◽  
Sergey Glukhov ◽  
Alexander Kuznetsov
Keyword(s):  
Magnetic Beads ◽  
Aroma Compound ◽  
Fluorescent Method ◽  
Volatile Organic ◽  
Ssdna Aptamer ◽  
Effect Transistor ◽  
Systematic Evolution ◽  
Dna Pool ◽  
Exponential Enrichment ◽  
Apparent Equilibrium

Furaneol is an aroma compound which occurs naturally in foods and is used as an artificial flavor. Detection of furaneol is required in food science and food processing industry. Capture- Systematic Evolution of Ligands by EXponential enrichment (SELEX) protocol was applied for the isolation of an aptamer binding to furaneol, a small volatile organic substance contributing to the flavor of various products. Thirteen cycles of selection were performed. The resulting DNA pool was cloned, using blunt-end cloning, and ninety-six plasmids were sequenced and analyzed. Eight oligonucleotides were selected as aptamer candidates and screened for the ability to bind to furaneol, using three different methods—magnetic-beads associated elution assay, SYBR Green I assay, and exonuclease protection assay. One of the candidates was further characterized as an aptamer. The apparent equilibrium constant was determined to be (1.1 ± 0.4) µM, by the fluorescent method. The reported aptamer was applied for development of the ion-sensitive field-effect transistor (ISFET)-based biosensor, for the analysis of furaneol, in the concentration range of 0.1–10 µM.

scholarly journals Development of aptamer-based inhibitors for CRISPR/Cas system

2020 ◽  
Author(s):  
Jing Zhao ◽  
Rika Inomata ◽  
Yoshio Kato ◽  
Makoto Miyagishi
Keyword(s):  
Genome Editing ◽  
In Vitro Selection ◽  
Unsolved Problem ◽  
Dna Aptamer ◽  
Cleavage Assay ◽  
Locked Nucleic Acids ◽  
Systematic Evolution ◽  
Exponential Enrichment ◽  
In Cells

Abstract The occurrence of accidental mutations or deletions caused by genome editing with CRISPR/Cas9 system remains a critical unsolved problem of the technology. Blocking excess or prolonged Cas9 activity in cells is considered as one means of solving this problem. Here, we report the development of an inhibitory DNA aptamer against Cas9 by means of in vitro selection (systematic evolution of ligands by exponential enrichment) and subsequent screening with an in vitro cleavage assay. The inhibitory aptamer could bind to Cas9 at low nanomolar affinity and partially form a duplex with CRISPR RNA, contributing to its inhibitory activity. We also demonstrated that improving the inhibitory aptamer with locked nucleic acids efficiently suppressed Cas9-directed genome editing in cells and reduced off-target genome editing. The findings presented here might enable the development of safer and controllable genome editing for biomedical research and gene therapy.

scholarly journals Immunochemical similarities between monoclonal antibacterial Waldenstrom's macroglobulins and monoclonal anti-DNA lupus autoantibodies.

1985 ◽  
Vol 161 (6) ◽  
pp. 1525-1538 ◽  
Author(s):  
Y Naparstek ◽  
D Duggan ◽  
A Schattner ◽  
M P Madaio ◽  
F Goni ◽  
...  
Keyword(s):  
Lupus Erythematosus ◽  
Variable Region ◽  
Antigen Binding ◽  
Waldenström’S Macroglobulinemia ◽  
Systemic Lupus ◽  
Antigen Binding Site ◽  
Waldenstrom's Macroglobulinemia ◽  
Waldenstrom’S Macroglobulinemia ◽  
Variable Region Genes ◽  
Waldenström's Macroglobulinemia

Six monoclonal IgM from patients with Waldenstrom's macroglobulinemia that react with Klebsiella polysaccharides were tested for their ability to bind to nucleic acid antigens. One of the macroglobulins bound to the polynucleotide poly(G), and one bound to poly(G), poly(I), and single-stranded DNA. The reaction with the polynucleotides was specifically inhibited by the Klebsiella polysaccharide K30. A monoclonal lupus anti-DNA antibody (16/6) was found to react weakly with the Klebsiella polysaccharides K30 and K21. Five of the Waldenstrom macroglobulins shared an idiotypic determinant with the 16/6 anti-DNA antibody. The reaction between the macroglobulins and the antiidiotype serum was specifically inhibited by Klebsiella polysaccharides, an indication that the idiotypic marker was in the antigen-binding site of the macroglobulins. These results indicate the existence of widely dispersed conserved variable region genes that encode idiotypically related immunoglobulins with the capacity to bind to both bacterial polysaccharides and nucleic acids. Such genes can be expressed by patients with either Waldenstrom's macroglobulinemia or systemic lupus erythematosus.

scholarly journals Structural analysis reveals TLR7 dynamics underlying antagonism

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Shingo Tojo ◽  
Zhikuan Zhang ◽  
Hiroyuki Matsui ◽  
Masahiro Tahara ◽  
Mitsunori Ikeguchi ◽  
...  
Keyword(s):  
Autoimmune Diseases ◽  
Lupus Erythematosus ◽  
Binding Pocket ◽  
Therapeutic Agents ◽  
Toll Like Receptor ◽  
Systemic Lupus ◽  
Detailed Mechanism ◽  
Cryo Electron Microscopy ◽  
Open Conformation ◽  
Targeting Strategy

Abstract Toll-like receptor 7 (TLR7) recognizes both microbial and endogenous RNAs and nucleosides. Aberrant activation of TLR7 has been implicated in several autoimmune diseases including systemic lupus erythematosus (SLE). Here, by modifying potent TLR7 agonists, we develop a series of TLR7-specific antagonists as promising therapeutic agents for SLE. These compounds protect mice against lethal autoimmunity. Combining crystallography and cryo-electron microscopy, we identify the open conformation of the receptor and reveal the structural equilibrium between open and closed conformations that underlies TLR7 antagonism, as well as the detailed mechanism by which TLR7-specific antagonists bind to their binding pocket in TLR7. Our work provides small-molecule TLR7-specific antagonists and suggests the TLR7-targeting strategy for treating autoimmune diseases.

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