scholarly journals Evaluation of aptamer specificity with or without primers using clinical samples for C-reactive protein by magnetic-assisted rapid aptamer selection

RSC Advances ◽  
2017 ◽  
Vol 7 (68) ◽  
pp. 42856-42865 ◽  
Author(s):  
Huan-Hao Li ◽  
Chih-Yung Wen ◽  
Chin-Yih Hong ◽  
Ji-Ching Lai
Keyword(s):  
Binding Sites ◽  
Clinical Samples ◽  
C Reactive Protein ◽  
Reactive Protein ◽  
Aptamer Selection ◽  
Systematic Evolution ◽  
Exponential Enrichment ◽  
Enrichment Process

Aptamers with primer binding sites are necessary for the SELEX (Systematic Evolution of Ligands by EXponential enrichment) process.

Pattern recognition of enrichment levels of SELEX-based candidate aptamers for human C-reactive protein

2017 ◽  
Vol 62 (3) ◽  
Author(s):  
Xinliang Yu ◽  
Ruqin Yu ◽  
Xiaohai Yang
Keyword(s):  
Pattern Recognition ◽  
Latent Variables ◽  
Molecular Descriptors ◽  
Principal Component ◽  
Support Vector ◽  
C Reactive Protein ◽  
Reactive Protein ◽  
Systematic Evolution ◽  
Model C ◽  
Exponential Enrichment

AbstractSelecting aptamers for human C-reactive protein (CRP) would be of critical importance in predicting the risk for cardiovascular disease. The enrichment level of DNA aptamers is an important parameter for selecting candidate aptamers for further affinity and specificity determination. This paper is the first report on pattern recognition used for CRP aptamer enrichment levels in the systematic evolution of ligands by exponential enrichment (SELEX) process, by applying structure-activity relationship models. After generating 10 rounds of graphene oxide (GO)-SELEX and 1670 molecular descriptors, eight molecular descriptors were selected and five latent variables were then obtained with principal component analysis (PCA), to develop a support vector classification (SVC) model. The SVC model (C=8.1728 and

scholarly journals Ultrarapid, Ultrasensitive One-Step Kinetic Immunoassay for C-Reactive Protein (CRP) in Whole Blood Samples: Measurement of the Entire CRP Concentration Range with a Single Sample Dilution

2002 ◽  
Vol 48 (2) ◽  
pp. 269-277 ◽  
Author(s):  
Piia Tarkkinen ◽  
Tom Palenius ◽  
Timo Lövgren
Keyword(s):  
Whole Blood ◽  
Solid Phase ◽  
Point Of Care ◽  
High Sensitivity ◽  
Clinical Samples ◽  
Cardiac Complications ◽  
Fluorescence Signal ◽  
C Reactive Protein ◽  
Reactive Protein ◽  
One Step

Abstract Background: Recently, measurement of very low concentrations of C-reactive protein (CRP) has gained popularity as a potential new means for predicting the risk of future cardiac complications. In this study, we demonstrate the feasibility of a kinetic, one-step microparticle assay for quantitative determination of extremely low and high CRP concentrations in the limited timeframe typical for point-of-care testing. Methods: A noncompetitive, kinetic CRP immunoassay was developed that uses individual, porous microparticles as the solid phase. The microparticles were covalently coated with a monoclonal capture antibody, and the monoclonal detection antibody was labeled with europium. The one-step binding reaction was stopped by washing after 2 min of incubation, and the fluorescence signal of individual particles was measured. Results: The analytical detection limit (mean of zero calibrator + 3 SD) was 0.00016 mg/L CRP. Clinical samples were diluted 400-fold before assay to cover the CRP concentration range of 0.064–1200 mg/L. The assay correlated well with the Dade Behring N High Sensitivity CRP assay (for 0–10 mg/L, r = 0.969, Sy|x = 0.68, n = 54; for 0–350 mg/L, r = 0.969, Sy|x = 11.7, n = 100). The within- and between-run CVs based on calculated concentrations were, respectively, 9–16% and 14% at 0.11 mg/L, 4.5–12% and 8.2% at 4.2 mg/L, and 3.5–6.3% and 4.4% at 105 mg/L, with a CV <15% at 0.2 mg/L and above. Conclusions: Use of the kinetic microparticle approach combined with time-resolved fluorometry allows ultrasensitive quantification of CRP in whole blood in 2 min with a linear assay range spanning more than four orders of magnitude.

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.

Serum Free Light Chain Assay: Shift Toward a Higher κ/λ Ratio

2019 ◽  
Vol 5 (1) ◽  
pp. 114-125 ◽  
Author(s):  
Barbara Rindlisbacher ◽  
Christof Schild ◽  
Florence Egger ◽  
Vera U Bacher ◽  
Thomas Pabst ◽  
...  
Keyword(s):  
Clinical Samples ◽  
Poor Correlation ◽  
Poor Agreement ◽  
C Reactive Protein ◽  
Serum Free ◽  
Reactive Protein ◽  
Serum Free Light Chain ◽  
Academic Center ◽  
Plasma Cell Disorders ◽  
Serum Free Light Chains

Abstract Background The analysis of serum free light chains (FLCs) is clinically relevant for the diagnosis and therapeutic management of clonal plasma cell disorders. This study compares the performance of monoclonal and polyclonal FLC κ and λ assays in clinical samples determined in a single academic center. Methods Serum FLCs were analyzed from 102 patients using the Freelite (Binding Site) and N Latex (Siemens) assays on the BN ProSpec System (Siemens). When available, data for protein electrophoresis, immunofixation, C-reactive protein, and estimated glomerular filtration rate (eGFR) were combined with FLC results to evaluate performance. Results Method evaluation showed acceptable imprecision and inaccuracy measures of <4.4% and 12.9%, respectively. Poor agreement between the methods was observed, including constant and proportional bias and poor correlation (Kendall τ, 0.671–0.901). The N Latex assay was not affected by the renal impairment estimated by eGFR, unlike the FLC κ/λ ratio results by the Freelite assay. With the Freelite assay, 98% of putative controls without monoclonal gammopathy (n = 42) showed a κ/λ ratio that was above the median of the standard diagnostic range or renal diagnostic range. A shift toward higher κ/λ ratios was also observed when retrospective data between 2011 and 2017 were compared. Conclusions Unlike the Freelite assay, κ/λ ratios analyzed with the N Latex assay were not affected by renal failure. Both methods showed acceptable performances using nephelometry, but they were poorly correlated. A shift toward κ/λ ratios might impair the specificity of borderline increased κ/λ results. This should be considered when interpreting FLC κ and λ results.

The Arabidopsis class I TCP transcription factor AtTCP11 is a developmental regulator with distinct DNA-binding properties due to the presence of a threonine residue at position 15 of the TCP domain

2011 ◽  
Vol 435 (1) ◽  
pp. 143-155 ◽  
Author(s):  
Ivana L. Viola ◽  
Nora G. Uberti Manassero ◽  
Rodrigo Ripoll ◽  
Daniel H. Gonzalez
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Class I ◽  
Binding Properties ◽  
Threonine Residue ◽  
Dna Binding Specificity ◽  
Systematic Evolution ◽  
Enrichment Experiments ◽  
Exponential Enrichment ◽  
Dna Binding Properties

The TCP domain is a DNA-binding domain present in plant transcription factors that modulate different processes. In the present study, we show that Arabidopsis class I TCP proteins are able to interact with a dyad-symmetric sequence composed of two GTGGG half-sites. TCP20 establishes symmetric interactions with the 5′ half of each strand, whereas TCP11 interacts mainly with the 3′ half. SELEX (systematic evolution of ligands by exponential enrichment) experiments with TCP15 and TCP20 indicated that these proteins have similar, although not identical, DNA-binding preferences and are able to interact with non-palindromic binding sites of the type GTGGGNCCNN. TCP11 shows a different DNA-binding specificity, with a preference for the sequence GTGGGCCNNN. The distinct DNA-binding properties of TCP11 are due to the presence of a threonine residue at position 15 of the TCP domain, a position that is occupied by an arginine residue in most TCP proteins. TCP11 also forms heterodimers with TCP15 that have increased DNA-binding efficiency. The expression in plants of a repressor form of TCP11 demonstrated that this protein is a developmental regulator that influences the growth of leaves, stems and petioles, and pollen development. The results suggest that changes in DNA-binding preferences may be one of the mechanisms through which class I TCP proteins achieve functional specificity.

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