Low pH capillary electrophoresis application to improve capillary electrophoresis-systematic evolution of ligands by exponential enrichment

Three-step evolutionary enhanced capillary electrophoresis-SELEX for aptamer selection of exosome vesicles

As various disease biomarkers, drugs/biomolecules carriers and physiological function regulator, exosomes play significant roles in various physiological and pathological process. Thus, the purification and detection of some exosome are of great significance, which make it necessary for the development of the recognition elements. Aptamers with high affinity and specificity exhibited well in the above areas. In this work, a new three-step evolutionary enhanced strategy based on capillary electrophoresis (CE)-SELEX was proposed for effective aptamer selection of exosome vesicles for the first time. Natural killer cells (NK) exosome was used as the model target. And the aptamer could be obtained in five round CE selection within three steps evolution including precise nucleic acid sequence convergence (with NK exosome specific proteins as targets in round 1st and 3rd), affinity evolution (with NK exosome as target in round 2nd and 4th) and specific evolution (negative selection in round 5th). Arising from the compatibility of CE-SELEX for exosome vesicles aptamer selection, and the proposed strategy, aptamer against NK exosome had been selected with good affinity (KD value of 27.6 nM) and excellent specificity. The as proposed CE-SELEX strategy paves a novel way for recognition element selection of exosome vesicles.

Selection and truncation of aptamers as fluorescence sensing platforms for selective and sensitive detection of nitrofurazone

Nitrofurazone (NFZ) is an antibiotic banned in many countries, as its residue seriously harms the human body. Herein, anti-NFZ aptamers were selected and identified based on the magnetic bead SELEX technique using a ssDNA library with a full length of 90 nucleotides (nt). Five full sequence candidate aptamers (NFZ8, NFZ24, NFZ28, NFZ34, and NFZ70) were obtained by secondary structure analysis. We optimized the entire sequence to obtain a truncated aptamer, a 16 nt sequence (NFZ8-1:5'-GTTCTATTGAAAAAAC-3') that showed the highest affinity for NFZ (K_d = 76.11 nM). The binding site of NFZ and aptamer NFZ8-1 was found to be "GAA" by molecular docking. In addition, utilizing the most special truncated aptamer NFZ8-1 as the identification probe, a graphene oxide fluorescent aptasensor is an innovative for the detection of NFZ residue that showed a wide linear reach from 1.25 to 160 ng/mL and a low limit of detection of 1.13 ng/mL. In the actual water environment sample detection, the recovery rate ranged from 95.21 to 113.66%, and the coefficient of variation ranged from 3.53 to 11.24%. These results demonstrate that the NFZ-truncated aptamer applied to the aptasensor provides a novel methodology for recognizing NFZ residues.

Oligonucleotide aptamers: Recent advances in their screening, molecular conformation and therapeutic applications

Aptamers are single stranded oligonucleotides with specific recognition and binding ability to target molecules, which can be obtained by Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Aptamers have the advantages of low molecular weight, low immunogenicity, easy modification and high stability. They play promising role in promoting food safety, monitoring the environment and basic research, especially in clinical diagnosis and therapeutic drugs. To date, great achievements regarding the selection, modifications and application of aptamers have been made. However, since it is still a challenge to obtain aptamers with high affinity in a more effective way, few aptamer-based products have already successfully entered into clinical use. This review aims to provide a thorough overview of the latest advances in this rapidly developing field, focusing on aptamer screening methods for different targets, the structure of the interaction between aptamers and target substances, and the challenges and potential of current therapeutic aptamers.

[Efficient screening for 8-oxoguanine DNA glycosylase binding aptamers via capillary electrophoresis]

8-氧代鸟嘌呤DNA糖基化酶(OGG1)是人体中重要的功能蛋白,在修复DNA氧化性损伤过程中起关键作用。氧化应激等引起的氧化损伤易导致炎症反应的发生,对OGG1的抑制可以一定程度上起到缓解作用;对癌细胞OGG1的抑制有望作为癌症治疗的新方法。目前的研究多集中于小分子对OGG1功能的影响和调控,而OGG1的适配体筛选尚未见报道。作为功能配体,适配体具有合成简单、高亲和力及高特异性等优点。该文筛选了OGG1的核酸适配体,结合毛细管电泳高效快速的优点建立了两种基于毛细管电泳-指数富集进化(CE-SELEX)技术的筛选方法:同步竞争法和多轮筛选法。同步竞争法利用单链结合蛋白(SSB)与核酸库中单链核酸的强结合能力,与目标蛋白OGG1组成竞争体系,并通过增加SSB浓度来增加竞争筛选压力,以去除与OGG1弱结合的核酸序列,一步筛选即可获得与OGG1强结合的核酸序列。多轮筛选法在相同孵育条件和电泳条件下,经3轮筛选获得OGG1的核酸适配体。比较两种筛选方法的筛选结果,筛选结果中频次最高的3条候选核酸适配体序列一致,其解离常数(K_D)值在1.71~2.64 μmol/L之间。分子对接分析结果表明候选适配体1(Apt 1)可能与OGG1中具有修复氧化性损伤功能的活性口袋结合。通过对两种筛选方法的对比,证明同步竞争法更加快速高效,对其他蛋白核酸适配体筛选方法的选择具有一定的指导意义。得到的适配体有望用于OGG1功能调控,以抑制其修复功能。

Capillary electrophoresis-based methodology for screening of oligonucleotide aptamers

As a new molecular recognition element, oligonucleotide aptamer not only has higher affinity and specificity to target molecules, but also has the advantages of wide recognition range, in vitro synthesis and chemical stability compared with conventional antibodies. Since a kind of screening method termed systematic evolution of ligands by exponential enrichment (SELEX) was reported, scientists have extensively researched the methodology of how to highly and efficiently screen out aptamers from a library consisting of a large number of random oligonucleotides. Certainly capillary electrophoresis-based screening methodologies, including nonequilibrium capillary electrophoresis of equilibrium mixtures, equilibrium capillary electrophoresis of equilibrium mixtures, non-SELEX, ideal-filter capillary electrophoresis, capillary transient isotachophoresis, etc., are revolutionary. Compared with conventional SELEX, these capillary electrophoresis-based methodologies show incomparable advantages such as the single-round screening of aptamers and increased successful screening rate. Methodology studies on the screening process of aptamers are comprehensively reviewed.

SELEX-based DNA Aptamer Selection: A Perspective from the Advancement of Separation Techniques

DNA aptamers, which are short, single-stranded DNA sequences that selectively bind to target substances (proteins, cells, small molecules, metal ions), can be acquired by means of the systematic evolution of ligands by exponential enrichment (SELEX) methodology. In the SELEX procedure, one of the keys for the effective acquisition of high-affinity and functional aptamer sequences is the separation stage to isolate target-bound DNA from unbound DNA in a randomized DNA library. In this review, various remarkable advancements in separation techniques for SELEX-based aptamer selection developed in this decade, are described and discussed, including CE-, microfluidic chip-, solid phase-, and FACS-based SELEX along with other methods.

Capillary Electrophoresis Involving in High Efficiency Screening for Aptamers

Systematic evolution of ligands by exponential enrichment (SELEX) is a universal technology for aptamer' screening. Accurate and efficient screening methods and strategy design are the key to success. This review briefly summarizes capillary electrophoresis (CE) involving in the efficient screening for aptamers in our group since 2007, including the application of CE in pre-screening, screening and post-screening process, classification and screening strategies against different protein targets, multiple screening modes, and screening for multi-scale targets. Finally, combined with the current progresses of aptamer screening, some remaining issues are discussed and the development prospects are proposed.

Evolution of multi-functional capillary electrophoresis for high-efficiency selection of aptamers

Aptamers have drawn considerable attention as newly emerging molecular recognition elements in clinical diagnostics, drug delivery, therapeutics, environmental monitoring, and food safety analyses. As the in vitro screening antibody analogs, aptamers are enabled to recognize various types of targets with high affinity and specificity like or even superior to antibodies. However, the restrictions and inefficiency of selection have been hampering their wider application. Among various modified systematic evolution of ligands by exponential enrichment (SELEX) methods, capillary electrophoresis (CE)-SELEX holds multiple functions and advantages with the powerful qualitative and quantitative analysis capabilities, less consumption of sample and analytical reagent, natural binding environment, higher screening efficiency, and availability in multiple modes. This review summarizes the key developments in the area of CE-SELEX by leading research groups, including our teams' ten years of research and experience to help researchers fully understand and utilize CE-SELEX. Aptamers' history, applications, as well as the SELEX developments, have been briefly described; the advantages of CE-SELEX are highlighted compared with the conventional SELEX methods. Further, we describe some essential CE-SELEX models and provide an overview of the CE-SELEX, including the targets and ssDNA library, every technical point in the selection process, and post-SELEX protocol. We expect this review will inspire more researchers to have insight into the screening problems from CE-SELEX viewpoint and will help to improve the selection efficiency and probability of success to meet the growing needs of aptamers' discovery in bioanalytical and medical fields.

High-efficiency selection of aptamers for bovine lactoferrin by capillary electrophoresis and its aptasensor application in milk powder

Capillary electrophoresis-based systematic evolution of ligands by exponential enrichment (CE-SELEX) is a high-efficient technique for aptamers selection, and has been evolved into many modes. In this study, we obtained the aptamer against bovine lactoferrin (BLF) with high affinity (dissociation constant, K_d = 20.74 ± 6.89 nM) and good specificity (>1000 folds) using single step CE-SELEX (ssCE-SELEX) mode. In the selection process, ssCE demonstrated high-efficiency selection with bulk K_d reaching at 0.19 ± 0.04 μM by only two rounds, as compared to capillary zone electrophoresis (CZE) mode with K_d of 0.39 ± 0.03 μM. Next-generation sequencing (NGS) was performed by two methods of high output (Hiseq) and medium output (Miseq) with different sequencing depths, and their same results of high-frequency sequences confirmed the reliability of the obtained sequences. Through affinity analysis, the primer region and single base mutation (SBM) were observed to affect the sequence structure and to result in affinity change. Besides, molecular dynamics (MD) simulation was performed to validate the binding affinity of the candidates with BLF by analyzing binding sites, interaction forces, and binding free energy. Moreover, BLF detection in milk powder matrices was completed successfully with the optimized CE-aptasensor. The signal response was in a good linear relationship (R² = 0.9930) with 4-128 nM of BLF and the detection limit was 1 nM. The obtained results of BLF in four milk powder samples were in an acceptable agreement with the labeled concentrations. This study presented a completed CE based process including aptamers selection, affinity characterization, and detection application, which also validated the high-efficiency selection of ssCE-SELEX mode.

Online reaction based single-step capillary electrophoresis-systematic evolution of ligands by exponential enrichment for ssDNA aptamers selection

Capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX) has proven to be an effective technique for aptamers selection. In this study, we present an online reaction based convenient single-step CE-SELEX (ssCE-SELEX) mode with human thrombin (H-Thr) as a model target. The selection progress was monitored through bulk K_d analysis, which showed more than a 1000-fold improvement over the initial library after two rounds of selection. Three selected candidate sequences presented high binding affinities against H-Thr with nanomolar (nM) K_d determined by nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM, 56.4-177.1 nM) and CE based non-linear fitting (CE-NLF, 98.2-199.7 nM). They also exhibited high specificities towards H-Thr compared with bovine thrombin, IgG, lysozyme, and lactoferrin. Meanwhile, the K_d results by isothermal titration calorimetry (ITC) confirmed the effective CE in measuring the aptamer affinity. In addition, three candidates were applied as aptasensors in the AuNPs based colorimetric assay, which showed visible color change and good linear relationships (R² > 0.93) with H-Thr concentration. Furthermore, molecular dynamics (MD) simulation was performed to validate the binding of the three candidates with H-Thr by binding sites and binding free energy. The ssCE-SELEX method avoids off-line incubation, saves time and sample, and may provide a universal and convenient method for aptamers selection.

Online reaction based single-step CE for Protein-ssDNA complex obtainment to assist aptamer selection

CE application in aptamer selection (CE-SELEX) shows more advantages than other selection methods. In this study, an online reaction based single-step CE (ssCE) mode was employed for fast obtaining protein-ssDNA complex. Using human thrombin (H-Thr) and its aptamer Apt29 as models, we accomplished the procedures of mixing, reaction, separation, detection and complex collection in single step online process, which took about 10 min to obtain the H-Thr/Apt29 complex. Important factors, affecting the aptamer and H-Thr interaction (buffer, ratio of aptamer and H-Thr amount), and complex separation and collection (voltage and temperature) were discussed. Later, the online reaction of H-Thr with an 80 nt ssDNA library was realized under optimized conditions, and the H-Thr/ssDNA complex was collected and subjected to PCR. By analyzing the PCR product through capillary gel electrophoresis, the resulting approximative 80 nt DNA length validated the ssDNA sequence in complex. To confirm the availability of ssCE mode, two ssDNA libraries with different lengths (56 nt and 82 nt ssDNA) and three proteins (platelet derived growth factor, PDGF-BB; lactoferrin protein, LF; and single-strand DNA binding protein, SSB) were utilized. Their complex peaks were also observed in electropherograms as expected. Additionally, the online incubation of ssDNA and H-Thr was achieved by stopping the separation voltage for some time when ssDNA passed the H-Thr zone. Our results show the ssCE mode has apparent merits of saving time and sample cost for aptamer selection against protein targets.

Trypsin enhances aptamer screening: A novel method for targeting proteins

A novel screening method for protein aptamer selection was developed in this study. Aptamers with high affinity and specificity to the surface recombinant antigen of Helicobacter pylori (HP-Ag) and to tumor markers carcinoembryonic antigen (CEA), cancer antigen 125 (CA125) and cancer antigen 19-9(CA19-9) were screened using trypsin enhanced screening method. Briefly, the target proteins above were immobilized onto 96-well polystyrene plates and incubated with a single-stranded DNA (ssDNA) library for aptamer selection. Then, trypsin was introduced to digest the proteins and obtain ssDNA that bound to the target proteins with high specificity. The concentration of ssDNA that shed from protein-ssDNA complexes was detected. After sequencing, the enrichment of target-specific aptamers was monitored and the affinity of each aptamer was analyzed. Urea, which has been reported in other article, was used to compare with trypsin. The results revealed that trypsin was more effective than urea for protein aptamer selection. The protocol used in this study provided a novel method for generating aptamers.

Aptamer selection and applications for breast cancer diagnostics and therapy

Aptamers are short non-coding, single-stranded oligonucleotides (RNA or DNA) developed through Systematic Evolution of Ligands by Exponential enrichment (SELEX) in vitro. Similar to antibodies, aptamers can bind to specific targets with high affinity, and are considered promising therapeutic agents as they have several advantages over antibodies, including high specificity, stability, and non-immunogenicity. Furthermore, aptamers can be produced at a low cost and easily modified, and are, therefore, called "chemical antibodies". In the past years, a variety of aptamers specifically bound to both breast cancer biomarkers and cells had been selected. Besides, taking advantage of nanomaterials, there were a number of aptamer-nanomaterial conjugates been developed and widely investigated for diagnostics and targeted therapy of breast cancer. In this short review, we first present a systematical review of various aptamer selection methods. Then, various aptamer-based diagnostic and therapeutic strategies of breast cancer were provided. Finally, the current problems, challenges, and future perspectives in the field were thoroughly discussed.

Multiple modes of capillary electrophoresis applied in peptide nucleic acid related study

Peptide Nucleic Acid (PNA) is a nucleic acid analogue, whose neutrally charged and hydrophobic backbone makes it more stable in vivo, so it might act as a potentially better protein probe as compared to aptamer. Currently the investigation of PNA and protein interaction is scarce. In this research, multiple modes of capillary electrophoresis were established and applied for PNA characterization and its interaction with ssDNA and protein. A 15-mer PNA having the same nucleobase sequence as 15-mer anti-thrombin DNA aptamer was chosen as PNA model for this study, its pI (7.71) was estimated by capillary isoelectric focusing (cIEF). Due to its neutral charge and strong hydrophobicity, three micellar electrokinetic chromatography (MEKC) modes containing (a) SDS, (b) Triton X-100 and (c) CTAB were compared for PNA related analysis. CTAB was not applicable for PNA analysis, while in 4mM SDS or 2mM Triton X-100, PNA and PNA-ssDNA complex can be identified directly. The significant peak of PNA-ssDNA complex helped in validating the two MEKC modes for PNA and target interaction study. Furthermore, the effect of SDS and Triton X-100 concentrations in the two MEKC modes on the protein target thrombin analysis was investigated by capillary zone electrophoresis (CZE). 4mM SDS caused thrombin denaturation. So in 2mM Triton X-100, interactions of PNA with thrombin, PNA with RNase A and a non-aptameric PNA (n-PNA) with thrombin were compared. PNA with thrombin exhibited strongest binding. In summary, cIEF mode for PNA pI determination, MECK mode for direct PNA, PNA-ssDNA and PNA-protein complex identification and CZE mode for the effect of surfactant in MEKC modes on protein target thrombin analysis were applied. Above results showed that multiple modes of CE provide rapid and very low-sample cost methods for PNA related studies.

The application of capillary electrophoresis for assisting whole-cell aptamers selection by characterizing complete ssDNA distribution

Whole-cell SELEX faces more difficulties than SELEX against purified molecules target. In this work, we demonstrate the application of capillary electrophoresis for assisting whole-cell aptamers selection by characterizing complete ssDNA distribution. We chose three cancer cell lines U251, Hela and PC3 as target, FAM labeled Sgc8c (a 41mer aptamer) and FAM labeled 41mer random ssDNA library as ssDNA model. CE conditions of running buffer and capillary length and inner diameter as well as UV and LIF detection were optimized. The distribution percentage of Sgc8c and ssDNA library against U251, Hela and PC3 was demonstrated, the relative peak area of their complex is 8.94%, 1.05% and 0.44% for Sgc8c and 9.03%, 1.04% and 0.12% for ssDNA library respectively. Under the chosen experimental conditions, binding ability comparison of three cell lines was U251>Hela>PC3, which was validated by laser confocol microscope. For each cell, distribution percentage of ssDNA library was compared with that of Sgc8c. Finally, whole-cell complex of U251-Sgc8c was confirmed by increase incubation time and fraction CE analysis.