Analytical biochemistry最新文献_第8页

Double alkylation with maleimide-PEG-biotin: An enrichment method for cysteine redox states 马来酰亚胺-聚乙二醇-生物素双烷基化：半胱氨酸氧化还原态的富集方法

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-05-06 DOI: 10.1016/j.ab.2025.115892

Jung Mi Lim , Rodney L. Levine

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Polyaniline-graphene oxide (PANI/GO)-grafted paper-based nanosensor for the detection of Helicobacter pylori 聚苯胺-氧化石墨烯接枝纸基幽门螺杆菌检测传感器

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-05-05 DOI: 10.1016/j.ab.2025.115891

Rachna Poria , Desmond Lutomia , Ankur Kaushal , Selva Kumar Ramasamy , Shagun Gupta

{"title":"Polyaniline-graphene oxide (PANI/GO)-grafted paper-based nanosensor for the detection of Helicobacter pylori","authors":"Rachna Poria , Desmond Lutomia , Ankur Kaushal , Selva Kumar Ramasamy , Shagun Gupta","doi":"10.1016/j.ab.2025.115891","DOIUrl":"10.1016/j.ab.2025.115891","url":null,"abstract":"<div><div>A polyaniline-graphene oxide (PANI-GO) nanocomposite-grafted DNA biosensor for detecting <em>Helicobacter pylori</em>-specific toxins, oncoprotein cytotoxin-associated gene A (<em>CagA</em>), has been reported. The nanocomposite was fabricated on Screen printed paper electrode (SPPE) and modified with a 5′NH<sub>2</sub>-labelled single-stranded DNA (ssDNA) probe specific to the <em>CagA</em> gene via an EDC/NHS cross-linker. Under optimized electrochemical experimental conditions, CV and DPV were used to analyse the performance of the developed biosensor. A linear dynamic range for <em>H. pylori</em> ssDNA was established between 0.00001 ng/μl and 0.1 ng/μl, with correlation coefficients of R<sup>2</sup> = 0.9813 for the CV and R<sup>2</sup> = 0.9343 for the DPV. The sensitivities of the developed sensor in the CV studies were 50.261 μA μL/ng∙mm<sup>2</sup> and 66.5 μA μL/ng∙mm<sup>2</sup> in the DPV studies. CV demonstrated an LOD of 0.0026 ng/μL, whereas the LOD of the DPV studies was 0.001 ng/μL. The developed sensor was validated using different concentrations of <em>H. pylori</em> ssDNA spiked in human stool samples. The results highlight the potential of the developed biosensor to detect and quantify <em>H. pylori</em> genomic DNA in a sensitive and reliable manner to aid in clinical diagnostics and pathogen detection applications.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"704 ","pages":"Article 115891"},"PeriodicalIF":2.6,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143923103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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A beginners guide to SELEX and DNA aptamers SELEX和DNA适体的初学者指南

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-05-02 DOI: 10.1016/j.ab.2025.115890

Cameron Stephens, Nina M. Goodey, Ueli Gubler

{"title":"A beginners guide to SELEX and DNA aptamers","authors":"Cameron Stephens, Nina M. Goodey, Ueli Gubler","doi":"10.1016/j.ab.2025.115890","DOIUrl":"10.1016/j.ab.2025.115890","url":null,"abstract":"<div><div>SELEX stands for \"Systematic Evolution of Ligands by Exponential Enrichment.” It is an <em>in vitro,</em> iterative, PCR-based, target-specific selection strategy used to generate single-stranded DNA (ssDNA) aptamers that bind a target of interest. Properly selected aptamers bind their targets with high affinity and specificity and have utility in a multitude of detection assays. They are thus similar to antibodies but have the advantage of being more stable and cheaper to produce. The SELEX process encompasses several steps, some of which are critical to the successful isolation of an aptamer. Careful analysis and optimization of the SELEX process are thus important. This review summarizes our own experience when we, as complete novices, were setting up the SELEX system in our lab. It is thus meant to give some general and practical but concise pointers for anyone interested in initiating their own SELEX experiments. As such, the review covers key elements of the SELEX process, including library design, target selection and immobilization strategies, aptamer binding conditions, partitioning techniques, and PCR optimization. We also discuss common pitfalls such as by-product formation and single-stranded DNA recovery challenges, along with practical strategies to overcome them. Emerging trends and post-SELEX considerations, such as sequencing, structure prediction, and chemical modifications, are included to guide beginners through every stage of aptamer development.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"703 ","pages":"Article 115890"},"PeriodicalIF":2.6,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143912286","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Inhibition of DNA glycoxidation by mannitol and Pyridoxamine: Implications for DNA-antibody development in diabetes and diabetic retinopathy 甘露醇和吡哆胺对DNA糖氧化的抑制作用：对糖尿病和糖尿病视网膜病变中DNA抗体发展的影响

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-05-02 DOI: 10.1016/j.ab.2025.115886

Rihab Akasha , Uzma Shahab , Ramendra Pati Pandey , Saif Khan , Paridhi Puri , Zeeshan Rafi , Sultan Alouffi , Saheem Ahmad

{"title":"Inhibition of DNA glycoxidation by mannitol and Pyridoxamine: Implications for DNA-antibody development in diabetes and diabetic retinopathy","authors":"Rihab Akasha , Uzma Shahab , Ramendra Pati Pandey , Saif Khan , Paridhi Puri , Zeeshan Rafi , Sultan Alouffi , Saheem Ahmad","doi":"10.1016/j.ab.2025.115886","DOIUrl":"10.1016/j.ab.2025.115886","url":null,"abstract":"<div><div>Chronic exposure to reactive carbonyl species such as glyoxal and methylglyoxal, along with hydroxyl radicals (<sup>•</sup>OH), leads to glycative and oxidative damage, contributing to insulin resistance and diabetic complications. Pyridoxamine (PM) is known to counteract these effects, but its potential synergy with mannitol (MN), a hydroxyl radical scavenger, remains unexplored. This study investigates the combined efficacy of MN and PM in preventing glycation and oxidative damage in vitro.</div><div>Calf thymus DNA was subjected to glycation using 10 mM glyoxal, oxidation via the Fenton reaction, and sequential glycoxidation (glycation followed by oxidation). The inhibitory effects of MN, PM, and their combination were assessed using NBT reduction for early glycation, GK-ribose for AGEs, TBARS for hydroxyl radicals, and spectroscopic analyses for AGEs formation. A clinical study also examined autoantibody prevalence in diabetes and diabetic retinopathy (DR).</div><div>Results showed that glycoxidated DNA exhibited structural alterations, with MN and PM individually reducing ketoamine content. Their combination further enhanced glycation and glycoxidation inhibition. Additionally, MN-PM co-administration synergistically reduced AGEs and hydroxyl radicals. Autoantibody levels were elevated in diabetes and DR. These findings suggest PM-MN co-administration as a promising strategy to mitigate diabetic complications.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"703 ","pages":"Article 115886"},"PeriodicalIF":2.6,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143912297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Development of a chemiluminescence enzyme immunoassay (CLEIA) for quantitating L1 protein in HPV vaccines

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-05-02 DOI: 10.1016/j.ab.2025.115889

ChengRui Fei , Huan Yang , SiJie Wang , WenZhi He , Xue Shen , Ying Zhang , YiHeng Jiang , Li Yang , XiaoJuan Li , Fan Wu , YaNan Wu , Qin Liu

{"title":"Development of a chemiluminescence enzyme immunoassay (CLEIA) for quantitating L1 protein in HPV vaccines","authors":"ChengRui Fei , Huan Yang , SiJie Wang , WenZhi He , Xue Shen , Ying Zhang , YiHeng Jiang , Li Yang , XiaoJuan Li , Fan Wu , YaNan Wu , Qin Liu","doi":"10.1016/j.ab.2025.115889","DOIUrl":"10.1016/j.ab.2025.115889","url":null,"abstract":"<div><div>The L1 protein serves as the principal capsid component of human papillomavirus (HPV). All globally commercialized HPV vaccines utilize virus-like particles (VLPs) formed through L1 protein self-assembly. Quantitative analysis of L1 protein concentration constitutes a critical parameter for evaluating the antigenic potency of HPV vaccines. In this study, we developed a chemiluminescent enzyme immunoassay (CLEIA) for precise quantification of L1 protein in bivalent HPV vaccines. Employing a sandwich immunoassay format, antigen-antibody complexes were immobilized on 96-well microplates using capture antibodies, followed by detection with HRP-conjugated secondary antibodies. Chemiluminescent signal amplification was achieved through enzymatic catalysis of luminol/hydrogen peroxide in the presence of enhancer molecules. Systematic optimization of experimental parameters yielded a validated methodology demonstrating excellent reproducibility (inter-assay CV < 4 %), accuracy (recovery rate 100.5 ± 2.8 % for 16L1 and 95.5 ± 6.4 % for 18L1), precision (inter-assay CV < 7 %) and sensitivity (limit of quantitation (LOQ) 0.0996 μg/mL for HPV16L1 and 0.1459 μg/mL for HPV18L1). This optimized assay provides a reliable analytical platform for quantitating L1 Protein in bivalent HPV vaccine.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"704 ","pages":"Article 115889"},"PeriodicalIF":2.6,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143943313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Triple DNAzyme cleavage mediated signal cascade for sensitive and reliable Kawasaki disease related microRNA analysis 三重DNAzyme切割介导的信号级联用于敏感可靠的川崎病相关microRNA分析

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-05-01 DOI: 10.1016/j.ab.2025.115887

Qunyan Ruan, Bina Zhao

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TransCNN: A novel architecture combining transformer and TextCNN for detecting N4-acetylcytidine sites in human mRNA transnn：一种结合transformer和TextCNN的新型结构，用于检测人类mRNA中的n4 -乙酰胞苷位点

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-04-29 DOI: 10.1016/j.ab.2025.115882

Shengli Zhang, Kai Liu, Yujie Xu

{"title":"TransCNN: A novel architecture combining transformer and TextCNN for detecting N4-acetylcytidine sites in human mRNA","authors":"Shengli Zhang, Kai Liu, Yujie Xu","doi":"10.1016/j.ab.2025.115882","DOIUrl":"10.1016/j.ab.2025.115882","url":null,"abstract":"<div><div>N4-acetylcytidine (ac4C), a pivotal post-transcriptional RNA modification, is central to understanding transcriptional regulation and diverse biological processes. As a key determinant of RNA structural stability and functional regulation, ac4C has been strongly associated with multiple human diseases. We can obtain a better understanding of regulation mechanism of gene expression by identifying ac4C sites rapidly and precisely. However, existing predictive approaches are constrained by limitations in feature representation and sequence context modeling, necessitating the development of advanced methodologies. In this study, we introduce a novel architecture named TransCNN that integrates transformer and Text convolutional neural network (TextCNN) to predict ac4C sites. TransCNN demonstrates superior performance compared to existing models on both 10-fold cross-validation and independent dataset with the accuracy of 83.27 % and 82.89 %, respectively. The enhanced performance of TransCNN is attributed to the transformer's ability to extract adaptive features and TextCNN's capability to form both narrow and broad connections within the sequence. This study aims to contribute significantly to the field by advancing the understanding and prediction of RNA modifications. The datasets and code used in this study are available at <span><span>https://github.com/liukai23157/</span><svg><path></path></svg></span>TransCNN.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"703 ","pages":"Article 115882"},"PeriodicalIF":2.6,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143898423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Metabolomics approach using HR-MAS NMR spectroscopy for the assessment of metabolic profiles of uterine fibroids 代谢组学方法使用HR-MAS核磁共振光谱评估子宫肌瘤的代谢谱

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-04-29 DOI: 10.1016/j.ab.2025.115885

Senem Arda Düz , Akın Mumcu , Berat Doğan , Erdinç Sarıdoğan , Görkem Tuncay , Taylan Onat , Abdullah Karaer

{"title":"Metabolomics approach using HR-MAS NMR spectroscopy for the assessment of metabolic profiles of uterine fibroids","authors":"Senem Arda Düz , Akın Mumcu , Berat Doğan , Erdinç Sarıdoğan , Görkem Tuncay , Taylan Onat , Abdullah Karaer","doi":"10.1016/j.ab.2025.115885","DOIUrl":"10.1016/j.ab.2025.115885","url":null,"abstract":"<div><div>The aim of this study is to determine dysregulated metabolites and metabolic pathways in uterine fibroids and in the myometrial tissue from which uterine fibroids are derived. Fifteen (15) patients underwent hysterectomy because of uterine fibroids and 14 controls were included in this study. <sup>1</sup>H HR-MAS NMR spectroscopy data were obtained from uterine fibroid tissue, the adjacent healthy myometrial tissue from cases, and myometrial tissue from controls. PCA and PLS-DA score plots from multivariate statistical analysis of pre-processed spectral data demonstrated a distinction between cases and control groups. The levels of lactate, alanine, glutamate, glutamine, methionine, acetone, isocitrate, choline, glycerophosphocholine, phosphocholine, <em>o</em>-phosphoethanolamine, taurine, myo-inositol, <em>p</em>-methylhistidine, phenylacetate, ascorbate, glucose, and methylhistidine were significantly higher in uterine fibroid tissue compared to the neighboring healthy myometrial tissue. Additionally, when adjacent healthy myometrial tissue was compared to control myometrial tissue, significantly lower levels of valine, leucine, isoleucine, ethanol, arginine, N-acetyl tyrosine, acetone, <em>p</em>-methylhistidine, glucose, phenylacetate, myo-inositol, and alpha-glucose were observed. The study provides a foundational framework by revealing the metabolomic heterogeneity of uterine fibroids. Strategies should be developed to target the metabolic alterations that contribute to the growth of these common tumors.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"704 ","pages":"Article 115885"},"PeriodicalIF":2.6,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143935883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

nCas9-based method for rolling-circle DNA substrate generation 基于ncas9的滚圈DNA底物生成方法

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-04-25 DOI: 10.1016/j.ab.2025.115883

Nischal Sharma, Kelsey S. Whinn, Harshad Ghodke, Antoine M. van Oijen, Jacob S. Lewis, Lisanne M. Spenkelink

{"title":"nCas9-based method for rolling-circle DNA substrate generation","authors":"Nischal Sharma, Kelsey S. Whinn, Harshad Ghodke, Antoine M. van Oijen, Jacob S. Lewis, Lisanne M. Spenkelink","doi":"10.1016/j.ab.2025.115883","DOIUrl":"10.1016/j.ab.2025.115883","url":null,"abstract":"<div><div>Rolling-circle DNA replication is a DNA-duplication mechanism whereby circular DNA templates are continuously copied to produce long DNA products. It is widely used in molecular diagnostics, DNA sequencing, nanotechnology, and <em>in vitro</em> DNA replication studies. The efficiency of rolling-circle replication reaction heavily relies on the quality of the rolling-circle DNA template. Existing methods to create rolling-circle DNA substrates often rely on unique restriction sites and have limited control over replication fork topology and position. To address these limitations, we present a straightforward, customizable, and efficient strategy for producing rolling-circle DNA substrates with control over gap size and fork position. Our method relies on the use of nickase Cas9 (nCas9), which can be programmed to target specific DNA sequences using guide RNAs. In a one-pot reaction, we target nCas9 to four sites on an 18-kb plasmid to create 8–11-bp fragments. These fragments are removed and a flap oligo is ligated, to construct a fork with precisely controlled flap length and gap size. We demonstrate the application of this DNA substrate in an <em>in vitro</em> single-molecule rolling-circle DNA-replication assay. With our method, any plasmid DNA can be converted into a rolling-circle template, permitting generation of more physiologically-relevant DNA templates.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"703 ","pages":"Article 115883"},"PeriodicalIF":2.6,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143881540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proximity rolling circle amplification based generation of lighting-up aptamer for sensitive and label-free MicroRNA analysis 基于邻近滚动圆扩增的点亮适体的产生，用于敏感和无标记的MicroRNA分析

IF 2.6 4区生物学

Analytical biochemistry Pub Date : 2025-04-25 DOI: 10.1016/j.ab.2025.115884

Chaogang Yuan , Lifang Cao , Honglian Shen , Yuexiang Zhang

{"title":"Proximity rolling circle amplification based generation of lighting-up aptamer for sensitive and label-free MicroRNA analysis","authors":"Chaogang Yuan , Lifang Cao , Honglian Shen , Yuexiang Zhang","doi":"10.1016/j.ab.2025.115884","DOIUrl":"10.1016/j.ab.2025.115884","url":null,"abstract":"<div><div>The dysregulated expression of microRNA (miRNA) has been strongly linked to pneumonia. However, ultrasensitive miRNA detection remains technically challenging due to their short sequences and low abundance in biological samples. Herein, we developed a catalytic hairpin assembly -triggered proximity rolling circle transcription system for synthesizing malachite green (MG)-binding RNA aptamers, enabling label-free and highly sensitive detection of miRNA-21. In this system, target miRNA-21 initiates hairpin probe structural rearrangement, promoting miRNA-21 recycling and activating dual rolling circle transcription reactions. The resulting long RNA transcripts undergo partial hybridization, yielding numerous functional MG RNA aptamers. Upon binding to MG dye, these aptamers generate a robust fluorescence signal, allowing ultrasensitive miRNA-21 detection at concentrations as low as 0.51 fM. The assay exhibits high specificity, discriminating miRNA-21 from single-base mismatched sequences, and shows promise for monitoring miRNA-21 expression in clinical samples. By combining the signal amplification of rolling circle transcription with the high-affinity recognition of MG aptamers, this method achieves a low background, superior signal-to-noise ratio, and exceptional sensitivity. Furthermore, the strategy can be readily adapted to detect other trace biomarkers by modifying the target-recognition sequence.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"703 ","pages":"Article 115884"},"PeriodicalIF":2.6,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143894737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0