The application of Aptamer in biomarker discovery

Li, Yongshu; Tam, Wanny; Yu, Yuanyuan; Zhang, Zhuo; Xue, Zhichao; Tsang, Chi-Man; Qiao, Xiaoting; Wang, Xiaokang; Wang, Weijing; Li, Yongyi; Tu, Yanyang; Gao, Yunhua

doi:10.1186/s40364-023-00510-8

Cited by 22 publications

(6 citation statements)

References 150 publications

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“…Specifically, the conserved nucleotide sites (TTCACCTACCG) were situated at the 5 ′ terminus of the random sequences, albeit with specific mutations. Then, a collection of 14 candidate aptamers (Apt-01, 02, 03, 04, 05, 07, 08, 09, 12,13,14,15,18,20) was generated by selecting the two most dominant sequences from each family of sequences and the M-fold web server was used to perform Gibbs free energy calculations and predictions of the secondary structure, which inform their thermodynamic stability. The average Gibbs free energy value of the 14 candidate aptamers in Table S5 is −11.62 ± 1.53, indicating that these 14 candidate aptamers have robust stability.…”

Section: Affinity and Specificity Of Selected Aptamersmentioning

confidence: 99%

Screening and Application of DNA Aptamers for Heparin-Binding Protein

Zhou,

Cao,

Huang

et al. 2024

Molecules

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Rapid detection of heparin-binding protein (HBP) is essential for timely intervention in sepsis cases. Current detection techniques are usually antibody-based immunological methods, which have certain problems, such as complexity and slow detection, and fall short in meeting the urgency of clinical needs. The application of an aptamer can address these concerns well. In this study, HBP-specific DNA aptamers were screened first. Among which, Apt-01, Apt−02, and Apt−13 had a high affinity for HBP, exhibiting impressive KD values of 3.42, 1.44, and 1.04 nmol/L, respectively. Then, the aptamer of HBP and its partially complementary primer probe were combined to form double-stranded DNA (dsDNA) and synthesize a circular DNA template. The template is complementary to the primer probe, but due to the presence of dsDNA, ExoIII cleaves C2-13 as an RCA primer probe, rendering the template unable to recognize the primer probe and preventing the RCA reaction from proceeding. When the target is present, it competes with the adapter for recognition and releases C2-13, exposing its 3′ end. After initiating the RCA at room temperature and reacting with SYBR GreenII at 37 °C for 20 min, fluorescence changes can be observed and quantitatively analyzed at a 530 nm wavelength, achieving quantitative biological analysis. Apt-01 was used to develop a fluorescent biosensor for HBP detection, which exhibited a good linear range (0.01 nmol/L to 10 nmol/L) and detection limit (0.0056 nmol/L). This advancement holds the potential to lay a solid groundwork for pioneering sensitive and specific methods for HBP detection and to significantly enhance the diagnostic processes for sepsis.

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Section: Affinity and Specificity Of Selected Aptamersmentioning

confidence: 99%

Screening and Application of DNA Aptamers for Heparin-Binding Protein

Zhou,

Cao,

Huang

et al. 2024

Molecules

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“…As artificial single-strand oligonucleotides, aptamers possess unique advantages compared to conventional antibodies. They can be flexible in design, have low immunogenicity, relative chemical/thermos stability, easy synthesis, as well as convenient modification [135,136]. In contrast to using aptamers, antibody-based methods excel in both analytical sensitivity and specificity and are therefore extensively employed to detect and quantify specific proteins [135].…”

Section: What Are the Advantages Of Affinity-capture-separation Analy...mentioning

confidence: 99%

“…Investigators should be careful to treat discovery platforms appropriately, confirming key results with additional methods, using comparisons to reference standards to obtain exact protein quantification [144], and specifically acquiring valid clinical biomarkers. Reliable clinical biomarkers are still limited, restricted by the suboptimal methods of biomarker discovery [135,136]. When using modern technologies in the diagnostic process, careful care must be taken to guarantee safe, efficient, and trusted care, and to avoid diagnostic errors that may lead to devastating consequences for the patient.…”

Section: What Are the Advantages Of Affinity-capture-separation Analy...mentioning

confidence: 99%

Human Sputum Proteomics: Advancing Non-Invasive Diagnosis of Respiratory Diseases with Enhanced Biomarker Analysis Methods

Guzman,

Guzman

2024

IJTM

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Many ailments can be diagnosed while they are asymptomatic, meaning that the patient has no signs or symptoms of a progressing disease. If caught in their initial stage of formation, these disorders can be effectively treated, leading to successful outcomes; curative therapies can halt illnesses from advancing, thus improving the quality of life and long-term survival of the patient. Still, cutting-edge upgrades in precision technologies are necessary for early, reliable, affordable, and rapid disease detection, but also vital for the well-being of people and the future of global public health. The emerging role and utility of non-invasive and repeatable diagnostic test approaches for the detection of health conditions have been exemplified by liquid biopsies based on genomic biomarkers. As such, biological fluids permit any measurable molecular indicator or signature (e.g., proteins) to provide valuable information on an individual’s wellness and/or disease. Among the bodily secretions used for non-invasive diagnostics is sputum, a complex viscous gel-like biopolymeric network that has gained growing recognition as a rich source of biomarkers of airway infections and pulmonary diseases, and serves as a determinant to reveal other illnesses. As per the World Health Organization, the burden of respiratory conditions is exacerbated by factors ranging from considerable subjection to air pollution and occupational contaminants to tobacco smoking and second-hand smoke, in addition to poor socio-economic status. Due to the likely increase in these determinants, respiratory tract ailments are on the rise, affecting the health of many individuals, in addition to putting stress on healthcare facilities and services worldwide. The aim of this study was to perform a narrative review of sputum constituents with an emphasis on proteins and glycoproteins assessed as possible biomarkers of lung and other organ diseases. A search was conducted using mucus, sputum proteomics, sputum biomarkers, and point-of-care testing as keywords employing Google, PubMed (MEDLINE), and Web of Science, selecting the most referenced and related papers of the last decade. We, therefore, highlight the need to use expectorated or induced sputum specimens as a routine sample source for testing valuable protein biomarkers to diagnose these chronic disorders, predict inflammation and disease progression, as well as monitor the effectiveness of treatments. Further, we discuss the urgent need for fast and reliable point-of-care methods to detect and quantify crucial protein biomarkers in sputum specimens, and the limitations faced when dealing with their complex matrices.

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“…[9][10][11] Aptamers, which are short, single-stranded DNA or RNA oligonucleotides with unique three-dimensional structures, 12 are extensively utilized in the development of biosensors due to their high specicity to the targets. 13 The aptamers of b-Lg have been screened using the exponentially enriched systematic ligand evolution technique (SELEX). 14 In addition, various techniques have been utilized to develop aptasensors for b-Lg detection, including uorescence detection, 15,16 surface-enhanced Raman spectroscopy, 17 electrochemistry, 18 and transient synchronous electrophoresis.…”

Section: Introductionmentioning

confidence: 99%