Development of Aptamer-Based Molecular Tools for Rapid Intraoperative Diagnosis and <i>In Vivo</i> Imaging of Serous Ovarian Cancer

Wang, Jing; Fang, Xiaona; Zhang, Chenchen; Ji, Haishuo; Pang, Qiushi; Li, Xuqing; Z, Luo; Wu, Qiang; Zhang, Liyun

doi:10.1021/acsami.1c02072

Cited by 17 publications

(17 citation statements)

References 46 publications

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“…Moreover, compared to antibodies, versatility of aptamers also permits chemical modifications to be performed at ease for diagnostic and therapeutic applications (Elskens et al 2020;Odeh, et al 2019). Due to their advantages, aptamers are widely used in diagnostics (Liu et al 2021;Citartan 2021), capturing assays (Citartan et al 2016), decontamination processes (Bilibana et al 2017), drug delivery (Thevendran et al 2020;Citartan 2019), therapeutics (Li et al 2021) and in vivo imaging (Wang et al 2021). Aptamers are generated through a process called Systemic Evolution of Ligands via Exponential Enrichment (SELEX).…”

Section: Introductionmentioning

confidence: 99%

Development of an optimization pipeline of asymmetric PCR towards the generation of DNA aptamers: a guide for beginners

Yeoh

Andrew

Tang

et al. 2022

World J Microbiol Biotechnol

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Asymmetric PCR is one of the most utilized strategies in ssDNA generation towards DNA aptamer generation due to its low cost, robustness and the low amount of starting template. Despite its advantages, careful optimization of the asymmetric PCR is still warranted to optimize the yield of ssDNA. In this present study, we have developed an extensive optimization pipeline that involves the optimization of symmetric PCR initially followed by the optimization of asymmetric PCR. In the asymmetric PCR, optimization of primer amounts/ratios, PCR cycles, annealing temperatures, template concentrations, Mg 2+ /dNTP concentrations and the amounts of Taq Polymerase was carried out. To further boost the generation of ssDNA, we have also integrated an additional single-stranded DNA generation method, either via lambda exonuclease or biotinstreptavidin-based separation into the optimization pipeline to further improve the yield of ssDNA generation. We have acquired 700 ± 11.3 and 820 ± 19.2 nM for A-PCR-lambda exonuclease and A-PCR-biotin-streptavidin-based separation, respectively. We urge to develop a separate optimization pipeline of asymmetric PCR for each different randomized ssDNA library before embarking on any SELEX studies.

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Section: Introductionmentioning

confidence: 99%

Development of an optimization pipeline of asymmetric PCR towards the generation of DNA aptamers: a guide for beginners

Yeoh

Andrew

Tang

et al. 2022

World J Microbiol Biotechnol

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“…Structure switching sensors such as electrochemical aptamer-based (E-AB) sensors rely on a measurable conformational change of the electrode-bound nucleic acid aptamer in the presence of a target. − Aptamers are single-stranded DNA or RNA oligonucleotides selected to bind to a specific target analyte through a process termed SELEX. − The interest in the development of aptamer-based sensors is growing because of the ability to detect virtually any analyte of interest through the selection of the nucleic acid sequence specific to the target analyte. However, the functionality of this class of sensing strategies, including electrochemical, aptamer-based sensors, is dependent on the target-induced conformational change of the nucleic acid measured by changes in the faradic current associated with the oxidation/reduction of a redox moiety at the 3′ position of the aptamer.…”

Section: Introductionmentioning

confidence: 99%

Effects of Nucleic Acid Structural Heterogeneity on the Electrochemistry of Tethered Redox Molecules

Sykes

White

2022

Langmuir

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The cation condensation-induced collapse of electrode-bound nucleic acids and the resulting change in the electrochemical signal is a useful tool to predict the structure and redox probe location of heterogeneous structures of surface-tethered DNA probesa common architecture employed in the development of electrochemical sensors. In this paper, we measure the faradaic current of an appended redox molecule at the 3′ position of the nucleic acid using cyclic voltammetry before and after nucleic acid collapse for various nucleic acid architectures and heterogeneous mixtures on the same electrode surface. The voltammetric peak current change with collapse correlates with the proximity of the redox molecules from the surface. For stem-loop probes, the terminal methylene blue is initially held closer to the surface, such that inducing collapse, by reducing the dielectric permittivity of the interrogation solution, results in a ∼30% increase in current. However, when incorporating pseudoknot probes that hold methylene blue further away from the electrode surface, the current change is much larger (∼120%), indicating a larger conformation change. Upon a 50:50 ratio of the two, we observe a change in current that relates to the ratiometric distribution of the probe used to make the surfaces. Additionally, using cyclic voltammetry, we find that the change between diffusion-limited and diffusion-independent peak currents is dependent upon the distinct structural characteristics of DNA probes on the surface (stem-loop or pseudoknot), as well as the ratios of different DNA probes on the surface. Thus, we demonstrate that the heterogeneous nature of DNA probes governs the corresponding electrochemical signals, which can lead to a better understanding on how to predict the structures of functional nucleic acids on electrode surfaces and how this affects surface-to-surface variability and electrochemical response.

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“…Since 1990, Tuerk and Ellington [12] applied SELEX technology to obtain aptamers that can specifically recognize T4 DNA polymerase firstly. Aptamers have developed continuously and become a new generation of molecular recognition probes, and it is widely used in medical diagnosis and molecular imaging, [13][14][15] environmental monitoring, [16,17] food safety and other fields. [18][19][20] There are various aptamer screening methods according to different targets, including cell, [21,22] virus [23] and tissue.…”

Section: Introductionmentioning

confidence: 99%

Screening and Specificity Analysis of Aptamer in Infiltrating Ductal Carcinoma of Breast

et al. 2022

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Breast cancer is a common malignant tumor disease in women, and early diagnosis has a better preventive effect on cancer. Aptamers, which are mainly screened by the exponential enrichment ligand phylogenetic technique, play an important role in the early diagnosis of cancer as early diagnostic molecules. In this study, aptamers identified specifically infiltrating ductal carcinoma of breast were obtained and their specificity was investigated. The aptamers of invasive ductal carcinoma of breast were screened based on Serum‐SELEX (Ser‐SELEX) technology, and sequences that specific binding were obtained by high‐throughput sequencing. The secondary structure of the aptamers was predicted by online software, the affinity and specificity of the aptamers were determined by q‐PCR and ELASA. After 13 rounds of screening, the aptamer IDC31 was obtained, and its secondary structure was predicted to have a stem ring structure. The q‐PCR results showed that the aptamer IDC31 had strong affinity and specificity for infiltrating ductal carcinoma of breast, and the dissociation constants were within the nanomolar range. The ELASA test showed that IDC31 had great specificity for breast invasive ductal carcinoma, and the detection rate was over 80 %. Therefore, the aptamer IDC31 could be used as an early diagnosis tool for breast invasive ductal carcinoma, which provided a possibility for the early diagnosis of breast invasive ductal carcinoma.

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Development of Aptamer-Based Molecular Tools for Rapid Intraoperative Diagnosis and In Vivo Imaging of Serous Ovarian Cancer

Cited by 17 publications

References 46 publications

Development of an optimization pipeline of asymmetric PCR towards the generation of DNA aptamers: a guide for beginners

Development of an optimization pipeline of asymmetric PCR towards the generation of DNA aptamers: a guide for beginners

Effects of Nucleic Acid Structural Heterogeneity on the Electrochemistry of Tethered Redox Molecules

Screening and Specificity Analysis of Aptamer in Infiltrating Ductal Carcinoma of Breast

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