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Article Citation - WoS: 10Citation - Scopus: 12Detection of Viruses by Probe-Gated Silica Nanoparticles Directly From Swab Samples(Elsevier, 2022) Tuna, Bilge Guvenc; Durdabak, Dilara Buse; Ercan, Meltem Kazak; Dogan, Soner; Kavruk, Murat; Dursun, Ali Dogan; Ozalp, Veli CengizViral infection has been one of the major health issues for human life. The real-time reverse transcription polymerase chain reaction (RT-PCR)-based detection has primarily been used for virus detection as a highly reliable procedure. However, it is a relatively long and multi-stage process. In addition, required skilled personnel and complex instrumentation presents difficulties in large scale monitoring efforts. Therefore, we report here a direct and fast detection method for CoV-2 genome as applied in the nose-throat swab samples without any further processing. The detection principle is based on fluorescein-loaded mesoporous silica nanoparticles capped by specific gene sequences probes immobilized on the surface of the nanoparticles. Upon hybridization with the target viral genome, the fluorescein molecules were released from the mesopores. Testing with synthetic oligonucleotides, the NSP12 gene-based detection resulted in a strong signal. Target detection time could be optimized to 15 min and the limit of detection was 1.4 RFU with 84% sensitivity with clinical samples (n = 43).Review Citation - WoS: 26Citation - Scopus: 23Real-Time Biosensing Bacteria and Virus With Quartz Crystal Microbalance: Recent Advances, Opportunities, and Challenges(Taylor & Francis inc, 2023) Bonyadi, Farzaneh; Kavruk, Murat; Ucak, Samet; Cetin, Barbaros; Bayramoglu, Gulay; Dursun, Ali D. D.; Ozalp, Veli C. C.Continuous monitoring of pathogens finds applications in environmental, medical, and food industry settings. Quartz crystal microbalance (QCM) is one of the promising methods for real-time detection of bacteria and viruses. QCM is a technology that utilizes piezoelectric principles to measure mass and is commonly used in detecting the mass of chemicals adhering to a surface. Due to its high sensitivity and rapid detection times, QCM biosensors have attracted considerable attention as a potential method for detecting infections early and tracking the course of diseases, making it a promising tool for global public health professionals in the fight against infectious diseases. This review first provides an overview of the QCM biosensing method, including its principle of operation, various recognition elements used in biosensor creation, and its limitations and then summarizes notable examples of QCM biosensors for pathogens, focusing on microfluidic magnetic separation techniques as a promising tool in the pretreatment of samples. The review explores the use of QCM sensors in detecting pathogens in various samples, such as food, wastewater, and biological samples. The review also discusses the use of magnetic nanoparticles for sample preparation in QCM biosensors and their integration into microfluidic devices for automated detection of pathogens and highlights the importance of accurate and sensitive detection methods for early diagnosis of infections and the need for point-of-care approaches to simplify and reduce the cost of operation.Article Citation - WoS: 5Citation - Scopus: 5Aptamer decorated PDA@magnetic silica microparticles for bacteria purification(Springer Wien, 2024) Kavruk, Murat; Babaie, Zahra; Kibar, Gunes; Cetin, Barbaros; Yesilkaya, Hasan; Amrani, Yassine; Ozalp, V. CengizOne significant constraint in the advancement of biosensors is the signal-to-noise ratio, which is adversely affected by the presence of interfering factors such as blood in the sample matrix. In the present investigation, a specific aptamer binding was chosen for its affinity, while exhibiting no binding affinity towards non-target bacterial cells. This selective binding property was leveraged to facilitate the production of magnetic microparticles decorated with aptamers. A novel assay was developed to effectively isolate S. pneumoniae from PBS or directly from blood samples using an aptamer with an affinity constant of 72.8 nM. The capture experiments demonstrated efficiencies up to 87% and 66% are achievable for isolating spiked S. pneumoniae in 1 mL PBS and blood samples, respectively.Article Biotechnological Preparedness for Novel Pandemics: Diagnostic Performance of IVDS Against SARS-CoV(Wiley, 2025) Kavruk, Murat; Ercan, Meltem; Borsa, Baris Ata; Ozalp, Veli Cengiz; Hernandez, Frank J.Although the COVID-19 pandemic has created many challenges and negative impacts around the world, some of which will persist into the future, its technological challenge has created a unique opportunity in a globalized world. It is a rare event that almost all of humanity to be directed towards a single goal and to try to produce solutions, but the necessity of a similar global action in the future has begun to enter the agenda again. The predictions made on the basis of countries and institutions against the possibility of a pandemic, which is defined as Disease X, are shaped by the experience of the COVID-19 pandemic. Technologically, one of the know-how we have gained in this pandemic is the performance of IVD and test systems in terms of quality and quantity. A comprehensive analysis of the products produced by combining biotechnology with different strategies has not been conducted. In this context, we have analyzed the technical preferences, limitations, and other performance parameters of IVDs and test kits that could be developed against a future Disease X. The performance parameters of 2,882 biotechnological products listed for use in the European Union have been analyzed, and areas that could be targeted for increased effectiveness have been identified. Our study is the first of its kind in this field and can serve as a guide for those who want to work on detection methods, diagnostics, and novel technologies for deployment in future pandemics.Article Citation - WoS: 3Citation - Scopus: 3Paper-Based Aptasensor Assay for Detection of Food Adulterant Sildenafil(Mdpi, 2024) Kavruk, Murat; Ozalp, Veli CengizSildenafil is used to treat erectile dysfunction and pulmonary arterial hypertension but is often illicitly added to energy drinks and chocolates. This study introduces a lateral flow strip test using aptamers specific to sildenafil for detecting its illegal presence in food. The process involved using graphene oxide SELEX to identify high-affinity aptamers, which were then converted into molecular gate structures on mesoporous silica nanoparticles, creating a unique signaling system. This system was integrated into lateral flow chromatography strips and tested on buffers and chocolate samples containing sildenafil. The method simplifies the lateral flow assay (LFA) for small molecules and provides a tool for signal amplification. The detection limit for these strips was found to be 68.2 nM (31.8 mu g/kg) in spiked food samples.
