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Smirnov VV, Drozd VS, Patra CK, Hussein Z, Rybalko DS, Kozlova AV, Nour MAY, Zemerova TP, Kolosova OS, Kalnin AY, El-Deeb AA. Towards the development of a DNA automaton: modular RNA-cleaving deoxyribozyme logic gates regulated by miRNAs. Analyst 2024; 149:1947-1957. [PMID: 38385166 DOI: 10.1039/d3an02178e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Advancements in DNA computation have unlocked molecular-scale information processing possibilities, utilizing the intrinsic properties of DNA for complex logical operations with transformative applications in biomedicine. DNA computation shows promise in molecular diagnostics, enabling precise and sensitive detection of genetic mutations and disease biomarkers. Moreover, it holds potential for targeted gene regulation, facilitating personalized therapeutic interventions with enhanced efficacy and reduced side effects. Herein, we have developed six DNAzyme-based logic gates able to process YES, AND, and NOT Boolean logic. The novelty of this work lies in their additional functionalization with a common DNA scaffold for increased cooperativity in input recognition. Moreover, we explored hierarchical input binding to multi-input logic gates, which helped gate optimization. Additionally, we developed a new design of an allosteric hairpin switch used to implement NOT logic. All DNA logic gates achieved the desired true-to-false output signal when detecting a panel of miRNAs, known for their important role in malignancy regulation. This is the first example of DNAzyme-based logic gates having all input-recognizing elements integrated in a single DNA nanostructure, which provides new opportunities for building DNA automatons for diagnosis and therapy of human diseases.
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Affiliation(s)
- Viktor V Smirnov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
| | - Valerya S Drozd
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
| | - Christina K Patra
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
| | - Zain Hussein
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Almetyevsk State Oil Institute, 2 Lenina St., Almetyevsk, 423450, Tatarstan, Russian Federation
| | - Daria S Rybalko
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
| | - Anastasia V Kozlova
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Almetyevsk State Oil Institute, 2 Lenina St., Almetyevsk, 423450, Tatarstan, Russian Federation
| | - Moustapha A Y Nour
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Almetyevsk State Oil Institute, 2 Lenina St., Almetyevsk, 423450, Tatarstan, Russian Federation
| | - Tatiana P Zemerova
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
| | - Olga S Kolosova
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Faculty of Industrial Drug Technology, Saint Petersburg State Chemical and Pharmaceutical University, 14, lit. A, st. Professor Popov, 197022, St. Petersburg, Russian Federation
| | - Arseniy Y Kalnin
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Institute of Chemistry, Saint Petersburg University, 7/9 Universitetskaya Nab., 199034 St. Petersburg, Russian Federation
| | - Ahmed A El-Deeb
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.
- Almetyevsk State Oil Institute, 2 Lenina St., Almetyevsk, 423450, Tatarstan, Russian Federation
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Tang F, Ding A, Xu Y, Ye Y, Li L, Xie R, Huang W. Gene and Photothermal Combination Therapy: Principle, Materials, and Amplified Anticancer Intervention. Small 2024; 20:e2307078. [PMID: 37775950 DOI: 10.1002/smll.202307078] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/19/2023] [Indexed: 10/01/2023]
Abstract
Gene therapy (GT) and photothermal therapy (PTT) have emerged as promising alternatives to chemotherapy and radiotherapy for cancer treatment, offering noninvasiveness and reduced side effects. However, their efficacy as standalone treatments is limited. GT exhibits slow response rates, while PTT is confined to local tumor ablation. The convergence of GT and PTT, known as GT-PTT, facilitated by photothermal gene nanocarriers, has attracted considerable attention across various disciplines. In this integrated approach, GT reciprocates PTT by sensitizing cellular response to heat, while PTT benefits GT by improving gene translocation, unpacking, and expression. Consequently, this integration presents a unique opportunity for cancer therapy with rapid response and improved effectiveness. Extensive efforts over the past few years have been dedicated to the development of GT-PTT, resulting in notable achievements and rapid progress from the laboratory to potential clinical applications. This comprehensive review outlines recent advances in GT-PTT, including synergistic mechanisms, material systems, imaging-guided therapy, and anticancer applications. It also explores the challenges and future prospects in this nascent field. By presenting innovative ideas and insights into the implementation of GT-PTT for enhanced cancer therapy, this review aims to inspire further progress in this promising area of research.
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Affiliation(s)
- Fang Tang
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen, 361005, China
- Future Display Institute in Xiamen, Xiamen, 361005, China
| | - Aixiang Ding
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen, 361005, China
| | - Yao Xu
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen, 361005, China
| | - Yingsong Ye
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen, 361005, China
| | - Lin Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen, 361005, China
- Future Display Institute in Xiamen, Xiamen, 361005, China
- Frontiers Science Center for Flexible Electronics (IFE), Northwestern Polytechnical University, Xi'an, 710072, China
| | - Rongjun Xie
- Fujian Key Laboratory of Materials Genome, College of Materials, Xiamen University, Xiamen, 361005, China
| | - Wei Huang
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen, 361005, China
- Future Display Institute in Xiamen, Xiamen, 361005, China
- Frontiers Science Center for Flexible Electronics (IFE), Northwestern Polytechnical University, Xi'an, 710072, China
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Naseroleslami M, Mousavi Niri N, Hosseinian SB, Aboutaleb N. DNAzyme loaded nano-niosomes attenuate myocardial ischemia/reperfusion injury by targeting apoptosis, inflammation in a NF-κB dependent mechanism. Naunyn Schmiedebergs Arch Pharmacol 2023; 396:2127-2136. [PMID: 36941384 DOI: 10.1007/s00210-023-02467-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 03/15/2023] [Indexed: 03/23/2023]
Abstract
Although DNAzymes have been found to reduce injury after myocardial ischemia/reperfusion (MI/R), their efficiency have been limited due to rapid degradation in vivo. Thus, this study was conducted to extend their half-life by encapsulation into nano‑niosomes and examine their cardioprotective effects in a rat model of myocardial infarction (MI). In order to synthesize nano‑niosomes, surface active agent film hydration method was used. Characterization of nano‑niosomes was performed using the atomic force microscopy (AFM). In order to establish MI/R model in rats, left anterior descending coronary artery (LAD) was ligated for 30 min. A single dose (150µL) of drug formulations was injected into the infarcted region. The cardiac function was evaluated using echocardiography. The expression of pro-inflammatory cytokines, apoptotic factors, and nuclear factor-κB (NF-κB) were evaluated using Western blot and immunohistochemistry, respectively. Particle size of only nano-niosomes was in the range of 60-90 nm, while a shift to 70-110 nm was seen after DNAzyme encapsulation. MI rats treated with DNAzyme‑loaded nano‑niosomes could markedly reduce Bax, caspase3, TNF-α, IL-1β, and NF-κB as well as increase Bcl-2 compared to only MI/R group. Collectively, our finding show that nano‑niosomes can be considered excellent drug delivery platforms to extend half-life and stability of DNAzyme, when it is used to reduce myocardial I/R injury.
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Affiliation(s)
- Maryam Naseroleslami
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Neda Mousavi Niri
- Department of Biotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Seyede Bahar Hosseinian
- Department of Biotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Nahid Aboutaleb
- Physiology Research Center, Iran University of Medical Sciences, Tehran, Iran.
- Department of Physiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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Kamali H, Golmohammadzadeh S, Zare H, Nosrati R, Fereidouni M, Safarpour H. The recent advancements in the early detection of cancer biomarkers by DNAzyme-assisted aptasensors. J Nanobiotechnology 2022; 20:438. [PMID: 36195928 PMCID: PMC9531510 DOI: 10.1186/s12951-022-01640-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 09/20/2022] [Indexed: 11/10/2022] Open
Abstract
Clinical diagnostics rely heavily on the detection and quantification of cancer biomarkers. The rapid detection of cancer-specific biomarkers is of great importance in the early diagnosis of cancers and plays a crucial role in the subsequent treatments. There are several different detection techniques available today for detecting cancer biomarkers. Because of target-related conformational alterations, high stability, and target variety, aptamers have received considerable interest as a biosensing system component. To date, several sensitivity-enhancement strategies have been used with a broad spectrum of nanomaterials and nanoparticles (NPs) to improve the limit and sensitivity of analyte detection in the construction of innovative aptasensors. The present article aims to outline the research developments on the potential of DNAzymes-based aptasensors for cancer biomarker detection.
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Affiliation(s)
- Hossein Kamali
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Pharmaceutics, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Shiva Golmohammadzadeh
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Pharmaceutics, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamed Zare
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Rahim Nosrati
- Cellular and Molecular Research Center, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Mohammad Fereidouni
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Hossein Safarpour
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran.
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Bhattacharya S, Saindane D, Prajapati BG. Liposomal Drug Delivery And Its Potential Impact On Cancer Research. Anticancer Agents Med Chem 2022; 22:2671-2683. [PMID: 35440318 DOI: 10.2174/1871520622666220418141640] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/08/2022] [Accepted: 02/24/2022] [Indexed: 11/22/2022]
Abstract
Liposomes are one of the most versatile drug carriers due to their functional properties, such as higher biocompatibility, the ability to encapsulate hydrophilic and hydrophobic products, and higher biodegradability. Liposomes are a better and more significant nanocarrier for cancer therapy. The key to developing a better cancer-targeted nanocarrier is the development of targeted liposomes using various approaches. Several traditional and novel liposome preparation methods are briefly discussed in this mini-review. The current state of liposome targeting, active and passive liposome targeting in cancer therapy, ligand directed targeting (antibody, aptamer, and protein/peptide-mediated targeting), and other miscellaneous approaches such as stimuli-responsive liposome-based targeting, autophagy inhibition mediated targeting, and curcumin loaded liposomal targeting are all discussed within. All of this gathered and compiled information will shed new light on liposome targeting strategies in cancer treatment and will pique the interest of aspiring researchers and academicians.
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Affiliation(s)
- Sankha Bhattacharya
- School of Pharmacy & Technology Management, SVKM'S NMIMS Deemed-to-be University, Shirpur, Maharashtra 425405
| | - Dnyanesh Saindane
- School of Pharmacy & Technology Management, SVKM'S NMIMS Deemed-to-be University, Shirpur, Maharashtra 425405
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Gaminda KAP; Department of Chemistry, The Open University of Sri Lanka, Nugegoda. DEOXYRIBOZYMES IN DETECTION OF PATHOGENIC BACTERIA. Biotechnol acta 2021; 14:5-20. [DOI: 10.15407/biotech14.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim. The purpose of the review was to analyze the use of DNAzyme biosensors for the detection of pathogens. In the recent years, deoxyribozymes (DNAzymes) have a significant impact as biosensors in diverse fields, from detection of metal ions in the environment to theranostic applications and detection of microorganisms. Although routinely used sophisticated instrumental methods are available to detect pathogenic bacterial contamination, they involve time-consuming, complicated sample pre-treatment and expensive instruments. As an alternative, pathogen-specific DNAzymes have demonstrated a series of advantages: a non-destructive rapid analysis technique with in situ and real-time detection of bacteria with high sensitivity and selectivity. A wide range of pathogen-specific DNAzymes has been developed using colorimetric and fluorescence-based detections for pathogenic bacterial contamination in various samples. The current review summarizes the in vitro selection of pathogen-specific DNAzymes, various strategies utilized in the sensor designs, and their potential use in theranostic applications.
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