Article
Chemistry, Multidisciplinary
Xiong Zheng, Mujing Yang, Tong Yang, Yun Chang, Shuzhen Peng, Qiuda Xu, Dandan Wang, Xiaoshun Zhou, Yong Shao
Summary: POH3 is designed to specifically bind with triplex DNA, resulting in a turn-on fluorescence response, and can be developed into a catalytic triplex DNAzyme for porphyrin metalation. The catalytic activity is initiated by the enhanced basicity of POH3 upon binding with the triplex DNA.
CHEMICAL COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Beatrix Peter, Barbara Majoros, Sandor Kurunczi, Andrea Violetta Acs, Inna Szekacs, Szilvia Bosze, Gabor M. Kovacs, Imre Boldizsar, Robert Horvath
Summary: Label-free grating-coupled interferometry (GCI) biosensing method was used to reveal the specific biomolecular interactions between two novel aryltetralin lignans and human serum albumin (HSA). The results suggest the potential medical application of these lignans without further optimization of their binding affinity to HSA.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Analytical
Lei Liao, Tingting Gong, Bingying Jiang, Ruo Yuan, Yun Xiang
Summary: A highly sensitive and label-free fluorescence sensor is developed for the detection of miR-21 in human sera. The sensor can detect miR-21 in low concentrations and selectively differentiate it from other control molecules.
Review
Engineering, Electrical & Electronic
Foozieh Sohrabi, Sajede Saeidifard, Seyedeh Mehri Hamidi
Summary: Plasmonic biosensing aims to provide ultra-high sensitivity and label-free detection of biomarkers. Integrating intensity and phase properties of light can increase signal to noise ratio and provide more information on phase changes.
OPTICAL AND QUANTUM ELECTRONICS
(2021)
Article
Biochemistry & Molecular Biology
Malwina Hyjek-Skladanowska, Brooke A. Anderson, Vitaliy Mykhaylyk, Christian Orr, Armin Wagner, Jaroslaw T. Poznanski, Krzysztof Skowronek, Punit Seth, Marcin Nowotny
Summary: This study investigates the structural and biochemical interactions between phosphorothioate-modified antisense oligonucleotides and annexin A2 protein. The researchers found that a unique mode of hydrophobic interactions accounts for the enhanced affinity of modified nucleic acids for the protein. This mechanism of interaction is not only observed for nucleic acid-binding proteins but also accounts for the association of phosphorothioate-modified oligonucleotides with other proteins.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Tomoki Sakamoto, Yudai Yamaoki, Takashi Nagata, Masato Katahira
Summary: Researchers successfully introduced oligodeoxynucleotides that can form triplex structures in vitro into living human cells and observed the characteristic signals of triplex structures through in-cell NMR spectra, providing the first evidence of the formation of parallel and antiparallel triplex structures in living human cells.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Mohamad Mahani, Maryam Taheri, Faten Divsar, Faeze Khakbaz, Alireza Nomani, Huangxian Ju
Summary: A new turn-on fluorescent assay based on triplex DNA labeled with N-doped carbon dots and gold nanoparticles was established for sensitive and selective detection of transcription factor NF-kB p50.
ANALYTICA CHIMICA ACTA
(2021)
Article
Chemistry, Physical
Vagif Nevruzoglu, Murat Tomakin, Melih Manir, Selcuk Demir, Fatih Saban Beris, Arif E. Cetin
Summary: Plasmonic nanoparticles with distinct nearfield properties are promising for label-free biosensing applications. A cryogenic temperature method for vacuum evaporation is proposed to produce nanoparticles with homogenous size distribution and high structural quality, enabling the excitation of plasmonic resonances with narrower linewidths and more controlled dimensions. The method shows enhanced refractive index sensitivity and larger spectral shifts within plasmonic resonances compared to the classical vacuum deposition technique.
Review
Chemistry, Analytical
Sin Yu Lam, Hill Lam Lau, Chun Kit Kwok
Summary: Small-molecule contaminants pose a great threat to human health and the environment, emphasizing the importance of developing affordable, user-friendly, and portable biosensors for rapid detection. This review summarizes the recent strategies used for Capture-SELEX and discusses the commonly used methods for detecting and characterizing small-molecule-aptamer interactions. The development of aptamer-based biosensors for various applications is also explored, along with the challenges and future possibilities in this field.
Article
Chemistry, Multidisciplinary
Ryan P. Connelly, Pedro F. Madalozzo, Jack E. Mordeson, Andrew D. Pratt, Yulia Gerasimova
Summary: The research demonstrates the conversion of a dapoxyl DNA aptamer into a sensor generating fluorescence signal at different wavelengths for detecting drug-resistant tuberculosis gene fragments. The promiscuity of the aptamer in binding to fluorogenic dyes has been discovered, laying the foundation for its application as a versatile sensing platform.
CHEMICAL COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Masaru Nakajima, Andrew D. Smith
Summary: This paper examines the problem of counting distinguishable RNA secondary structures, particularly for circular sequences, using dynamic programming and group theory methods to address the issue of symmetry.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2023)
Article
Genetics & Heredity
Gongwang Yu, Hanbing Zhu, Xiaoshu Chen, Jian-Rong Yang
Summary: The study investigates the secondary structure characteristics of mRNAs and their importance in function and evolution. It is found that specific folding of mRNAs may be an adaptive trait associated with important genes or sites, potentially providing the advantage of modulating ribosome movement. This reveals a novel aspect of the RNA structurome with functional and evolutionary implications.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Article
Spectroscopy
Lei Liao, Jianglong Yao, Ruo Yuan, Yun Xiang, Bingying Jiang
Summary: In this study, a fluorescence strategy based on transcriptional amplification of lighting-up aptamers was developed for label-free, low background and sensitive monitoring of FEN1, with a low detection limit, allowing for early-stage cancer diagnosis.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2023)
Article
Biophysics
Ruiyun Zhou, Chen Wang, Yuxin Huang, Kang Huang, Yingli Wang, Wendao Xu, Lijuan Xie, Yibin Ying
Summary: This study investigates the integration of graphene with THz metasurface into a microfluidic cell for sensitive biosensing in liquid environment, demonstrating high sensitivity in detecting DNA sequences of Escherichia coli O157:H7. The results suggest the potential of the proposed graphene-metasurface microfluidic biosensor for label-free biosensing applications.
BIOSENSORS & BIOELECTRONICS
(2021)
Article
Biochemical Research Methods
Thomas Binet, Berangere Avalle, Miraine Davila Felipe, Irene Maffucci
Summary: AptaMat, a simple and sensitive algorithm, has been developed for comparing the secondary structures of single-stranded nucleic acids (ssNAs). It outperforms other commonly used metrics in discriminating similar structures and correctly classifying RFAM families during clustering.
Review
Biochemistry & Molecular Biology
Carme Fabrega, Anna Clua, Ramon Eritja, Anna Avino
Summary: Nucleoside and nucleobase antimetabolites are important chemotherapeutic agents for cancer treatment and other diseases. Prodrug strategies have been developed to avoid side effects. This review describes the use of nucleoside antimetabolite-modified oligonucleotides as prodrugs, which are enzymatically degraded to generate active nucleotides inside cells. It discusses the potential of these modified oligonucleotides in biomedical applications, including the improvement of antiproliferative properties and the development of DNA nanostructures and protein nanoparticles for enhanced cancer therapy.
CURRENT MEDICINAL CHEMISTRY
(2023)
Article
Nanoscience & Nanotechnology
Daheui Choi, Kihak Gwon, Hye Jin Hong, Harihara Baskaran, Olalla Calvo-Lozano, Alan M. Gonzalez-Suarez, Kyungtae Park, Jose M. de Hoyos-Vega, Laura M. Lechuga, Jinkee Hong, Gulnaz Stybayeva, Alexander Revzin
Summary: Human pluripotent stem cells have great potential for cell therapeutics and disease modeling. Researchers have developed heparin-containing microcapsules that promote stem cell aggregation and can deliver growth factors. They also found that coating the microcapsules with tannic acid can enhance their biological activity and increase pluripotency expression.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Correction
Biochemistry & Molecular Biology
Anna Clua, Santiago Grijalvo, Namrata Erande, Swati Gupta, Kristina Yucius, Raimundo Gargallo, Stefania Mazzini, Muthiah Manoharan, Ramon Eritja
Article
Chemistry, Multidisciplinary
Seonhwa Lee, Alan M. Gonzalez-Suarez, XuHai Huang, Olalla Calvo-Lozano, Sonja Suvakov, Laura M. Lechuga, Vesna D. Garovic, Gulnaz Stybayeva, Alexander Revzin
Summary: Extracellular vesicles (EVs) are lipid bilayer nanovesicles that contain important biological information for disease diagnosis. This paper presents a nanoparticle-enabled immunoassay integrated with an electrochemical plate for quantifying the expression of podocin and nephrin in urinary EVs. The electrochemical immunoassay revealed a higher podocin to nephrin ratio in preeclamptic women compared to healthy controls, suggesting the potential of this ratio for disease diagnosis.
Review
Pharmacology & Pharmacy
Carme Fabrega, Anna Avino, Natalia Navarro, Andreia F. Jorge, Santiago Grijalvo, Ramon Eritja
Summary: In this study, the conjugation of oligonucleotides with lipids and peptides for the development of therapeutics with improved pharmacokinetics is reviewed.
Article
Pharmacology & Pharmacy
Altea Soto, Manuel Nieto-Diaz, Enrique Martinez-Campos, Ana Noalles-Dols, Maria Asuncion Barreda-Manso, Felipe Reviriego, Helmut Reinecke, David Reigada, Teresa Munoz-Galdeano, Irene Novillo, Alberto Gallardo, Juan Rodriguez-Hernandez, Ramon Eritja, Anna Avino, Carlos Elvira, Rodrigo M. Maza
Summary: MicroRNAs (miRNAs) are short RNA oligonucleotides that regulate protein expression to control cells' function. miRNA therapeutics have high specificity and low toxicity, but face challenges in delivery. Polymeric vehicles, like EPA copolymers, show promise as miRNA carriers for neural cells. This study synthesized and characterized different copolymers and evaluated their ability to condense miRNA, their size, charge, cytotoxicity, cell binding and internalization ability, and endosomal escape capacity. The results suggest that EPA and its copolymers could be effective for miRNA delivery to neural cells.
Article
Nanoscience & Nanotechnology
Olalla Calvo-Lozano, Laura Hernandez-Lopez, Leyre Gomez, Arnau Carne-Sanchez, Cornelia von Baeckmann, Laura M. Lechuga, Daniel Maspoch
Summary: In this study, metal-organic cages or polyhedra (MOCs/MOPs) were integrated into a nanophotonic sensor for the rapid and real-time detection of small pollutant molecules in water. The sensor, which incorporates Rh(II)-based MOPs as chemical receptors, does not require sample pretreatment and provides fast and accurate results. The detection limits for two common pollutants, 1,2,3-benzotriazole (BTA) and imidacloprid (IMD), were both below the corresponding toxicity thresholds defined by the European Chemicals Agency (ECHA). This research opens the possibility of implementing competitive sensor devices for in situ environmental monitoring by combining innovative chemical receptors with state-of-the-art photonic sensing technologies.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Analytical
Laila Bchara, Ramon Eritja, Raimundo Gargallo, Fernando Benavente
Summary: A capillary electrophoresis method with UV detection has been developed for analyzing the folding equilibrium of i-motif DNA. Multivariate curve resolution-alternating least-squares (MCR-ALS) has been used to separate folded and unfolded species and estimate melting temperatures (Tm).
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Judit Rodriguez, Arnau Dominguez, Anna Avino, Gigliola Borgonovo, Ramon Eritja, Stefania Mazzini, Raimundo Gargallo
Summary: Cytosine-rich DNA sequences can form i-motif structures, which have the potential to modulate gene expression in vivo. The stability of i-motif structures is low at neutral pH, but can be increased by adding neighboring moieties or DNA ligands. This study investigated the relative effects of these structural moieties and ligands on i-motif stabilization using spectroscopic techniques and multivariate data analysis methods. The results showed that the duplex is responsible for stabilizing the i-motif structure at neutral pH, while the T:T base pair has little effect. Among the selected DNA-binding ligands, the G-quadruplex ligand BA41 interacts with the duplex but shows little interaction and stabilization within the i-motif.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Editorial Material
Biochemistry & Molecular Biology
Montserrat Terrazas, Ramon Eritja, Daniela Montesarchio
Article
Materials Science, Multidisciplinary
Ariana Rueda, Julian I. Mendoza, Lorena Alba-Castellon, Eloi Parlade, Eric Volta-Duran, David Paez, Anna Avino, Ramon Eritja, Esther Vazquez, Antonio Villaverde, Ramon Mangues, Ugutz Unzueta
Summary: This study reports a simple and straightforward method for the one-step production and site-directed cysteine conjugation of disulfide-containing non-antibody thiolated carrier proteins. The method allows for the development of stable, homogeneous, and efficient nanomedicines.
SCIENCE CHINA-MATERIALS
(2023)
Article
Chemistry, Organic
Natalia Navarro, Sergio Serantes, Anna Avino, Carme Fabrega, Ramon Eritja
Summary: The field of therapeutic oligonucleotides has grown significantly in recent years, but their cellular internalization remains a major limitation. This study presents different strategies for enhancing cellular uptake through specialized solid supports and lipid conjugation, which were validated through in vitro cell experiments.
Article
Chemistry, Multidisciplinary
Virginia Martin-Nieves, Luis Miguel Menendez-Mendez, Carme Fabrega, Susana Fernandez, Yogesh S. Sanghvi, Miguel Ferrero, Ramon Eritja
Summary: Nucleosides and their analogues, especially l-nucleosides, are important molecules with potential antiviral and antiproliferative activity. They have emerged as a new class of therapeutic agents due to their comparable biological activity, improved toxicological properties, and greater metabolic stability compared to d-nucleosides. l-nucleosides can also be used as building blocks for l-oligonucleotides, which have similar physical properties as d-oligonucleotides but are resistant to nuclease degradation, non-toxic, and immunologically passive. The synthesis and incorporation of 2'-O-methyl/2'-O-MOE-l-nucleoside pyrimidine derivatives into G-rich oligonucleotides were described, showing their potential in providing enhanced nuclease resistance without significant impact on nucleic acid structural properties.
Article
Biochemistry & Molecular Biology
Anna Avino, Carlos Cuestas-Ayllon, Manuel Gutierrez-Capitan, Lluisa Vilaplana, Valeria Grazu, Veronique Noe, Eva Balada, Antonio Baldi, Alex J. Felix, Eva Aubets, Simonas Valiuska, Arnau Dominguez, Raimundo Gargallo, Ramon Eritja, M-Pilar Marco, Cesar Fernandez-Sanchez, Jesus Martinez de la Fuente, Carlos J. Ciudad
Summary: An innovative analytical approach based on sandwich oligonucleotide hybridization has been developed, which can be adapted to multiple biosensing devices for the rapid detection of pathogens.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)