Article
Biochemical Research Methods
Hosub Lim, Junhyuck Chang, Kyung-il Kim, Youngkwang Moon, Saebom Lee, Byoungsang Lee, Jung Heon Lee, Jinkee Lee
Summary: In this study, an on-chip aptamer selection device using graphene oxide-coated magnetic nanoparticles and a multilayered microfluidic device was developed. Through 8 cycles of selection process, an aptamer with a dissociation constant of 18.6 +/- 1.5 μM was screened within approximately 2 hours for each cycle, providing a novel label-free screening technology for achieving high-quality aptamers.
Article
Chemistry, Analytical
An T. H. Le, Tong Ye Wang, Svetlana M. Krylova, Stanislav S. Beloborodov, Sergey N. Krylov
Summary: This study reveals the dependence of the partitioning of protein-DNA complexes on experimental conditions. By comparing two modes of capillary electrophoresis, NECEEM and IFCE, the optimal conditions for separating protein targets of different sizes can be determined. IFCE is preferable for large-size protein targets, while NECEEM should be the method of choice for small-size protein targets.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Junku Takao, Reina Nagai, Tatsuro Endo, Hideaki Hisamoto, Kenji Sueyoshi
Summary: This study introduces a novel aptamer selection method based on microscale electrophoretic filtration, which enables simple operations, highly effective separation, and the use of relatively inexpensive apparatus.
Article
Biochemistry & Molecular Biology
Katja Schilling-Loeffler, Rachel Rodriguez, Jacquelina Williams-Woods
Summary: This study characterized seven previously described norovirus aptamers for their target affinity, structure, and potential applications. Four aptamers showed affinity for GII.4 strains, while three also exhibited affinity toward GII.3 and GI.7. Circular dichroism analysis revealed that most aptamers exhibited a B-DNA structure, with one displaying a G-quadruplex hybrid structure. These findings provide a knowledge base for future norovirus detection and extraction assay development using aptamer technology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Chemistry, Multidisciplinary
Lucy F. Yang, Melissa Ling, Nataly Kacherovsky, Suzie H. Pun
Summary: This review discusses the discovery process of aptamers, known as systematic evolution of ligands by exponential enrichment (SELEX), and their applications in biosensors and separations. Aptamers, with similar binding affinity and specificity as antibodies, have shown great potential in various fields. They have been utilized in biosensors for virus detection, such as SARS-CoV-2, and in separations for purifying specific molecules or cell types.
Article
Microbiology
Qing Yu, Mengmeng Li, Mingzhu Liu, Shuaishuai Huang, Gaoxue Wang, Taixia Wang, Pengfei Li
Summary: The study generated three DNA aptamers (LBVA1, LBVA2, and LBVA3) against LMBV-infected fathead minnow cells through SELEX technology. These aptamers exhibited efficient antiviral activities in vitro, indicating their potential in developing effective anti-viral treatments.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Hongli Fan, Yaxiong Liu, Jiamei Dong, Zhuoya Luo
Summary: The research team successfully developed an aptamer specific for beclomethasone (BEC) and a quantum dot-based assay (QDA) for BEC detection. The QDA method showed high sensitivity and accuracy, suitable for detecting BEC in Traditional Chinese Medicine (TCM).
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Debora Ferreira, Joaquim Barbosa, Diana A. Sousa, Catia Silva, Luis D. R. Melo, Meltem Avci-Adali, Hans P. Wendel, Ligia R. Rodrigues
Summary: This study identified two specific aptamers targeting highly metastatic breast cancer cells, showing potential for clinical applications in the treatment and diagnosis of triple-negative breast cancer.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Hiraku Takada, Kaede Kijima, Akira Ishiguro, Akira Ishihama, Tomohiro Shimada
Summary: This study reveals that the master regulator FlhDC mediates all flagellum-forming genes in E. coli through a transcriptional regulatory cascade. The researchers also identified new target genes involved in the sugar utilization phosphotransferase system, sugar catabolic pathway of glycolysis, and other carbon source metabolic pathways. The results suggest that FlhDC activates these new targets, providing coordinated regulation between flagella formation, operation, and energy production.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Debleena Basu, Sourabrata Chakraborty, Riddhi Pal, Tarun Kumar Sharma, Siddik Sarkar
Summary: Aptamers are short sequences of synthetic oligonucleotides that can bind specifically to their target with similar or higher sensitivity compared to antibodies. The in-vitro selection process, known as SELEX, involves a combination of chemistry and molecular biology. Chemical modifications are made to enhance stability in biofluids, with a focus on maintaining sensitivity and specificity. Aptamer applications have expanded beyond in-vitro systems to include molecular imaging for disease pathology and treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Chemistry, Multidisciplinary
Hu Lingling, Liu Ke, Ren Guolan, Liang Jiangong, Wu Yuan
Summary: Proteins are essential in all life domains and precise regulation of their activity is crucial for understanding biological processes and therapeutic applications. Nucleic acid aptamers obtained through SELEX have specific protein recognition characteristics similar to antibodies and can help regulate their activity. This minireview covers the selection of protein-binding aptamers using SELEX, membrane protein analysis techniques based on aptamer-mediated target recognition, aptamer-mediated functional regulation of proteins (including membrane receptors and non-membrane proteins such as thrombin), as well as the potential challenges and prospects of aptamer-mediated protein manipulation, providing useful information for researchers in this field.
CHEMICAL RESEARCH IN CHINESE UNIVERSITIES
(2022)
Review
Chemistry, Multidisciplinary
Liu Ke, Jin Yu, Liang Jiangong, Wu Yuan
Summary: Aptamers are short single-stranded DNA or RNA oligonucleotides obtained through in vitro SELEX. They possess high specificity and affinity but their commercial applications are still limited. Chemical modifications have been conducted to enhance their performance, showing promising prospects for future development.
CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE
(2021)
Article
Chemistry, Multidisciplinary
Obtin Alkhamis, Yi Xiao
Summary: The selection stringency, specifically the target concentration, affects the outcome of SELEX. Excessively high target concentrations promote enrichment of low-affinity binders and suppress the enrichment of high-affinity aptamers. Understanding these principles is crucial for obtaining high-quality aptamers.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Yang Lin, Cho-Yi Chen, Yu-Chia Ku, Li-Chin Wang, Chia-Chien Hung, Zhi-Qian Lin, Bing-Hong Chen, Jui-Tse Hung, Yi-Chen Sun, Kai-Feng Hung
Summary: we modify the conventional method to improve the efficiency in the identification of the aptamer, a single strand of nucleic acid with binding specificity to the target molecule, showing as a proof of concept that this approach is particularly useful to select aptamers that can selectively bind to cells presenting a particular peptide by the major histocompatibility complex (MHC) on the cell surface.
Article
Biochemical Research Methods
Mubarak Umar, Chun-Yin Chan, Chun Kit Kwok
Summary: The RNA G-quadruplex (rG4)-SELEX method generates L-RNA aptamers to target rG4 structures, effectively suppressing G-quadruplex-mediated interactions. This Protocol Extension improves aptamer discovery speed, showcasing the utility of L-RNA aptamers. The detailed procedure expands the current rG4 toolkit, facilitating exploration of innovative rG4-related applications.
Article
Immunology
Lana Dbeibo, Julia J. van Rensburg, Sara N. Smith, Kate R. Fortney, Dharanesh Gangaiah, Hongyu Gao, Juan Marzoa, Yunlong Liu, Harry L. T. Mobley, Stanley M. Spinola
INFECTION AND IMMUNITY
(2018)
Article
Biochemistry & Molecular Biology
Sebastien Crepin, Elizabeth N. Ottosen, Katharina Peters, Sara N. Smith, Stephanie D. Himpsl, Waldemar Vollmer, Harry L. T. Mobley
MOLECULAR MICROBIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
Sebastien Crepin, Elizabeth N. Ottosen, Courtney E. Chandler, Anna Sintsova, Robert K. Ernst, Harry L. T. Mobley
MOLECULAR MICROBIOLOGY
(2020)
Article
Biology
Anna Sintsova, Arwen E. Frick-Cheng, Sara Smith, Ali Pirani, Sargurunathan Subashchandrabose, Evan S. Snitkin, Harry Mobley
Article
Microbiology
Wanghsu Jiang, Wimal Ubhayasekera, Michael C. Breed, Allison N. Norsworthy, Nina Serr, Harry L. T. Mobley, Melanie M. Pearson, Stefan D. Knight
Article
Microbiology
Laura A. Mike, Andrew J. Stark, Valerie S. Forsyth, Jay Vornhagen, Sara N. Smith, Michael A. Bachman, Harry L. T. Mobley
Summary: The study identifies a close relationship between capsule biosynthesis and hypermucoviscosity in Klebsiella pneumoniae, with central metabolism playing a key regulatory role. Certain metabolic genes specifically impact only one of these properties, with genes related to the TCA cycle playing a significant role.
Article
Microbiology
Mark T. Anderson, Aric N. Brown, Ali Pirani, Sara N. Smith, Amanda L. Photenhauer, Yuang Sun, Evan S. Snitkin, Michael A. Bachman, Harry L. T. Mobley
Summary: Bloodstream infections, caused by Gram-negative species, are a significant public health burden due to high mortality rates and treatment costs. A study characterizing infection kinetics and bacterial replication rates of six common pathogens in a murine model revealed different colonization abilities in major organs. While some species replicated rapidly in the liver or kidney, others were steadily cleared from targeted organs during infection, highlighting the complex dynamics of bacterial replication and immune-mediated clearance. Insights from this study may aid in developing strategies to combat bloodstream infections in the future.
Article
Immunology
Allyson E. Shea, Jolie A. Stocki, Stephanie D. Himpsl, Sara N. Smith, Harry L. T. Mobley
Summary: Uropathogenic Escherichia coli (UPEC) causes urinary tract infections (UTI) in nearly half of women worldwide, and the role of the ila locus in UPEC uropathogenesis remains unclear. This study found that the ila locus is related to bladder cell adherence and invasion, and its loss may affect the fitness of UPEC during UTI.
INFECTION AND IMMUNITY
(2022)
Review
Microbiology
Aric N. Brown, Mark T. Anderson, Michael A. Bachman, Harry L. T. Mobley
Summary: ArcAB, a member of the bacterial transcriptional regulator two-component system family, acts as a sensor of oxygen consumption. This review provides an overview of the structure and function of ArcAB proteins and discusses the literature on its role as an oxygen consumption sensor. The regulation of ArcAB activity is primarily mediated by the bacterial quinone pool, but the exact mechanism is still not fully understood. The review also explores the involvement of ArcAB in regulating central metabolic pathways and its potential interactions with other regulatory systems.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2022)
Article
Microbiology
Arwen E. Frick-Cheng, Anna Sintsova, Sara N. Smith, Ali Pirani, Evan S. Snitkin, Harry L. T. Mobley
Summary: More than half of women will experience a urinary tract infection (UTI), with uropathogenic Escherichia coli (UPEC) causing the majority of cases. Iron acquisition systems play a crucial role in UPEC pathogenesis, and this study reveals the importance of the ferric citrate uptake system as an alternative iron source when other siderophores are limited. Understanding these iron acquisition mechanisms is important for developing new strategies to combat UTI.
Article
Immunology
Sophia Mason, Jay Vornhagen, Sara N. Smith, Laura A. Mike, Harry L. T. Mobley, Michael A. Bachman
Summary: Healthcare-acquired infections, particularly caused by Klebsiella pneumoniae, are a major concern for hospitalized patients and long-term-care facilities. Previous studies have linked the ter operon to infection in colonized patients. This study further explores the role of the ter operon in enhancing fitness during gut colonization and bladder infection.
INFECTION AND IMMUNITY
(2023)
Article
Microbiology
A. E. Shea, A. E. Frick-Cheng, S. N. Smith, H. L. T. Mobley
Summary: This study demonstrates that phenotypic characteristics can be used to predict the severity of urinary tract infection caused by uropathogenic Escherichia coli (UPEC) strains. These characteristics can help differentiate UPEC from other E. coli strains and reduce the overuse of antibiotics.
Article
Microbiology
Melanie M. Pearson, Sapna Pahil, Valerie S. Forsyth, Allyson E. Shea, Harry L. T. Mobley
Summary: Ordered transposon libraries are a valuable resource for studying bacterial species, especially those with difficult methods for targeted genetic mutations. In this study, we constructed an ordered transposon library for the bacterial urinary tract pathogen Proteus mirabilis strain HI4320. The library enables large-scale screens and facilitates the study of P. mirabilis biology. However, the library's coverage of predicted genes was lower than expected due to unmapped insertions and a high proportion of mixed clones and multiple transposon insertion events. Future library construction can be improved by addressing these challenges.
MICROBIOLOGY SPECTRUM
(2022)
Article
Immunology
Melanie M. Pearson, Allyson E. Shea, Sapna Pahil, Sara N. Smith, Valerie S. Forsyth, Harry L. T. Mobley
Summary: Animal models for host-microbial interactions are valuable but lacking for many microbes. This study introduces a method called organ agar, which enables screening of mutant libraries without physiological bottlenecks. The authors demonstrate that growth defects on organ agar accurately predict bacterial colonization deficiencies in a murine model. The method is also useful for identifying unknown links between biosynthetic genes and swarming motility.
INFECTION AND IMMUNITY
(2023)
Meeting Abstract
Urology & Nephrology
Anna Sintsova, Ali Pirani, Sargurunathan Subashchandrabose, Evan Snitkin, Harry L. T. Mobley
JOURNAL OF UROLOGY
(2019)