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Reducing Measurement Deviation by Metastable DNA Probes for Aptamer Thermodynamic Characterization.
Anal Chem
January 2025
Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.
DNA reaction equilibrium-based calculations have great potential in thermodynamic characterization, but their widespread applications are hindered by significant measurement deviation of equilibrium concentration. Here, we report the advantages of metastable DNA hybridization in reducing quantification deviation of equilibrium concentration and propose a universal and standardized strategy for measuring aptamer binding energy, termed metastable DNA reference calorimetry (MDRC). We built different MDRC-based algorithms tailored to different aptamer binding models, enabling the calculation of thermodynamic parameters for aptamers with one or more binding sites.
View Article and Find Full Text PDFComputer Simulation of Sulfated Cyclodextrin-Based Enantioselective Separation of Weak Bases With Partial, High-Concentration Filling of the Chiral Selector and Analyte Detection on the Cathodic Side.
Electrophoresis
January 2025
Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
Computer simulation was utilized to characterize the electrophoretic processes occurring during the enantioselective capillary electrophoresis-mass spectrometry (CE-MS) analysis of ketamine, norketamine, and hydroxynorketamine in a system with partial filling of the capillary with 19 mM (equals 5%) of highly sulfated γ-cyclodextrin (HS-γ-CD) and analyte detection on the cathodic side. Provided that the sample is applied without or with a small amount of the chiral selector, analytes become quickly focused and separated in the thereby formed HS-γ-CD gradient at the cathodic end of the sample compartment. This gradient broadens with time, remains stationary, and gradually reduces its span from the lower side due to diffusion such that analytes with high affinity to the anionic selector become released onto the other side of the focusing gradient where anionic migration and defocusing occur concomitantly.
View Article and Find Full Text PDFDirected evolution of antimicrobial peptides using multi-objective zeroth-order optimization.
Brief Bioinform
November 2024
School of Computer Science and Technology, Harbin Institute of Technology, HIT Campus, Shenzhen University Town, Nanshan District, Shenzhen 518055, Guangdong, China.
Antimicrobial peptides (AMPs) emerge as a type of promising therapeutic compounds that exhibit broad spectrum antimicrobial activity with high specificity and good tolerability. Natural AMPs usually need further rational design for improving antimicrobial activity and decreasing toxicity to human cells. Although several algorithms have been developed to optimize AMPs with desired properties, they explored the variations of AMPs in a discrete amino acid sequence space, usually suffering from low efficiency, lack diversity, and local optimum.
View Article and Find Full Text PDFPost-synthesis surface modification of Cu/Zr metal azolate framework: A pathway to highly sensitive electrochemical biosensors for atrazine detection.
Anal Chim Acta
February 2025
Dept. of Electronic Materials Engineering, Kwangwoon University, Seoul, 01897, Republic of Korea. Electronic address:
Background: Atrazine (ATZ), a pesticide that poses serious health problems, is observed in the environment, thereby prompting its periodic monitoring and control using functional biosensors. However, established methods for ATZ detection have limited applicability. Two-dimensional (2D) metal azolate frameworks (MAF) have a higher surface area per unit volume and provide easier access to active sites.
View Article and Find Full Text PDFImproving 1-year liver allograft survival hazard ratios.
BMJ Open Qual
January 2025
Mayo Clinic, Rochester, Minnesota, USA.
Background: The Scientific Registry for Transplant Recipients (SRTR) publishes outcomes of all transplant centres in the USA two times a year. The outcomes are publicly available and used by insurance payers and patients to assess the performance of a programme. Poor performance can result in temporary suspension or termination of a transplant programme.
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