We have tried to construct synthetic polymers for sequence-specific recognition and complexation of longer deoxynucleotide sequences. For this purpose, we developed a method of template-directed polymerization of basic pair specific DNA ligands such as basic dyes. The template-directed polymerization consists in a copolymerization of various dyes of different specificities staying simultaneously in a binding equilibrium with DNA. In the present paper, we describe the synthesis and the properties of base pair specific monomers especially designed for performance of radical chain polymerization reactions in aqueous medium at room temperature. Different acrylamide derivatives of well-known dyes, such as AT-specific malachite green and GC-specific phenyl neutral red, were synthesized and studied for their ability of base pair specific complex formation with DNA of different base composition. Partition equilibrium dialysis and dye titration agarose gel electrophoresis were used to ensure for several dyes that they may be incorporated into different polymers via copolymerization of their acrylamido derivatives with various small base-unspecific monomers without substantial change of their binding parameters. Furthermore, we demonstrate that acrylamide and other small acrylamide derivatives can be used as building blocks for the synthesis of polymeric links between base pair specific monomers. The results and their consequences for template polymerization reactions are discussed.

Download full-text PDF

Source
http://dx.doi.org/10.1021/bi00513a024DOI Listing

Publication Analysis

Top Keywords

pair specific
20
base pair
16
synthesis properties
8
template-directed polymerization
8
specific monomers
8
polymerization reactions
8
acrylamide derivatives
8
base
5
pair
5
specific
5

Similar Publications

SARS-CoV-2 CoCoPUTs: analyzing GISAID and NCBI data to obtain codon statistics, mutations, and free energy over a multiyear period.

Virus Evol

January 2025

Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA.

A consistent area of interest since the beginning of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been the sequence composition of the virus and how it has changed over time. Many resources have been developed for the storage and analysis of SARS-CoV-2 data, such as GISAID (Global Initiative on Sharing All Influenza Data), NCBI, Nextstrain, and outbreak.info.

View Article and Find Full Text PDF

Advancing cancer therapy with custom-built alternating electric field devices.

Bioelectron Med

January 2025

School of Pharmacy, Biodiscovery Institute & Boots Science Building, University of Nottingham, Nottingham, NG7 2RD, UK.

Background: In glioblastoma (GBM) therapy research, tumour treating fields by the company Novocure™, have shown promise for increasing patient overall survival. When used with the chemotherapeutic agent temozolomide, they extend median survival by five months. However, there is a space to design alternative systems that will be amenable for wider use in current research.

View Article and Find Full Text PDF

Preparation of the immobilized α-adrenoceptor column by the ultra-high affinity protein pair CL7/Im7 and its application in drug-protein interaction analysis.

J Chromatogr B Analyt Technol Biomed Life Sci

January 2025

Northwest University Chang An Hospital, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, Shaanxi 710069, China; Department of Clinical Pharmaceutics, Chang An District Hospital, Xi'an, Shaanxi 710118, China. Electronic address:

Immobilizing the target protein on a solid surface with controlled orientation, high specificity, and maintained activity is a proven strategy to enhance the stability of the protein. In this study, we employed an ultra-high affinity protein pair consisting of a mutant of colicin E7 Dnase and its corresponding inhibitor, immunity protein 7(Im7), to develop an immobilized α-adrenoceptor (α-AR) column. Briefly, we expressed α-AR fused with CL7 as a tag at its C-terminus in Escherichia coli cells.

View Article and Find Full Text PDF

Optimizing Point-in-Space Continuous Monitoring System Sensor Placement on Oil and Gas Sites.

ACS Sustain Resour Manag

January 2025

Department of Applied Mathematics and Statistics, Colorado School of Mines, Golden, Colorado 80401, United States.

We propose a generic, modular framework to optimize the placement of point-in-space continuous monitoring system sensors on oil and gas sites aiming to maximize the methane emission detection efficiency. Our proposed framework substantially expands the problem scale compared to previous related studies and can be adapted for different objectives in sensor placement. This optimization framework is comprised of five steps: (1) simulate emission scenarios using site-specific wind and emission information; (2) set possible sensor locations under consideration of the site layout and any site-specific constraints; (3) simulate methane concentrations for each pair of emission scenario and possible sensor location; (4) determine emissions detection based on the site-specific simulated concentrations; and (5) select the best subset of sensor locations, under a given number of sensors to place, using genetic algorithms combined with Pareto optimization.

View Article and Find Full Text PDF

Prolonged exposure to high environmental temperatures results in an accumulated heat load that induces a heat stress (HS) response in dairy cattle. Heat stress compromises dairy farm profitability by reducing milk yield, altering milk composition, and hindering reproductive performance. The ability to alternate between carbohydrate and lipid sources for energy production is termed metabolic flexibility (Met Flex).

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!