Search results for "nukleotidit"
showing 5 items of 5 documents
Computational approach to design of aptamers to the receptor binding domain of SARS-CoV-2
2021
The aim of the research. In this work, in silico selection of DNA-aptamers to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein was performed using molecular modeling methods. Material and methods. A new computational approach to aptamer in silico selection is based on a cycle of simulations, including the stages of molecular modeling, molecular docking, molecular dynamic simulations, and quantum chemical calculations. To verify the obtained calculated results flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods were applied. Results. An initial library consisted of 256 16-mer oligonucleotides was modeled. Based on molecular docking results, th…
Selective trapping of oligos to triangular gold nanoparticles utilizing dielectrophoresis
2014
Triangular shaped particles are an interesting research topic since there are three plasmonically active tips, which can be utilized in new molecular sensing application systems. In this research we used dielectrophoretic force to trap thiol-modified (5’- end) and Cy3-dye-labeled (3’-end) single-stranded DNA (ssDNA) oligonucleotides, size 40 nt (about 22 nm long), to the corners of the gold triangles. These gold triangles were 20 nm thick and side length was 1 μm. The trapping experiment was done under AC-circuit and the gathering of the oligos to the triangles was studied in situ under confocal microscope. The theoretical values for dielectrophoretic force with different voltages were simu…
Structure‐ and Interaction‐Based Design of Anti‐SARS‐CoV‐2 Aptamers
2022
Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. This study aims to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with …
Liikunnan ja hera- tai proteiinijuomadieetin vaikutukset sirtuiinien 1-7 ilmentymiseen LCR-rottien raajalihaksessa
2014
Anne Mäkinen (2014). Liikunnan ja hera- tai proteiinijuomadieettien vaikutukset sirtuiinien 1-7 ilmentymiseen LCR -rottien raajalihaksessa. Liikuntabiologian laitos, Jyväskylän yliopisto, Liikuntafysiologian pro gradu-tutkielma, 41 s. Histonit ja muut kromosomaaliset proteiinit pakkautuvat DNA:n (deoksiribonukleiinihapon) tumaan. Histonideasetylaasit kontrolloivat osaltaan geenien ilmentymistä. Ryhmän III histonideasetylaaseja nimitetään sirtuiineiksi, joita on seitsemän kappaletta ja niiden toiminta on riippuvainen NAD+:sta (nikotiinihappoamidiadeniinidinukleotidi). Tutkimuksissa on todettu liikunnan lisäävän joidenkin sirtuiinien ilmentymistä, mutta proteiinin tai heran vaikutuksia sirtui…
The Role of Small-Angle X-Ray Scattering and Molecular Simulations in 3D Structure Elucidation of a DNA Aptamer Against Lung Cancer
2021
Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here we present a general optimization procedure for finding most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated aptamer LC-18t was developed. A three-dimensional shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and m…