The assessment of three dimensional modelling design for single strand DNA aptamers for computational chemistry application
| Autor: | Mohamad Zulkeflee Sabri, Mohd. Zulkhairi Abdul Rahim, Sharifah Mariam Sayed Hitam, Azzmer Azzar Abdul Hamid |
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| Rok vydání: | 2020 |
| Předmět: |
0303 health sciences
Oligonucleotide Aptamer 030303 biophysics Organic Chemistry Biophysics Protein Data Bank (RCSB PDB) RNA Dimensional modeling Computational biology DNA Aptamers Nucleotide Molecular Dynamics Simulation Biochemistry 03 medical and health sciences chemistry.chemical_compound Molecular dynamics Protein structure Computational Chemistry chemistry Nuclear Magnetic Resonance Biomolecular 030304 developmental biology |
| Zdroj: | Biophysical chemistry. 267 |
| ISSN: | 1873-4200 |
| Popis: | Aptamers are oligonucleotides and peptides around 15-100 bases in length and are suitable as detection probes or as therapeutics molecules. There are growing interests in the aptamer screening approach through computational simulation methods. DNA and RNA modelling lacks of validation on their predicted 3D structures due to less number of validation tools, unlike protein structures. We suggest an approach to design the stem-loop/hairpin for the three dimensional structure of DNA aptamers through serial applications of computational prediction methods by comparing the simulated structures with the experimental data deposited in PDB Data bank, followed by MD simulations. The result shows minimal structural differences were observed between the designed and the original NMR aptamers, and the stem-loop conformational structures were also retained during the MD thus suggesting the proposed aptamers designing methods are able to synthesize a high quality molecular structure of hairpin aptamers, comparable to the NMR structures. |
| Databáze: | OpenAIRE |
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