Design and characterization of symmetric nucleic acids via molecular dynamics simulations
| Autor: | Bhyravabhotla Jayaram, Saher Afshan Shaikh, Pradeep Pant |
|---|---|
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Stereochemistry media_common.quotation_subject Biophysics Molecular Dynamics Simulation 010402 general chemistry 01 natural sciences Biochemistry Asymmetry Biomaterials 03 medical and health sciences chemistry.chemical_compound Molecular dynamics Transcription (biology) Nucleic Acids Directionality Nucleotide media_common chemistry.chemical_classification Base Sequence Organic Chemistry General Medicine 0104 chemical sciences 030104 developmental biology chemistry Chemical bond Nucleic acid Nucleic Acid Conformation DNA B-Form DNA |
| Zdroj: | Biopolymers. 107(4) |
| ISSN: | 1097-0282 |
| Popis: | Asymmetry (5'→3') associated with each strand of the deoxyribonucleic acid (DNA) is inherent in the sugar-phosphate backbone connectivity and is essential for replication and transcription. We note that this asymmetry is due to one single chemical bond (C3' to C2' ) in each nucleotide unit, and the absence of this bond results in directionally symmetric nucleic acids. We also discovered that creation of an extra chemical bond (C5' to C2' ) can lead to a symmetric backbone. Keeping their potential synthetic and therapeutic interest in mind, we designed a few novel symmetric nucleic acids. We investigated their conformational stability and flexibility via detailed all atom explicit solvent 100-ns long molecular dynamics simulations and compared the resulting structures with that of regular B-DNA. Quite interestingly, some of the symmetric nucleic acids retain the overall double helical structure indicating their potential for integration in physiological DNA without causing major structural perturbations. |
| Databáze: | OpenAIRE |
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