1. Properties of phosphoramide benzoazole oligonucleotides (PABAOs). II. Structure and hybridization efficiency of N-benzoxazole derivatives.
- Author
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Yushin II, Golyshev VM, Novgorodtseva AI, and Lomzov AA
- Subjects
- Nucleic Acid Hybridization, Nucleic Acid Conformation, Molecular Dynamics Simulation, Benzoxazoles chemistry, Benzoxazoles chemical synthesis, Oligonucleotides chemistry, Oligonucleotides chemical synthesis, Phosphoramides chemistry, DNA chemistry
- Abstract
New phosphate-modified nucleic acid derivatives are of great significance in basic research and biomedical applications. We have recently developed a new class of phosphoramide benzoazole oligonucleotides (PABAOs). In this work, th properties of N-benzoxazole oligodeoxyribonucleotides have been thoroughly examined. We have demonstrated the convenient automated solid-phase synthesis of oligomers with a different number of modifications (up to six) at various positions. Optical properties, thermal stability, structure, and dynamics of PABAO/DNA complexes have been investigated. The N-benzoxazole-modified phosphate group is uncharged at neutral pH and has a pKa value of 8.52. Structural analysis performed by the CD spectroscopy and MD simulation indicate B-form of PABAO/DNA duplexes. The thermal stability of PABAO/DNA complexes bearing N-benzoxazole is reduced by 2.5-6.2° per modification compared to native duplexes at standard and near physiological buffer conditions. The performed study underlines a great potential of phosphoramide benzoazole oligonucleotides for basic research, applied sciences, and biotechnology., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Alexander A. Lomzov reports a relationship with Russian Science Foundation that includes: funding grants. Alexander A. Lomzov has patent #RU2823099C1 licensed to ICBFM SB RAS. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)
- Published
- 2024
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