Properties of phosphoramide benzoazole oligonucleotides (PABAOs). II. Structure and hybridization efficiency of N-benzoxazole derivatives

IF 2.5 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochemical and biophysical research communications Pub Date : 2024-11-13 DOI:10.1016/j.bbrc.2024.150997

Ivan I. Yushin, Victor M. Golyshev, Alina I. Novgorodtseva, Alexander A. Lomzov

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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.

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磷酰胺苯并唑寡核苷酸（PABAOs）的特性。II.N-苯并恶唑衍生物的结构和杂交效率。

新的磷酸修饰核酸衍生物在基础研究和生物医学应用中具有重要意义。我们最近开发了一类新的磷酰胺苯并噁唑寡核苷酸（PABAOs）。在这项工作中，我们对 N-苯并噁唑寡核苷酸的性质进行了深入研究。我们展示了在不同位置进行不同数量（最多六次）修饰的寡聚体的便捷自动化固相合成。我们对 PABAO/DNA 复合物的光学特性、热稳定性、结构和动力学进行了研究。经 N-苯并恶唑修饰的磷酸基团在中性 pH 值下不带电，pKa 值为 8.52。通过 CD 光谱和 MD 模拟进行的结构分析表明 PABAO/DNA 双链体为 B 型。在标准和接近生理的缓冲条件下，含有 N-苯并恶唑的 PABAO/DNA 复合物的热稳定性比原生双链体每改性一次降低 2.5-6.2° 。这项研究强调了磷酰胺苯并噁唑寡核苷酸在基础研究、应用科学和生物技术方面的巨大潜力。

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来源期刊

Biochemical and biophysical research communications 生物-生化与分子生物学

CiteScore

6.10

自引率

0.00%

发文量

1400

审稿时长

14 days

期刊介绍： Biochemical and Biophysical Research Communications is the premier international journal devoted to the very rapid dissemination of timely and significant experimental results in diverse fields of biological research. The development of the "Breakthroughs and Views" section brings the minireview format to the journal, and issues often contain collections of special interest manuscripts. BBRC is published weekly (52 issues/year).Research Areas now include: Biochemistry; biophysics; cell biology; developmental biology; immunology ; molecular biology; neurobiology; plant biology and proteomics