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首页> 外文期刊>Chemistry: A European journal >Rational design for cooperative recognition of specific nucleobases using β-cyclodextrin-modified DNAs and fluorescent ligands on DNA and RNA scaffolds
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Rational design for cooperative recognition of specific nucleobases using β-cyclodextrin-modified DNAs and fluorescent ligands on DNA and RNA scaffolds

机译：使用β-环糊精修饰的DNA和DNA和RNA支架上的荧光配体协同识别特定核碱基的合理设计

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摘要

We propose a binary fluorimetric method for DNA and RNA analysis by the combined use of two probes rationally designed to work cooperatively. One probe is an oligonucleotide (ODN) conjugate bearing a β-cyclodextrin (β-CyD). The other probe is a small reporter ligand, which comprises linked molecules of a nucleobase-specific heterocycle and an environment-sensitive fluorophore. The heterocycle of the reporter ligand recognizes a single nucleobase displayed in a gap on the target labeled with the conjugate and, at the same time, the fluorophore moiety forms a luminous inclusion complex with nearby β-CyD. Three reporter ligands, MNDS (naphthyridine-dansyl linked ligand), MNDB (naphthyridine-DBD), and DPDB (pyridine-DBD), were used for DNA and RNA probing with 3′-end or 5′-end modified β-CyD-ODN conjugates. For the DNA target, the β-CyD tethered to the 3′-end of the ODN facing into the gap interacted with the fluorophore sticking out into the major groove of the gap site (MNDS and DPDB). Meanwhile the β-CyD on the 5′-end of the ODN interacted with the fluorophore in the minor groove (MNDB and DPDB). The results obtained by this study could be a guideline for the design of binary DNA/RNA probe systems based on controlling the proximity of functional molecules.
机译：我们结合合理设计的两种探针共同使用，提出了一种用于DNA和RNA分析的二元荧光法。一种探针是带有β-环糊精（β-CyD）的寡核苷酸（ODN）缀合物。另一探针是小的报告配体，其包含核碱基特异性杂环和环境敏感的荧光团的连接分子。报告配体的杂环识别在缀合物标记的靶标上的缺口中显示的单个核碱基，同时，荧光团部分与附近的β-CyD形成发光的包合物。使用三个报告子配体MNDS（萘啶-腺苷连接的配体），MNDB（萘啶-DBD）和DPDB（吡啶-DBD）对3'端或5'端修饰的β-CyD-进行DNA和RNA探测。 ODN共轭物。对于DNA靶标，拴在ODN面向间隙的3'-末端的β-CyD与伸出间隙位点主要凹槽（MNDS和DPDB）的荧光团相互作用。同时，ODN的5'端的β-CyD与小沟（MNDB和DPDB）中的荧光团相互作用。这项研究获得的结果可能是基于控制功能分子的接近度来设计二元DNA / RNA探针系统的指南。

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