The European Physical Journal E ( IF 1.8 ) Pub Date : 2021-03-08 , DOI: 10.1140/epje/s10189-021-00030-z Maksym V Karachevtsev 1 , Vladimir A Valeev 1 , Victor A Karachevtsev 1
|
Abstract
Hybrids formed by DNA/RNA and graphene family nanomaterials are considered as potentially useful multifunctional agents in biosensing and nanomedicine. In this work, we study the noncovalent interaction between double-stranded (ds) RNA, polyadenylic:polyuridylic acids (poly(A:U)) and graphene oxide/graphene (GO/Gr) using UV absorption spectroscopy and molecular dynamics (MD) simulations. RNA melting showed that relatively long ds-RNA is adsorbed onto GO (at an ionic strength of \(\sim 0.1~\hbox {M}\)) at that a large fraction of RNA maintains the duplex structure. It was revealed that this fraction decreases over long time (during a few days), indicating a slow adsorption process of the long polymer. MD simulations showed that the adsorption of duplex (rA)\(_{15}\): (rU)\(_{15}\) or (rA)\(_{30}\): (rU)\(_{30}\) on graphene starts with the interaction between \(\pi \)-systems of graphene and base pairs located at a duplex tail. In contrast to relatively long duplex (rA)\(_{30}\): (rU)\(_{30}\) which keeps parallel arrangement along the graphene surface, the shorter one ((rA)\(_{15}\): (rU)\(_{15}\)) always adopts a perpendicular orientation relative to graphene even in case of the initial parallel orientation. It was found out that (rA)\(_{30}\): (rU)\(_{30}\) forms the stable hybrid with graphene keeping essential fraction of the duplex, while (rA)\(_{15}\): (rU)\(_{15}\) demonstrates the duplex unzipping into two single strands with time. The interaction energies between adenine/uracil stacked with graphene as well between nucleotides in water environment were determined.
Graphic abstract
中文翻译：
双链多核苷酸poly(A:U)与石墨烯/氧化石墨烯的相互作用
摘要
由 DNA/RNA 和石墨烯家族纳米材料形成的混合物被认为是生物传感和纳米医学中潜在有用的多功能试剂。在这项工作中，我们使用紫外吸收光谱和分子动力学 (MD) 研究了双链 (ds) RNA、聚腺苷酸：聚尿苷酸 (poly(A:U)) 和氧化石墨烯/石墨烯 (GO/Gr) 之间的非共价相互作用模拟。RNA 熔解显示相对长的 ds-RNA 被吸附到 GO 上（离子强度为\(\sim 0.1~\hbox {M}\)），因为大部分 RNA 保持双链结构。结果表明，该分数随着时间的推移（几天内）而减少，表明长聚合物的吸附过程缓慢。MD 模拟表明双链体的吸附 (rA) \(_{15}\) : (rU)\(_{15}\)或 (rA) \(_{30}\) : (rU) \(_{30}\)在石墨烯上始于\(\pi \) - 石墨烯和位于双链尾的碱基对。与相对较长的双链体 (rA) \(_{30}\) 相比： (rU) \(_{30}\)沿石墨烯表面保持平行排列，较短的双链体((rA) \(_{15 }\) : (rU) \(_{15}\) ) 即使在初始平行取向的情况下，也始终采用相对于石墨烯的垂直取向。发现 (rA) \(_{30}\) : (rU) \(_{30}\)与石墨烯形成稳定的杂化物，保持双链体的基本部分，而 (rA)\(_{15}\) : (rU) \(_{15}\)展示了双链体随着时间解压缩成两条单链。测定了与石墨烯堆叠的腺嘌呤/尿嘧啶之间以及水环境中核苷酸之间的相互作用能。
京公网安备 11010802027423号