PROBING THE STACKING INTERACTION IN NUCLEIC ACIDS

探究核酸中的堆积相互作用

• 批准号: 7601489
• 负责人: MARGARET MANDZIUK
• 金额: $ 0.03万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-01 至 2008-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7601489
• 关键词: Base Pairing; Complex; Computer Retrieval of Information on Scientific Projects Database; Electronics; Failure; Funding; Grant; Hydrogen Bonding; Institution; Link; Methods; Nucleic Acids; Numbers; Oligonucleotides; Research; Research Personnel; Resources; Source; Structure; Sugar Phosphates; United States National Institutes of Health; base; improved

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Whereas the ab-initio electronic structure methods are successful in calculations involving hydrogen bonding between nucleic acids bases, they fail when applied to stacking interaction. That failure has been attributed to the inadequate ellectronic correlations and it is implied that expansion of the basis set may improve the results. I would like to explore a conceptually different approach to stacking and perform calculations for complexes involving hydrogenated and/or dehydrogenated radicals of nucleic acid bases and base pairs. The exploratory calculations will be performed at the B3LYP/aug-cc-pVDZ level. Inspite of using a rather modest basis set for this problem, the calculations will require significant computational resources due to the large number of atoms in the considered clusters. If successful, the exploratory calculations will be extended to include the phosphate-sugar links between the bases and to calculate structures of small oligonucleotides.

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 虽然从头算电子结构方法在涉及核酸碱基之间氢键的计算中是成功的，但当应用于堆积相互作用时，它们却失败了。这一失败归因于不充分的电子关联，这意味着扩大基组可能会改善结果。我想探索一种概念上不同的堆积方法，并对含有核酸碱基和碱基对的氢化和/或脱氢自由基的络合物进行计算。探索性计算将在B3LYP/Aug-cc-pVDZ水平上进行。尽管使用了一个相当适度的基组来解决这个问题，但由于所考虑的团簇中的大量原子，计算将需要大量的计算资源。如果成功，探索性计算将扩大到包括碱基之间的磷酸-糖键，并计算小分子寡核苷酸的结构。