The Effect of Monovalent Cation Binding on DNA Hairpin Stability

单价阳离子结合对 DNA 发夹稳定性的影响

• 批准号: 0748271
• 负责人: Nancy Stellwagen
• 金额: $ 34.5万
• 依托单位: University of Iowa
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-03-01 至 2012-02-29
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0748271&HistoricalAwards=false
• 关键词: Effect; Monovalent; Cation; Binding; DNA

In this research supported by the Analytical and Surface Chemistry Program, Professor Stellwagen and her group will study the binding of monovalent cations to DNA hairpins, and the effect of monovalent cation binding on hairpin stability, using capillary electrophoresis. The current structure-prediction algorithms do not reliably predict DNA hairpin stability, indicating that the interactions leading to hairpin formation are not properly included in the folding routines. Since hairpin structures in single-stranded DNA oligomers are only marginally stable, they are difficult to study by conventional methods such as ultraviolet absorption or differential scanning calorimetry. By contrast, free solution capillary electrophoresis can detect hairpin formation and cation binding directly, because electrophoretic mobility depends on both the shape and the effective charge of the analyte. Broader impact of the proposed research: An important aspect of the project is its contribution to the training of undergraduate students and recent graduates in the biochemical and/or biophysical sciences. There are also scientific and technological broader impacts. Unexpected hairpin formation in single-stranded DNA oligomers can interfere with the hybridization of DNA oligomers to their target DNA or RNA sequences, creating difficulties in the design of multiplex PCR reactions and the interpretation of microarray experiments. Hairpin formation can also interfere with the effectiveness of DNA oligonucleotides used as antisense gene therapy agents. Hence, it is important to be able to predict hairpin formation in DNA oligomers and to understand the factors contributing to hairpin stability. The capillary electrophoresis methods that we have developed to measure monovalent cation binding to DNA are of general utility and can be used to measure the binding of other ligands to other analytes. .

在这项由分析和表面化学计划支持的研究中，Stellwagen教授和她的团队将使用毛细管电泳研究单价阳离子与DNA发夹的结合，以及单价阳离子结合对发夹稳定性的影响。 目前的结构预测算法不能可靠地预测DNA发夹的稳定性，这表明导致发夹形成的相互作用没有正确地包括在折叠程序中。 由于单链DNA寡聚体中的发夹结构仅在边缘上稳定，因此难以通过常规方法如紫外吸收或差示扫描量热法来研究。 相比之下，自由溶液毛细管电泳可以直接检测发夹形成和阳离子结合，因为电泳迁移率取决于分析物的形状和有效电荷。 拟议研究的更广泛影响：该项目的一个重要方面是其对生物化学和/或生物物理科学本科生和应届毕业生的培训的贡献。还有更广泛的科学和技术影响。单链DNA寡聚体中意外的发夹形成可干扰DNA寡聚体与其靶DNA或RNA序列的杂交，从而在多重PCR反应的设计和微阵列实验的解释中产生困难。 发夹形成也可以干扰用作反义基因治疗剂的DNA寡核苷酸的有效性。 因此，能够预测DNA低聚物中发夹的形成并了解影响发夹稳定性的因素非常重要。 我们已经开发的用于测量单价阳离子与DNA结合的毛细管电泳方法具有通用性，并且可以用于测量其他配体与其他分析物的结合。.