Diffusion of Confined DNA

ID：MPS/DMR/BMAT（7623）1206045 PI：Dorfman，Kevin ORG：明尼苏达大学标题：受限DNA的扩散智力优势：纳米通道受限DNA是一种直接从基因组DNA获得序列特异性信息的新兴技术。 随着这项新技术的发展，人们对受限的半柔性链物理学重新产生了兴趣。 虽然30多年前由de Gennes和Odijk开发的经典理论为柔性链的延伸和扩散性提供了完整的描述，但实验数据表明这些理论并不能描述半柔性链，如DNA在大部分限制范围内。 模拟提供了具体的证据，证明在Odijk和de Gennes所描述的极限之间存在两种制度：一种“扩展的de Gennes”制度和一种“过渡制度”，但这些最先进的理论仍然未经检验。 本实验方案的具体目标是：（1）测试在过渡和扩展的de Gennes区域中DNA延伸的预测，（2）开发一个适当的定义，用于解释表面性质的受限DNA的有效宽度，和（3）测试在过渡和扩展的de Gennes区域中DNA扩散系数的预测。 拟议的实验利用一种新的方法来制造相对便宜的原型纳米通道与物理研究所需的精度。 更广泛的意义：纳米通道限制是一种新兴的DNA条形码编码方法，它可以将DNA拉伸，并从线性化的DNA中光学“读取”荧光基因组信息。 DNA条形码快速提供基因组规模的信息，具有双酶对分辨率，作为第二代基因组测序和杂交微阵列的重要补充。 用于DNA条形码化的纳米通道尺寸通常位于过渡区或扩展的de Gennes区。 本项目所获得的基本结果将为这些器件的进一步工程化提供基础。 在这个项目中的研究将培养研究生和本科生在纳米纤维，聚合物物理和传输现象。 代表性不足的少数民族的参与将进一步增加通过夏季研究计划与化学系在格兰布林州立大学，HBCU。 参加“能源和U”计划将促进3-12年级学生对科学和工程的兴趣。 “能量和U”是一个互动程序，通过戏剧性的能量转换演示，以适合年龄的方式教授热力学第一定律。 每年有数千名学生参加该项目，其中包括许多来自市中心和贫困学校的学生。

ID: MPS/DMR/BMAT(7623) 1206045 PI: Dorfman, Kevin ORG: University of MinnesotaTitle: Diffusion of Confined DNAINTELLECTUAL MERIT: Nanochannel confined DNA is an emerging technology for obtaining sequence specific information directly from genomic DNA. The development of this new technology has been accompanied by a renewed interest in the physics of confined, semi-flexible chains. While the classical theories developed more than 30 years ago by de Gennes and Odijk provide a complete description for the extension and diffusivity of a flexible chain, experimental data indicate that these theories do not describe semi-flexible chains such as DNA over most of the range of confinement. Simulations have provided concrete evidence for the existence of two regimes between the limits described by Odijk and de Gennes: an "extended de Gennes" regime and a "transition regime," but these state-of-the-art theories remain untested. The specific aims of this experimental proposal are: (1) test the predictions for the extension of DNA in the transition and extended de Gennes regime, (2) develop a proper definition for the effective width of confined DNA that accounts for surface properties, and (3) test the predictions for the diffusion coefficients of DNA in the transition and extended de Gennes regimes. The proposed experiments take advantage of a new approach to fabricate relatively inexpensive prototype nanochannels with the precision required for physical studies. This project should lead to a comprehensive, quantitative understanding of the extension and diffusion of DNA in confinement.BROADER IMPACTS: Nanochannel confinement is an emerging method for DNA barcoding, where the DNA is stretched and fluorescent genomic information is optically "read" from the linearized DNA. DNA barcoding rapidly provides genome-scale information with kilobase pair resolution, serving as an important complement to second-generation genome sequencing and hybridization microarrays. The nanochannel sizes used for DNA barcoding normally lie in the transition regime or the extended de Gennes regime. The fundamental results gained from this project will provide the foundation for the further engineering of these devices. The research in this project will train graduate and undergraduate students in nanofabrication, polymer physics, and transport phenomena. The participation of underrepresented minorities will be increased further through a summer research program with the Chemistry Department at Grambling State University, an HBCU. Participation in the "Energy and U" program will promote interest in science and engineering in students in grades 3-12. "Energy and U" is an interactive program that teaches the first law of thermodynamics in an age-appropriate manner through dramatic demonstrations of energy conversion. Thousands of students attend the program each year, including many students from inner city and underprivileged schools.