Epigenetic profiling by near-field UV-Raman scattering in nanochannels

通过纳米通道中的近场紫外拉曼散射进行表观遗传分析

基本信息

批准号：
8193129
负责人：
Hans Hallen
金额：
$ 18.66万
依托单位：
NORTH CAROLINA STATE UNIVERSITY RALEIGH
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-09-18 至 2013-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8193129
关键词：
Achievement Antibodies Arts Base Composition Cells Chromatin Chromatin Modeling Chromosomes Cytosine DNA DNA Binding Data Data Quality Detection Development Devices Dyes Environmental Risk Factor Epigenetic Process Evolution Fluorescence Fungal Genome GC Rich Sequence Genes Genetic Materials Genetic Risk Genomics Goals Haploidy Haplotypes Histones Human Genome Hybrids Imagery Individual Label Libraries Location Malignant Neoplasms Maps Measures Metals Methods Methylation Modeling Modification Molecular Analysis Monitor Nature Neoplasm Metastasis Optics Population Process Property Research Resolution Scanning Signal Transduction Staging Stem cells Stretching Structure Surface Techniques Technology Testing Ursidae Family Yeasts anticancer research cancer stem cell chromatin modification driving force genome sequencing genome-wide histone modification improved nanochannel nanofluidic performance tests programs reconstitution single molecule tool tumor

项目摘要

DESCRIPTION (provided by applicant): Epigenetic programming has emerged as a central theme in cancer development. Here we propose a new technique for monitoring the methylation state, chromatin status, and histone modification of genomic sized molecules, ideally whole chromosomes. The proposed method combines stretching of genetic material in nanofluidic channels, and subsequent optical readout by UV-resonant Raman scattering under near-field enhancement. We expect a resolution of about 1 kbp or better. The technique will provide a tool for single-molecule studies probing the epigenetic diversity of cell populations, and should be able to yield information about the importance and evolution of progenitor cell within tumors. The proposed research is exploratory in nature, but will provide significant improvements over the current art because of its capability to handle long molecules, high resolution, and label-free detection. Our strategy toward our goal is to establish a number of milestones along the way, which by themselves are significant achievements. In the first stage, we will nanochannel stretching of DNA that is labeled using methylation-specific fluorescent markers. We also aim at demonstrating chromatin stretching, and visualization of histones using specific antibodies. In the next stage, we will demonstrate that near-field enhancement of fluorescence by metal structures that are integrated with the nanofluidic device. The resolution should improve by a factor of 10. We will then investigate the near-field UV-resonant Raman signatures of specific DNA and chromatin constructs on test structures on wafers. Finally, we will integrate our findings to demonstrate near-field UV-resonant Raman of DNA scanned through nanochannels. Further, we will use the best technology proven in the course of the project, Raman or fluorescence, chromatin or bare DNA, to construct an epigenetic map of genomic model DNA or reconstituted chromatin from yeasts. We propose a new technique for monitoring the epigenetic programming state of genomic sized molecules, ideally whole chromosomes. The proposed method combines stretching of genetic material in nanofluidic channels, and subsequent optical readout by UV-resonant Raman scattering under near-field enhancement. We expect the method to become a valuable tool in cancer research.

描述（由申请人提供）：表观遗传编程已成为癌症发展的中心主题。在这里，我们提出了一种新技术，用于监测基因组大小的分子（最好是整个染色体）的甲基化状态、染色质状态和组蛋白修饰。所提出的方法结合了纳米流体通道中遗传物质的拉伸以及在近场增强下通过紫外共振拉曼散射进行的后续光学读出。我们预计分辨率约为 1 kbp 或更好。该技术将为探索细胞群表观遗传多样性的单分子研究提供工具，并且应该能够产生有关肿瘤内祖细胞的重要性和进化的信息。拟议的研究本质上是探索性的，但由于其处理长分子、高分辨率和无标记检测的能力，将比现有技术提供重大改进。我们实现目标的策略是一路上建立多个里程碑，这些里程碑本身就是重大成就。在第一阶段，我们将对使用甲基化特异性荧光标记物标记的 DNA 进行纳米通道拉伸。我们还旨在展示染色质拉伸以及使用特定抗体的组蛋白可视化。在下一阶段，我们将演示与纳米流体装置集成的金属结构对荧光的近场增强。分辨率应提高 10 倍。然后，我们将研究晶圆测试结构上特定 DNA 和染色质结构的近场紫外共振拉曼特征。最后，我们将整合我们的研究结果来展示通过纳米通道扫描的 DNA 的近场紫外共振拉曼。此外，我们将使用项目过程中经过验证的最佳技术，拉曼或荧光、染色质或裸DNA，构建基因组模型DNA或酵母重组染色质的表观遗传图谱。我们提出了一种新技术来监测基因组大小的分子（最好是整个染色体）的表观遗传编程状态。所提出的方法结合了纳米流体通道中遗传物质的拉伸以及近场增强下通过紫外共振拉曼散射进行的后续光学读出。我们期望该方法成为癌症研究中的一个有价值的工具。

项目成果

期刊论文数量（7）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Fluctuation modes of nanoconfined DNA.

纳米限制 DNA 的波动模式。

DOI：
10.1063/1.3675207
发表时间：
2012
期刊：
Journal of applied physics
影响因子：
3.2
作者：
Karpusenko,Alena;Carpenter,JoshuaH;Zhou,Chunda;Lim,ShuangFang;Pan,Junhan;Riehn,Robert
通讯作者：
Riehn,Robert

Collapse of DNA under alternating electric fields.

DNA 在交变电场下的塌陷。

DOI：
10.1103/physreve.92.012714
发表时间：
2015
期刊：
Physical review. E, Statistical, nonlinear, and soft matter physics
影响因子：
0
作者：
Zhou,Chunda;Riehn,Robert
通讯作者：
Riehn,Robert

Chromatin modification mapping in nanochannels.

纳米通道中的染色质修饰图谱。

DOI：
10.1063/1.4833257
发表时间：
2013
期刊：
Biomicrofluidics
影响因子：
3.2
作者：
Lim,ShuangFang;Karpusenko,Alena;Blumers,AnselL;Streng,DianaE;Riehn,Robert
通讯作者：
Riehn,Robert

Collapse of DNA in ac electric fields.

DOI：
10.1103/physrevlett.106.248103
发表时间：
2011-06-17
期刊：
Physical review letters
影响因子：
8.6
作者：
Zhou C;Reisner WW;Staunton RJ;Ashan A;Austin RH;Riehn R
通讯作者：
Riehn R

Probing transient protein-mediated DNA linkages using nanoconfinement.

使用纳米限制探测瞬时蛋白质介导的 DNA 连接。

DOI：
10.1063/1.4882775
发表时间：
2014
期刊：
Biomicrofluidics
影响因子：
3.2
作者：
Roushan,Maedeh;Kaur,Parminder;Karpusenko,Alena;Countryman,PrestonJ;Ortiz,CarlosP;FangLim,Shuang;Wang,Hong;Riehn,Robert
通讯作者：
Riehn,Robert