Molecular Recognition in Microarrays: A Computer Simulation Study

摘要：DNA微阵列的分子识别：计算机模拟研究项目概述：DNA微阵列已经彻底改变了生物学研究的方式，使在一个实验中分析数千个基因成为可能。微阵列被用于基因分析、毒理基因组学、药物发现、途径生物化学和法律的鉴定。尽管这种强大的技术已经被科学界热情地采用，但它还远未成熟。关于如何设计最大灵敏度和特异性的微阵列存在相当大的不确定性。需要对影响微阵列性能的各种因素之间的相互作用有一个基本的了解。 拟议的研究有两个基本目标。第一个目标是为设计具有最大灵敏度和特异性的微阵列制定指导方针。这将通过进行蒙特卡罗模拟的吸附和分子识别的晶格模型DNA靶分子的晶格模型探针分子拴到微阵列表面。DNA基本上是纳米级的。 系统地探讨了影响微阵列灵敏度和特异性的因素，包括：探针序列、长度和浓度;靶序列、长度和浓度;探针和靶的核苷酸组成、间隔区长度和温度。这项研究的结果将与我们的实验合作者Stefan Franzen教授的结果以及文献中的数据进行比较。第二个目标是开发一种新的计算工具，可用于提高解释微阵列数据的准确性。这将通过建立一个新的DNA分子的中间分辨率模型，然后进行隐式溶剂不连续分子动力学模拟的吸附目标模型DNA分子（完美匹配和错配）的微阵列表面含有探针模型DNA分子。一个多尺度建模方法将被用来提取模型中的能量和几何参数从显式溶剂CHARMM模拟计算的平均力的潜力。这里的一个子目标是量化表面杂交和批量杂交之间的差异，然后使用这些信息来修改和改进目前用于将微阵列数据与完美匹配和错配相关联的基于批量的理论模型。该项目这一部分的结果将与我们的合作者Erdogan Gulari教授的实验结果进行比较。这两个项目合在一起应该能给我们一个DNA微阵列中分子识别的良好物理图像。 拟议研究的更广泛影响如下。这项拟议中的研究可能会对医学研究领域产生影响。DNA微阵列在当今癌症研究中被大量使用，因为研究人员正在努力识别肿瘤中表达的基因，或者识别可能作为化疗潜在靶点的遗传标记（癌基因）。 除了培训两名研究生外，还将通过以下两项活动促进研究和教育。(1)DNA在微阵列上的杂交将被用作PI的本科化学工程热力学课程开发的一些示例的基础，并插入到她正在编写的本科化学工程热力学教科书中。(2)将准备一份介绍基因组学基础知识并最终介绍DNA微阵列的幻灯片，以便通过网络传播。PI将继续开展大量非正式活动，以扩大妇女的机会。由于她是第一批被任命为化学工程学院在美国的女性之一，PI现在被视为学术界的年轻成员的榜样，因此作为一个非正式的导师，许多女学生（本科生和研究生）在NCSU，以及女性教师和未来的女性教师在美国各地。 PI吸引了不成比例的女研究生加入她的研究小组;在过去五年中，她指导的16名研究生中，有9名是女性。

ABSTRACTMolecular Recognition in Microarrays: A Computer Simulation StudyProject Summary:DNA microarrays have revolutionized the way that biological research is done, enablingthe analysis of thousands of genes in a single experiment. Microarrays are being used in gene profiling, toxicogenomics, drug discovery, pathway biochemistry, and legal identification. Even though this powerful technique has been enthusiastically adopted by the scientific community, it is far from mature. Considerable uncertainty exists about how to design microarrays for maximum sensitivity and specificity. A fundamental understanding of the interplay between the various factors that affect microarray performance is needed. The proposed research has two basic objectives. The first objective is to develop guidelines for designing microarrays with maximum sensitivity and specificity. This will be accomplished by performing Monte Carlo simulations of the adsorption and molecular recognition of lattice model DNA target molecules by lattice model probe molecules tethered to a microarray surface. DNA is basically at the nano-scale. The factors that affect the sensitivity and specificity of microarrays will be systematically explored including: the probe sequence, length and concentration; the target sequence, length and concentration; the nucleotide compositions of the probe and target, the spacer length, and the temperature. Results from this study will be compared to those of our experimental collaborator, Professor Stefan Franzen and to data in the literature. The second objective is to develop a new computational tool that can be used to improve accuracy in interpreting microarray data. This will be accomplished by building a new intermediate resolution model of DNA molecules and then performing implicit-solvent discontinuous molecular dynamics simulations of the adsorption of target model DNA molecules (both perfect match and mismatch) on microarray surfaces containing probe model DNA molecules. A multiscale modeling approach will be used to extract the energetic and geometrical parameters in the model from potentials of mean force calculated during explicit-solvent CHARMM simulations. A sub-objective here is to quantify the difference between hybridization on surfaces and hybridization in bulk, and then to use this information to modify and improve the bulk-based theoretical models currently used to correlate microarray data on perfect matches and mismatches. Results from this part of the project will be compared to experimental results of our collaborator Professor Erdogan Gulari. Taken together these two projects should give us a goodphysical picture of molecular recognition in DNA microarrays. The broader impacts of the proposed research are the following. The proposed research could have an impact on the world of medical research. DNA microarrays are heavily used in cancer research today as researchers struggle to identify genes that are expressed in tumors, or toidentify genetic markers (oncogenes) that could serve as potential targets for chemotherapy. In addition to training two graduate students, research and education will be fostered by the following two activities. (1) Hybridization of DNA on microarrays will be used as the basis for a number of examples that will be developed for the PI's undergraduate chemical engineering thermodynamics course, and inserted into an undergraduate chemical engineering thermodynamics textbook that she is writing. (2) A power point presentation describing the basics of genomics and culminating in a description of DNA microarrays will be prepared for dissemination via the web.The PI will continue her considerable but informal activities to broaden the opportunitiesfor women. Since she was one of the first women to be appointed to a chemical engineering faculty in the US, the PI is now viewed as a role model by younger members of the academic community, and hence serves as an informal mentor to many women students (undergraduate and graduate) at NCSU, as well as to women faculty and prospective women faculty across the US. The PI attracts a disproportionate number of women graduate students to her research group; of the 16 graduate students that she has advised over the past five years, 9 have been women.