Enhanced DNA microarray performance with patterned probe

描述(申请人提供)：建议研究的目标是开发一种显著提高杂交测序(SBH)性能的方法，从而降低成本并提高DNA测序速度。如果成功，GeneSpectrum公司正在开发的技术将把这种测序的成本降低100倍。当前DNA测序技术的局限性和对DNA序列信息日益增长的需求决定了对快速、廉价的DNA序列测定方法的需求，特别是在人类健康的应用中。杂交测序是20世纪80年代末90年代初提出的一种有效的DNA测序方法。事实证明，这种方法效率低下，基本上被放弃了。我们发现了一种设计和解释阵列的新方法，它大大增加了可以从阵列中提取的信息量，这将使SBH成为一种可行的技术。我们的方法依赖于包含天然碱基和通用碱基的寡核苷酸探针阵列。在这项提议的背景下，通用碱基被定义为当与DNA结合时，与所有四个同源碱基杂交得同样好的核苷酸类似物。通用碱基用于将天然碱基排列成寡核苷酸探针中的模式。这些图案化的寡核苷酸阵列使我们能够使用独特的算法，从而产生高效的序列重建。在过去的两年里，我们研究了几个分子在我们的图案化探针中作为通用碱基的能力。我们最近发现了一种方法，通过使用特定的天然碱基混合物来制造万能碱基的替代品，我们称之为“半简并”碱。其结果是描述了一种形成可立即测试和使用的图案化探针的方法。该项目的目标是证明半简并碱基将在阵列、图案化的探针中起到通用碱基的作用。

DESCRIPTION (provided by applicant): The goal of the proposed research is to develop a method for significantly improving the performance of sequencing by hybridization (SBH), thus decreasing the cost and increasing the speed of sequencing DNA. If successful, the technology that GeneSpectrum Inc. is developing will reduce the cost of such sequencing by 100 fold. The limitations of current DNA sequencing technology and the growing appetite for DNA sequence information define a need for a rapid, inexpensive method for DNA sequence determination, particularly in applications to human health. Sequencing by hybridization was proposed as an efficient method for sequencing DNA in the late 1980s and early 1990s. The method proved to be inefficient and was essentially abandoned. We have discovered a novel approach to the design and interpretation of arrays that provides a large increase in the amount of information that can be extracted from the array and that will make SBH a viable technique. Our method relies on arrays of oligonucleotide probes that contain natural bases and universal bases. In the context of this proposal universal bases are defined as nucleotide analogs that, when incorporated into DNA, hybridize equally well with all four of the cognate bases. The universal bases are used to arrange the natural bases into patterns in the oligonucleotide probes. Arrays of these patterned oligonucleotides allow us to use unique algorithms that result in highly efficient sequence reconstruction. In the last two years, we have investigated the ability of several molecules to function as the universal base in our patterned probes. We have recently discovered a method to make surrogates of universal bases by using specific mixtures of natural bases, which we refer to as "semi-degenerate" bases. The result is the delineation of a method to form patterned probes that can be tested and used immediately. The objective of the project proposed here is to demonstrate that semi-degenerate bases will function in arrayed, patterned probes as universal bases.