Enhanced DNA microarray performance with patterned probe

描述（由申请人提供）：拟议研究的目标是开发一种方法，用于显著提高杂交测序（SBH）的性能，从而降低成本并提高DNA测序的速度。如果成功，基因谱公司的技术。将使测序成本降低100倍。目前DNA测序技术的局限性和对DNA序列信息日益增长的需求，决定了需要一种快速、廉价的DNA序列测定方法，特别是在人类健康的应用中。杂交测序在20世纪80年代末和90年代初被提出作为DNA测序的有效方法。这种方法被证明是无效的，基本上被放弃了。我们已经发现了一种新的方法来设计和解释阵列，提供了大量的增加，可以从阵列中提取的信息，这将使SBH一个可行的技术。我们的方法依赖于含有天然碱基和通用碱基的寡核苷酸探针阵列。在该提议的上下文中，通用碱基被定义为核苷酸类似物，当掺入DNA中时，其与所有四个同源碱基同样良好地杂交。通用碱基用于将天然碱基排列成寡核苷酸探针中的模式。这些图案化寡核苷酸的阵列使我们能够使用独特的算法，导致高效的序列重建。在过去的两年中，我们已经研究了几种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，通过使用天然碱基的特定混合物来制造通用碱基的替代物，我们称之为“半简并”碱基。其结果是描绘了一种方法，以形成图案化的探针，可以立即测试和使用。这里提出的项目的目标是证明半简并碱基将在阵列化的图案化探针中作为通用碱基发挥作用。

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.