Real-time Multiplex Single-Molecule DNA Sequencing

描述（由申请人提供）：基因组测序已经彻底改变了生物学和医学。在过去10年中，测序成本降低了5倍，这推动了许多生物体基因组序列数据可用性的爆炸式增长。尽管取得了这些进展，但由于常规测序的成本过高，序列数据的绝大多数价值尚未实现。目前基于毛细管电泳的测序技术可能无法实现成本的数量级降低。需要替代测序技术。在这里，我们提出利用DNA聚合酶作为一个快速和节俭的测序引擎，实时监测DNA聚合。Nanofluidics, Inc.是从康奈尔大学分拆出来的，明确地利用技术进步，使实时单分子测序系统成为可能。第一种是光学约束技术，即零模波导（ZMW），它可以在DNA聚合过程中实时检测单个核苷酸的掺入。第二种，末端磷酸盐荧光标记，是一种将荧光团连接到核苷酸上的方法，这样它们在结合后就会自动从DNA链上移除。通过使DNA结构不受荧光团的阻碍，这种方法即使使用100%的标记核苷酸替代也可以进行高度的过程结合。这些技术的结合消除了缓慢而昂贵的反应洗涤或解除聚合酶阻断的需要。由于聚合酶是自由运行的，只要聚合酶继续合成，序列读取就可以进行，合成过程可以长达数十万个碱基。ZMW和聚合酶都很小，系统没有流体或运动部件，使该技术适用于高度复用。该项目的目标是将这些技术应用到四色、实时、多重单分子DNA测序系统中，使哺乳动物基因组测序到2008年的成本为5万美元，到2010年的成本为1000美元。

DESCRIPTION (provided by applicant): Genome sequencing has revolutionized biology and medicine. A 5-fold decrease in sequencing cost over the past 10 years has fueled an explosive growth in the availability of genome sequence data for numerous organisms. Despite these advances, the vast majority of the value from sequence data has yet to be realized, as the cost of routine sequencing is prohibitive. Current sequencing technologies based on capillary electrophoresis will likely not allow order-of-magnitude decreases in cost. Alternative sequencing technologies are required. Here we propose to use DNA polymerase enzyme as a fast and frugal sequencing engine by monitoring DNA polymerization in real-time. Nanofluidics, Inc. was established as a spin-out from Cornell University explicitly to leverage 2 technological advances that enable real-time single-molecule sequencing system. The first is an optical confinement technology, the zero-mode waveguide (ZMW), which allows detection of single nucleotide incorporation in real-time during processive DNA polymerization. The second, terminal-phosphate fluorescent labeling, is a method of attaching fluorophores to nucleotides such that they are automatically removed from the DNA strand after incorporation. By leaving the DNA structure un-hindered with fluorophores, this method allows highly processive incorporation even using 100% replacement with labeled nucleotides. The combination of these technologies eliminates the need for slow and expensive washing of the reaction or un-blocking of the polymerase. Because the polymerase is free-running, the sequence read can proceed as long as the polymerase continues synthesizing, which can be as long as hundreds of thousands of bases. Both the ZMW and the polymerase are small, and the system has no fluidics or moving parts, making the technology amenable to high degrees of multiplexing. The goal of this program is to deploy these technologies in a 4-color, real-time, multiplex single-molecule DNA sequencing system that will enable sequencing of a mammalian genome for $50,000 by 2008, and $1000 by 2010.