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Some combinatorial problems concerning DNA arrays.

机译：有关DNA阵列的一些组合问题。

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摘要

DNA arrays are a powerful technology for accessing biological information. Such arrays are currently expensive, and so it is crucial to reduce the costs of using these technologies. We visit four problems within the array field, one concerned with analysis and three with fabrication of such arrays.; Sequencing by hybridization (SBH) is a theoretical technique for recovering sequence information from an array consisting of all possible oligonucleotides of a given length. This SBH technique has been shown to make inefficient use of arrays. Revising the experimental design to use pools of targets is shown to enable far more efficient use of arrays.; Arrays can be manufactured by in situ synthesis techniques. Such techniques rarely err, but those errors that do occur must be detected. Oligonucleotides with the same sequence but constructed using differing synthesis steps can be used to check for errors in manufacturing. We show how relatively small sets of such oligonucleotides may be constructed to detect any single step manufacturing error.; The in situ synthesis technique of photolithography leads to two optimization problems. First, unintended illumination of areas leads to mis-synthesis of some oligonucleotides. This unintended illumination can be reduced by rearranging the locations at which probes are synthesized on the substrate. Second, the photomasks used for lithography are most efficiently constructed by constructing a small cover of the open areas with rectangles. Solutions that improve on existing techniques for both of these problems are discussed.; In all of these cases, combinatorial models lead to improved efficiency of array techniques. Such efficiency gains may lead to cheaper arrays.
机译：DNA阵列是访问生物学信息的强大技术。这种阵列目前很昂贵，因此降低使用这些技术的成本至关重要。我们访问了阵列领域中的四个问题，一个与分析有关，三个与此类阵列的制造有关。杂交测序（SBH）是一种理论技术，可从由给定长度的所有可能的寡核苷酸组成的阵列中回收序列信息。该SBH技术已被证明无法有效利用数组。修改实验设计以使用目标池显示出能够更有效地使用阵列。阵列可以通过原位合成技术制造。这样的技术很少出错，但是必须检测确实发生的那些错误。具有相同序列但使用不同合成步骤构建的寡核苷酸可用于检查制造中的错误。我们展示了如何构建相对较小的此类寡核苷酸组以检测任何一步制造错误。光刻的原位合成技术导致两个优化问题。首先，区域的意外照明会导致某些寡核苷酸的错误合成。通过在基板上重新排列合成探针的位置，可以减少这种意外照明。其次，用于光刻的光掩模是通过用矩形覆盖开口区域的一小部分来最有效地构造的。讨论了针对这两个问题改进现有技术的解决方案。在所有这些情况下，组合模型可提高阵列技术的效率。这样的效率提高可以导致更便宜的阵列。

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  • 作者

    Hubbell, Earl.;

  • 作者单位

    University of Southern California.;

  • 授予单位 University of Southern California.;
  • 学科 Mathematics.; Biology Genetics.; Computer Science.
  • 学位 Ph.D.
  • 年度 2001
  • 页码 92 p.
  • 总页数 92
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类 数学;遗传学;自动化技术、计算机技术;
  • 关键词

  • 入库时间 2022-08-17 11:47:18

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