School of Materials Science and Engineering, Georgia Institute of Technology, 771 Ferst Dr. NW, Atlanta, GA 30332-0245, USA.
711 Human Performance Wing, Air Force Research Laboratory, Wright Patterson AFB, OH 45433, USA.
Molecules. 2019 Apr 21;24(8):1572. doi: 10.3390/molecules24081572.
In contrast to sophisticated high-throughput sequencing tools for genomic DNA, analytical tools for comparing secondary structure features between multiple single-stranded DNA sequences are less developed. For single-stranded nucleic acid ligands called aptamers, secondary structure is widely thought to play a pivotal role in driving recognition-based binding activity between an aptamer sequence and its specific target. Here, we employ a competition-based aptamer screening platform called CompELS to identify DNA aptamers for a colloidal target. We then analyze predicted secondary structures of the aptamers and a large population of random sequences to identify sequence features and patterns. Our secondary structure analysis identifies patterns ranging from position-dependent score matrixes of individual structural elements to position-independent consensus domains resulting from global alignment.
与用于基因组 DNA 的复杂高通量测序工具相比，用于比较多个单链 DNA 序列之间二级结构特征的分析工具的发展还不够完善。对于称为适体的单链核酸配体，二级结构被广泛认为在驱动适体序列与其特定靶标之间基于识别的结合活性中起着关键作用。在这里，我们采用一种称为 CompELS 的基于竞争的适体筛选平台来鉴定用于胶体靶标的 DNA 适体。然后，我们分析鉴定的适体和大量随机序列的预测二级结构，以确定序列特征和模式。我们的二级结构分析确定了从依赖位置的各个结构元素的评分矩阵到通过全局比对产生的位置独立的共识结构域的模式。
