Nucleic Acids Research Lab, Department of Chemistry, University of Delhi, Delhi 110007, India.
Nucleic Acids Research Lab, Department of Chemistry, University of Delhi, Delhi 110007, India; Cluster Innovation Center, University of Delhi, Delhi 110007, India.
Int J Biol Macromol. 2018 May;111:455-461. doi: 10.1016/j.ijbiomac.2018.01.053. Epub 2018 Jan 10.
Sequence recognition and conformational polymorphism enable DNA to emerge out as a substantial tool in fabricating the devices within nano-dimensions. These DNA associated nano devices work on the principle of conformational switches, which can be facilitated by many factors like sequence of DNA/RNA strand, change in pH or temperature, enzyme or ligand interactions etc. Thus, controlling these DNA conformational changes to acquire the desired function is significant for evolving DNA hybridization biosensor, used in genetic screening and molecular diagnosis. For exploring this conformational switching ability of cytosine-rich DNA oligonucleotides as a function of pH for their potential usage as biosensors, this study has been designed. A C-rich stretch of DNA sequence (5'-TCCCCCAATTAATTCCCCCA-3'; SG20c) has been investigated using UV-Thermal denaturation, poly-acrylamide gel electrophoresis and CD spectroscopy. The SG20c sequence is shown to adopt various topologies of i-motif structure at low pH. This pH dependent transition of SG20c from unstructured single strand to unimolecular and bimolecular i-motif structures can further be exploited for its utilization as switching on/off pH-based biosensors.
序列识别和构象多态性使 DNA 成为在纳米尺寸范围内制造器件的重要工具。这些与 DNA 相关的纳米器件基于构象开关的原理工作，这些开关可以通过多种因素来实现，如 DNA/RNA 链的序列、pH 值或温度的变化、酶或配体相互作用等。因此，控制这些 DNA 构象变化以获得所需的功能对于开发 DNA 杂交生物传感器非常重要，该传感器用于遗传筛选和分子诊断。为了探索富含胞嘧啶的 DNA 寡核苷酸作为生物传感器的 pH 功能的这种构象转换能力，设计了这项研究。使用 UV-热变性、聚丙烯酰胺凝胶电泳和 CD 光谱法研究了 DNA 序列（5'-TCCCCCAATTAATTCCCCCA-3'；SG20c）中的 C 丰富区。结果表明，SG20c 序列在低 pH 值下采用各种 i-motif 结构的拓扑结构。SG20c 从无规卷曲的单链到单分子和双分子 i-motif 结构的这种 pH 依赖性转变，可以进一步被开发用于作为开/关 pH 基生物传感器的用途。
