Alkali cation-mediated topology displayed by an exonic G-rich sequence of <i>TRPA1 gene</i>

G-rich sequences are intrinsic parts of the genome, widespread in promoters, telomeres, or other regulatory regions. The in vivo existence and biological significance have established the functional aspect of G-quadruplex structures and thus have developed immense interest in exploring their therapeutic aspects. Herein, using biophysical methods, we examined the structural status and comprehensive cation-dependence of a 17-bp G-rich genomic sequence (SKGT17) located in the coding region of the human TRPA1 gene, known to be associated with various neurovascular, cardiovascular, and respiratory conditions. TRPA1 is primarily seen as a therapeutic target for the development of novel analgesics. Bioinformatics analysis has suggested that 17-bp quadruplex motif is a binding site for transcription factor 'Sp1'. The formation and recognition of SKGT17 G-quadruplex might impact its regulatory functioning. Biophysical studies confirmed that the presence of alkali metal ions facilitated the formation of G-quadruplex in parallel topology. Native gel further substantiated the formation of a biomolecular species. Circular dichroism (CD), UV-thermal melting (Tm), and CD melting confirmed the formation of parallel G-quadruplex with metal ion-dependent stability. The stability of the G-quadruplex formed is found to be significantly high in the presence of K+ ions than that of other ions. Intriguingly, we have also established that this segment of the TRAP1 gene favors G-quadruplex formation over its participation in the corresponding duplex formation under K+ ions conditions. This study attempts to explain the rationale for the stabilization of G-quadruplex in the presence of alkali metal ions and may add to a better understanding and insights into DNA-metal ions interactions. Communicated by Ramaswamy H. Sarma富含鸟嘌呤的序列（G-rich sequences）是基因组的固有组成部分，广泛分布于启动子、端粒及其他调控区域。其体内存在性与生物学意义确立了G-四链体（G-quadruplex）结构的功能属性，由此引发了学界对其治疗应用探索的极大兴趣。 本研究借助生物物理方法，对位于人类TRPA1基因编码区的17bp富含鸟嘌呤基因组序列SKGT17的结构状态与全面的阳离子依赖性展开了分析。该序列已被证实与多种神经血管、心血管及呼吸系统疾病相关。TRPA1主要被视为开发新型镇痛药物的治疗靶点。 生物信息学分析表明，该17bp四链体基序是转录因子Sp1的结合位点。SKGT17 G-四链体的形成与识别可能会影响其调控功能。 生物物理研究证实，碱金属离子的存在可促进平行拓扑结构G-四链体的形成。非变性凝胶电泳实验进一步证实了生物分子聚集体的形成。圆二色性（CD）、紫外热解链（Tm）及CD热解链实验均证实，该平行拓扑结构G-四链体的稳定性依赖于金属离子的存在。研究发现，相较于其他离子，K+存在时形成的G-四链体稳定性显著更高。 有趣的是，本研究还证实，在K+离子条件下，TRAP1基因的该片段更倾向于形成G-四链体，而非参与形成对应的双链结构。本研究旨在阐明碱金属离子稳定G-四链体的内在机制，或可为深入理解DNA与金属离子的相互作用提供新的认知与见解。 本文由Ramaswamy H. Sarma转交。