CD spectra reveal the state of G-quadruplexes and i-motifs in repeated and other DNA sequences.

IF 2.4 Q3 BIOPHYSICS Biophysical reports Pub Date : 2025-03-12 Epub Date: 2024-11-27 DOI:10.1016/j.bpr.2024.100187
Levi Diggins, Daniel Ross, Sundeep Bhanot, Rebecca Corallo, Rachel Daley, Krishna Patel, Olivia Lewis, Shane Donahue, Jacob Thaddeus, Lauren Hiers, Christopher Syed, David Eagerton, Bidyut K Mohanty
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Abstract

The B-DNA of the genome contains numerous sequences that can form various noncanonical structures including G-quadruplex (G4), formed by two or more stacks of four guanine residues in a plane, and intercalating motif (i-motif [iM]) formed by alternately arranged C-C+ pairs. One of the easy yet sensitive methods to study G4s and iMs is circular dichroism (CD) spectroscopy, which generates characteristic G4 and iM peaks. We have analyzed and compared the effects of various environmental factors including pH, buffer composition, temperature, flanking sequences, complimentary DNA strands, and single-stranded DNA binding protein (SSB) on the CD patterns of G4s and iMs generated by two groups of DNA molecules, one containing tandem repeats of GGGGCC and CCCCGG from the C9ORF72 gene associated with amyotrophic lateral sclerosis and frontotemporal dementia, and the second containing polyG/polyC clusters from oncogene promoter-proximal regions without such tandem repeats. Changes in pH caused drastic changes in CCCCGG-iM and GGGGCC-G4 and the changes were dependent on repeat numbers and G-C basepairing. In contrast, with the DNA sequences from the promoter-proximal regions of oncogenes, iMs disassembled upon pH changes with the peak slowly shifting to lower wavelength but the G4s did not show significant change. Complementary DNA strands and flanking DNA sequences also regulate G4 and iM formation. The SSB disassembled both G4s and iMs formed by almost all sequences suggesting an in vivo role for SSBs in the disassembly of G4s and iMs during DNA replication and other DNA transactions.

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CD光谱揭示了重复和其他DNA序列中g -四联体和i-基序的状态。
基因组的B DNA包含许多可以形成各种非规范结构的序列,包括g-四重体(G4),由两个或更多四个鸟嘌呤残基在一个平面上堆叠形成,以及由C-C+对交替排列形成的插层基序(i-motif, iM)。圆二色(CD)光谱是研究G4和iM的一种简便而灵敏的方法,它可以产生G4和iM的特征峰。我们分析并比较了各种环境因素,包括pH、缓冲液成分、温度、侧翼序列、互补DNA链和单链DNA结合蛋白(SSB)对两组DNA分子产生的G4s和iMs的CD模式的影响,其中一组DNA分子含有与肌萎缩性侧索硬化症(ALS)和额颞叶痴呆(FTD)相关的C9ORF72基因GGGGCC和CCCCGG的串联重复序列;第二种包含来自癌基因启动子-近端区域的polyG/polyC簇,没有这种串联重复序列。pH变化引起ccggg - im和GGGGCC-G4的剧烈变化,其变化依赖于重复数和G:C碱基配对。相比之下,在癌基因启动子-近端DNA序列中,iMs随着pH的变化而解体,峰值缓慢向较低波长移动,但G4s没有明显变化。互补DNA链和侧翼DNA序列也调节G4和iM的形成。单链DNA结合蛋白SSB可以拆卸几乎所有序列形成的G4s和iMs,这表明在体内,SSB在DNA复制和其他DNA交易过程中参与了G4s和iMs的拆卸。
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Biophysical reports
Biophysical reports Biophysics
CiteScore
2.40
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审稿时长
75 days
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