Assembly of supramolecular DNA complexes containing both G-quadruplexes and i-motifs by enhancing the G-repeat-bearing capacity of i-motifs

Abstract

The single-step assembly of supramolecular complexes containing both i-motifs and G-quadruplexes (G4s) is demonstrated. This can be achieved because the formation of four-stranded i-motifs appears to be little affected by certain terminal residues: a five-cytosine tetrameric i-motif can bear ten-base flanking residues. However, things become complex when different lengths of guanine-repeats are added at the 3′ or 5′ ends of the cytosine-repeats. Here, a series of oligomers d(XGiXC5X) and d(XC5XGiX) (X = A, T or none; i < 5) are designed to study the impact of G-repeats on the formation of tetrameric i-motifs. Our data demonstrate that tetramolecular i-motif structure can tolerate specific flanking G-repeats. Assemblies of these oligonucleotides are polymorphic, but may be controlled by solution pH and counter ion species. Importantly, we find that the sequences d(TGiAC5) can form the tetrameric i-motif in large quantities. This leads to the design of two oligonucleotides d(TG4AC7) and d(TGBrGGBrGAC7) that self-assemble to form quadruplex supramolecules under certain conditions. d(TG4AC7) forms supramolecules under acidic conditions in the presence of K+ that are mainly V-shaped or ring-like containing parallel G4s and antiparallel i-motifs. d(TGBrGGBrGAC7) forms long linear quadruplex wires under acidic conditions in the presence of Na+ that consist of both antiparallel G4s and i-motifs.

5′-(CGA) n sequence-assisted pH-controlled assembly of supramolecular DNA nanostructure

“…To this end, SG1 (S1–G 6 –S2) and CSG1 (CS2–G 6 –CS1) with completely symmetrical sequences were constructed; meanwhile, SG2 and CSG2 were also constructed by adding TT mismatches in both sides of G 6 to increase the flexibility of chains (table 1) [21]. …”

“…Optimal soft ionization conditions were obtained based on previous methods [21]. This system can measure m/z in the range of 50–3000.…”

“…By using ESI-MS, we can obtain accurate information on association preference of G-rich and C-rich DNA strands in various solution conditions [26] and have built a novel DNA nanostructure with both G-quadruplex and i-motif based on ESI-MS determinations [21]. In this work, we attempted to construct G-quadruplex-based supramolecular nanostructures and regulate the assembly of the nanostructures by connecting a specific 5′-(CGA) n sequence which can form pH-dependent DNA duplex.…”

Construction of nanostructures based on quadruplex DNA scaffolds

“…基于四链DNA以上结构的性质, 本课题组 [78] (c) 滑动的"结型"DNA单体结构组装为"结型"DNA纳米结构及其进一步转化为"四链+双链"型DNA纳米结构的流程示意图; (d), (e)"结型"DNA 纳米结构和转化的"四链+双链"型DNA纳米结构的原子力形貌表征 [73] Figure 10 (Color online) Schematic illustration of the construction of DNA nanostructures composed of I-motifs and duplexes, and the structural switch of different types of DNA nanostructures, and gel electrophoresis or atomic force microscope images of these DNA nanostructures. (a) I-motif-linked DNA nanostructures formed by C1Sn and C2Sn were mediated by various lengths of T-spacers.…”

“…(a) Assembly process of DNA Pillars; (b) and (c) DNA pillar-directed AuNP assemblies and the TEM images [74] ; (d)-(g) various I-motif-programmed DNA nanocircles and their AFM images [75] 评 述 12(a)). 在此基础上, 结合G碱基修饰对于四分子G-四链体结构构型影响的相关报道 [79] , 本课题组 [78] 进 一步设计了d(TG Br GG Br GAC7)序列(G Br 表示G碱基的 8号位的H被Br取代), 实验结果表明它在酸性钾离子 条件下可以形成"四分子反平行G-四链体+I-motif"模 式的线型DNA纳米结构(图12(b)). Figure 12 (Color online) Schematic illustration of the self-assembly of quadruplex nanostructures containing both G-quadruplexes and I-motifs, and AFM images of assembled DNA nanostructures [78] .…”