Effect of C(60) fullerene on the duplex formation of i-motif DNA with complementary DNA in solution

Rational design of guiding elements to control folding topology in i-motifs with multiple quadruplexes

Nucleic acids are versatile scaffolds that accommodate a wide range of precisely defined operational characteristics. Rational design of sensing, molecular computing, nanotechnology, and other nucleic acid devices requires precise control over folding conformations in these macromolecules. Here, we report a new approach that empowers well-defined conformational transitions in DNA molecular devices. Specifically, we develop tools for precise folding of multiple DNA quadruplexes (i-motifs) within the same oligonucleotide strand. To accomplish this task, we modify a DNA strand with kinetic control elements (hairpins and double stranded stems) that fold on a much faster timescale and consequently guide quadruplexes toward the targeted folding topology. To demonstrate that such guiding elements indeed facilitate formation of the targeted folding topology, we thoroughly characterize the folding/unfolding transitions through a combination of thermodynamic techniques, size exclusion chromatography (SEC) and small-angle X-ray scattering (SAXS). Furthermore, we extend SAXS capabilities to produce a direct insight on the shape and dimensions of the folded quadruplexes by computing their electron density maps from solution scattering data.

Fluorescein-Stabilized i-Motif DNA and Its Unfolding Leading to a Stronger Adsorption Affinity

Several previous studies have indicated that polydeoxycytidine (poly-C) DNA has an anomalously high affinity for different types of surfaces. It was hypothesized that the formation of an i-motif structure could be a factor responsible for this enhanced affinity, but this is against the notion that a folded molecule should have fewer interactions with a surface. Herein, the properties of poly-C DNA were examined in detail, focusing on the presence or absence of a FAM (carboxyfluorescein) label and its subsequent adsorption on graphene oxide. Fluorescence and CD spectroscopy studies indicated that FAM can stabilize an i-motif structure in C15 DNA. In particular, the fluorescence of FAM is drastically quenched when the DNA is folded. This structure is irreversibly unfolded upon heating. Furthermore, the unfolded structure has an even higher affinity for graphene oxide than the folded structure. Finally, a large portion of the folded C15 unfolds upon desorption from graphene oxide, and unfolding could happen upon adsorption or desorption of the DNA. This study provides a method to further enhance the adsorption stability of poly-C DNA and calls for care when investigating the potential effects of dye labels on DNA.

Stabilization of an intermolecular i-motif by lipid modification of cytosine-oligodeoxynucleotides

This paper describes the stabilization of an intermolecular i-motif by lipophilic modification on the 3'-terminus of oligonucleotides. The hydrophobic aliphatic chain connected at the 3'-terminus of a trinucleotide (dC)3 promoted the formation of an i-motif and significantly enhanced the quadruplex's stability. The impact of lipophilic modification on i-motif's thermal stability was studied by UV-thermal denaturation melting experiments and isothermal titration calorimetry. We found that alkyl chains containing more than 14 carbon atoms could elevate the i-motif structure's stability in a wide range of pH and concentrations.

Structural Characteristics of Pneumolysin and Its Domains in a Biomimetic Solution

Pneumolysin (PLY) and its truncated fragments, domains 1-3 (D_1-3), and domain 4 (D₄), were purified as recombinant proteins after being cloned and over-expressed in Escherichia coli. The three-dimensional structures of these proteins were quantitatively investigated in a biomimetic condition, phosphate buffered saline (PBS) by synchrotron X-ray scattering. X-ray scattering analysis revealed important structural features including structural parameters. PLY was present as a monomeric form in PBS. The monomeric form resembled its crystallographic structure with a discrepancy of only 6.3%, confirming that PLY forms a stable structure and, thus, retains its structure in the crystalline state and even in PBS solution. D₄ was also present as a monomeric form, but its structure was very different from that of the corresponding part in the crystallographic PLY structure; the discrepancy was 92.0%. Such a dissimilar structure might originate from a less folded-chain conformation. This result suggested that the structure of D₄ is highly dependent on the crystalline or solution state and further on the presence or absence of the D_1-3 unit. In contrast, D_1-3 was dimeric rather than monomeric. Its structure was close to the most probable dimeric form of the corresponding part in the crystallographic PLY structure with 13.1% discrepancy. This fact indicated that the D_1-3 unit forms a stable structure and, indeed, such structure is well maintained in the crystalline state as well as in PBS although presented as a dimer. This result further supported that the whole structural stability of PLY is mainly attributed to the structure of D_1-3. All of PLY, D_1-3, and D₄ revealed aggregation tendencies during purification and storage. Overall, the structural characteristics of PLY and its domains in PBS may correlate to the PLY oligomer formation yielding large pore structures for the penetration of cell membranes.

Reversible Redox Activity by Ion-pH Dually Modulated Duplex Formation of i-Motif DNA with Complementary G-DNA

The unique biological features of supramolecular DNA have led to an increasing interest in biomedical applications such as biosensors. We have developed an i-motif and G-rich DNA conjugated single-walled carbon nanotube hybrid materials, which shows reversible conformational switching upon external stimuli such as pH (5 and 8) and presence of ions (Li⁺ and K⁺). We observed reversible electrochemical redox activity upon external stimuli in a quick and robust manner. Given the ease and the robustness of this method, we believe that pH- and ion-driven reversible DNA structure transformations will be utilized for future applications for developing novel biosensors.

Length-Dependent Diblock DNA with Poly-cytosine (Poly-C) as High-Affinity Anchors on Graphene Oxide

DNA-functionalized graphene oxide (GO) is a popular system for biosensor development and directed materials assembly. Compared to covalent attachment, simple physisorption of DNA has been more popular, and a DNA sequence with a strong affinity on GO is highly desirable. Recently, we found that poly-cytosine (poly-C) DNA can strongly adsorb on many common nanomaterials, including GO. To identify an optimal length of poly-C DNA, we herein designed a series of diblock DNA sequences containing between 0 and 30 cytosines. The displacement of a random sequenced DNA by poly-C DNA was demonstrated, confirming the desired diblock structure on GO with the poly-C block anchoring on the surface and the other block available for hybridization. The adsorption density of poly-C containing DNA did not vary much as the length of the poly-C block increased, suggesting the conformation of the anchoring DNA on the GO was quite independent of the DNA length. With a longer poly-C block, the efficiency of surface hybridization of the other block increased, while nonspecific adsorption of noncomplementary DNA was inhibited more. Compared to poly-adenine (poly-A)-containing DNAs, which were previously used for the same purpose, poly-C DNA adsorption is more stable. Using four types of 15-mer DNA homopolymers as the intended anchoring sequences, the C₁₅ DNA had the best hybridization efficiency. This work has suggested the optimal length for the poly-C block to be 15-mer or longer, and it has provided interesting insights into the DNA/GO biointerface.

Probing the self-assembled nanostructures of functional polymers with synchrotron grazing incidence X-ray scattering

For advanced functional polymers such as biopolymers, biomimic polymers, brush polymers, star polymers, dendritic polymers, and block copolymers, information about their surface structures, morphologies, and atomic structures is essential for understanding their properties and investigating their potential applications. Grazing incidence X-ray scattering (GIXS) is established for the last 15 years as the most powerful, versatile, and nondestructive tool for determining these structural details when performed with the aid of an advanced third-generation synchrotron radiation source with high flux, high energy resolution, energy tunability, and small beam size. One particular merit of this technique is that GIXS data can be obtained facilely for material specimens of any size, type, or shape. However, GIXS data analysis requires an understanding of GIXS theory and of refraction and reflection effects, and for any given material specimen, the best methods for extracting the form factor and the structure factor from the data need to be established. GIXS theory is reviewed here from the perspective of practical GIXS measurements and quantitative data analysis. In addition, schemes are discussed for the detailed analysis of GIXS data for the various self-assembled nanostructures of functional homopolymers, brush, star, and dendritic polymers, and block copolymers. Moreover, enhancements to the GIXS technique are discussed that can significantly improve its structure analysis by using the new synchrotron radiation sources such as third-generation X-ray sources with picosecond pulses and partial coherence and fourth-generation X-ray laser sources with femtosecond pulses and full coherence.

Structural Characteristics of Amphiphilic Cyclic and Linear Block Copolymer Micelles in Aqueous Solutions

The structural characteristics of aqueous micelles composed of amphiphilic cyclic poly(n-butyl acrylate-b-ethylene oxide) (cyclic PBA-b-PEO) or a linear analogue (i.e., linear poly(n-butyl acrylate-b-ethylene oxide-b-n-butyl acrylate) (linear PBA-b-PEO-b-PBA)) were examined for the first time using synchrotron X-ray scattering techniques and quantitative data analysis. The scattering data were analyzed using a variety of methodologies in a comprehensive complementary manner. These analyses provided details of the structural information about the micelles. Both micelles were found to consist of a core and a fuzzy shell; however, the cyclic block copolymer had a strong tendency to form micelles with core and shell parts that were more compact and dense than the corresponding parts of the linear block copolymer micelles. The PBA block of the cyclic copolymer was found to form a hydrophobic core with a density that exceeded the density of the homopolymer in the bulk state. The structural differences originated primarily from the topological difference between the cyclic and linear block copolymers. The elimination of the chain end groups (which introduced entropy and increased the excess excluded volume) from the amphiphilic block copolymer yielded more stable dense micelles in solution.

Fundamental aspects of the nucleic acid i-motif structures

The latest research on fundamental aspects of i-motif structures is reviewed with special attention to their hypothetical rolein vivo.

Stabilization and induction of oligonucleotide i-motif structure via graphene quantum dots

DNA i-motif structures have been found in telomeric, centromeric DNA and many in the promoter region of oncogenes; thus they might be attractive targets for gene-regulation processes and anticancer therapeutics. We demonstrate in this work that i-motif structures can be stabilized by graphene quantum dots (GQDs) under acidic conditions, and more importantly GQDs can promote the formation of the i-motif structure under alkaline or physiological conditions. We illustrate that the GQDs stabilize the i-motif structure through end-stacking of the bases at its loop regions, thus reducing its solvent-accessible area. Under physiological or alkaline conditions, the end-stacking of GQDs on the unfolded structure shifts the equilibrium between the i-motif and unfolded structure toward the i-motif structure, thus promoting its formation. The possibility of fine-tuning the stability of the i-motif and inducing its formation would make GQDs useful in gene regulation and oligonucleotide-based therapeutics.

pH-dependent structures of ferritin and apoferritin in solution: disassembly and reassembly

The pH-dependent structures of the ferritin shell (apoferritin, 24-mer) and the ferrihydrite core, under physiological conditions that permit enzymatic activity, were investigated by synchrotron small-angle X-ray scattering (SAXS). The solution structure of apoferritin was found to be nearly identical to the crystal structure. The shell thickness and hollow core volumes were estimated. The intact hollow spherical apoferritin was stable over a wide pH range, 3.40-10.0, and the ferrihydrite core was stable over the pH range 2.10-10.0. The apoferritin subunits underwent aggregation below pH 0.80, whereas the ferrihydrite cores aggregated below pH 2.10 as a result of the disassembly of the ferritin shell under the strongly acidic conditions. As the pH decreased from 3.40 to 0.80, apoferritin underwent stepwise disassembly by first forming a hollow sphere with two holes, then a headset-shaped structure, and, finally, rodlike oligomers. As the pH was increased from pH 1.96, the disassembled rodlike oligomers recovered only to the headset-shaped structure, and the disassembled headset-shaped intermediates recovered only to the hollow spherical structure with two hole defects. The apoferritin hole defects that formed during the disassembly process did not heal as the pH was increased to neutral or slightly basic conditions. The pH-induced apoferritin disassembly and reassembly processes were not fully reversible, although they were pseudoreversible over a limited pH range, between 10.0 and 2.66.