Ball with hair: modular functionalization of highly stable G-quadruplex DNA nano-scaffolds through N2-guanine modification

Application of nanotechnology in the diagnosis and treatment of acute pancreatitis

Acute pancreatitis (AP) is a common digestive system disease. The severity of AP ranges from mild edema in the pancreas to severe systemic inflammatory responses leading to peripancreatic/pancreatic necrosis, multi-organ failure and death. Improving the sensitivity of AP diagnosis and developing alternatives to traditional methods to treat AP have gained the attention of researchers. With the continuous rise of nanotechnology, it is being widely used in daily life, biomedicine, chemical energy and many other fields. Studies have demonstrated the effectiveness of nanotechnology in the diagnosis and treatment of AP. Nanotechnology has the advantages of simplicity, rapidity and sensitivity in detecting biomarkers of AP, as well as enhancing imaging, which helps in the early diagnosis of AP. On the other hand, nanoparticles (NPs) have oxidative stress inhibiting and anti-inflammatory effects, and can also be loaded with drugs as well as being used in anti-infection therapy, providing a new approach for the treatment of AP. In this article, we elaborate and summarize on the potential of nanoparticles for diagnostic and therapeutic applications in AP from the current reported literature and experimental results to provide useful guidelines for further research on the application of nanotechnology.

Four-Layered Intramolecular Parallel G-Quadruplex with Non-Nucleotide Loops: An Ultra-Stable Self-Folded DNA Nano-Scaffold

A four-stranded scaffold of nucleic acids termed G-quadruplex (G4) has found growing applications in nano- and biotechnology. Propeller loops are a hallmark of the most stable intramolecular parallel-stranded G4s. To date, propeller loops have been observed to span only a maximum of three G-tetrad layers. Going beyond that would allow creation of more stable scaffolds useful for building robust nanodevices. Here we investigate the formation of propeller loops spanning more than three layers. We show that native nucleotide sequences are incompatible toward this goal, and we report on synthetic non-nucleotide linkers that form a propeller loop across four layers. With the established linkers, we constructed a four-layered intramolecular parallel-stranded G4, which exhibited ultrahigh thermal stability. Control on loop design would augment the toolbox toward engineering of G4-based nanoscaffolds for diverse applications.

Recent progress in non-native nucleic acid modifications

While Nature harnesses RNA and DNA to store, read and write genetic information, the inherent programmability, synthetic accessibility and wide functionality of these nucleic acids make them attractive tools for use in a vast array of applications.

Selective functionalization at N2-position of guanine in oligonucleotides via reductive amination

Chemo- and site-specific modifications in oligonucleotides have wide applicability as mechanistic probes in chemical biology. However, methods that label specific sites in nucleic acids are scarce, especially for labeling DNA/RNA from biological or enzymatic sources rather than synthetic ones. Here we have employed a classical reaction, reductive amination, to selectively functionalize the N²-amine of guanosine and 2'-deoxyguanosine monophosphate (GMP/dGMP). This method specifically modifies guanine in DNA and RNA oligonucleotides, while leaving the other nucleobases unaffected. Using this approach, we have successfully incorporated a reactive handle chemoselectively into nucleic acids for further functionalization and downstream applications.

Characterization of different biodegradable scaffolds in tissue engineering

The aim of the present study was to compare the characteristics of acellular dermal matrix (ADM), small intestinal submucosa (SIS) and Bio‑Gide scaffolds with acellular vascular matrix (ACVM)‑0.25% human‑like collagen I (HLC‑I) scaffold in tissue engineering blood vessels. The ACVM‑0.25% HLC‑I scaffold was prepared and compared with ADM, SIS and Bio‑Gide scaffolds via hematoxylin and eosin (H&E) staining, Masson staining and scanning electron microscope (SEM) observations. Primary human gingival fibroblasts (HGFs) were cultured and identified. Then, the experiment was established via the seeding of HGFs on different scaffolds for 1, 4 and 7 days. The compatibility of four different scaffolds with HGFs was evaluated by H&E staining, SEM observation and Cell Counting Kit‑8 assay. Then, a series of experiments were conducted to evaluate water absorption capacities, mechanical abilities, the ultra‑microstructure and the cytotoxicity of the four scaffolds. The ACVM‑0.25% HLC‑I scaffold was revealed to exhibit the best cell proliferation and good cell architecture. ADM and Bio‑Gide scaffolds exhibited good mechanical stability but cell proliferation was reduced when compared with the ACVM‑0.25% HLC‑I scaffold. In addition, SIS scaffolds exhibited the worst cell proliferation. The ACVM‑0.25% HLC‑I scaffold exhibited the best water absorption, followed by the SIS and Bio‑Gide scaffolds, and then the ADM scaffold. In conclusion, the ACVM‑0.25% HLC‑I scaffold has good mechanical properties as a tissue engineering scaffold and the present results suggest that it has better biological characterization when compared with other scaffold types.

Manipulating DNA G-Quadruplex Structures by Using Guanosine Analogues

The ability to control the folding topology of DNA G-quadruplexes allows for rational design of quadruplex-based scaffolds for potential use in various therapeutic and technological applications. By exploiting the distinct conformational properties of some base- and sugar-modified guanosine surrogates, conformational transitions can be induced through their judicious incorporation at specific sites in the quadruplex core. Changes may involve tetrad polarity inversions with conservation of the global fold or complete refolding to new topologies. Reliable predictions relating to low-energy conformers formed upon specific chemical perturbations of the system and the rational design of modified sequences suffer from our still limited understanding of the subtle interplay of various favorable and unfavorable interactions within a particular quadruplex scaffold. However, aided by an increasing number of systematic substitution experiments and high-resolution structures of modified quadruplex variants, critical interactions, in addition to glycosidic bond angle propensities, are starting to emerge as important contributors to modification-driven quadruplex refolding.

Tolerance of N2-heteroaryl modifications on guanine bases in a DNA G-quadruplex

To systematically determine the effect of N²-heteroaryl modification on the stability of G-quadruplex structures, six types of N²-heteroarylated deoxyguanosines were incorporated into oligonucleotides with intramolecular quadruplex-forming sequences obtained from the human telomere sequence.

Polymorphism of G4 associates: from stacks to wires via interlocks

We examined the assembly of DNA G-quadruplexes (G4s) into higher-order structures using atomic force microscopy, optical and electrophoretic methods, NMR spectroscopy and molecular modeling. Our results suggest that parallel blunt-ended G4s with single-nucleotide or modified loops may form different types of multimers, ranging from stacks of intramolecular structures and/or interlocked dimers and trimers to wires. Decreasing the annealing rate and increasing salt or oligonucleotide concentrations shifted the equilibrium from intramolecular G4s to higher-order structures. Control antiparallel and hybrid G4s demonstrated no polymorphism or aggregation in our experiments. The modification that mimics abasic sites (1',2'-dideoxyribose residues) in loops enhanced the oligomerization/multimerization of both the 2-tetrad and 3-tetrad G4 motifs. Our results shed light on the rules that govern G4 rearrangements. Gaining control over G4 folding enables the harnessing of the full potential of such structures for guided assembly of supramolecular DNA structures for nanotechnology.

In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids?

Synthetic analogs of natural nucleotides have long been utilized for structural studies of canonical and noncanonical nucleic acids, including the extensively investigated polymorphic G-quadruplexes (GQs). Dependence on the sequence and nucleotide modifications of the folding landscape of GQs has been reviewed by several recent studies. Here, an overview is compiled on the thermodynamic stability of the modified GQ folds and on how the stereochemical preferences of more than 70 synthetic and natural derivatives of nucleotides substituting for natural ones determine the stability as well as the conformation. Groups of nucleotide analogs only stabilize or only destabilize the GQ, while the majority of analogs alter the GQ stability in both ways. This depends on the preferred syn or anti N-glycosidic linkage of the modified building blocks, the position of substitution, and the folding architecture of the native GQ. Natural base lesions and epigenetic modifications of GQs explored so far also stabilize or destabilize the GQ assemblies. Learning the effect of synthetic nucleotide analogs on the stability of GQs can assist in engineering a required stable GQ topology, and exploring the in vitro action of the single and clustered natural base damage on GQ architectures may provide indications for the cellular events.

Rotation of Guanine Amino Groups in G-Quadruplexes: A Probe for Local Structure and Ligand Binding

Nucleic acids are dynamic molecules whose functions may depend on their conformational fluctuations and local motions. In particular, amino groups are dynamic components of nucleic acids that participate in the formation of various secondary structures such as G-quadruplexes. Here, we present a cost-efficient NMR method to quantify the rotational dynamics of guanine amino groups in G-quadruplex nucleic acids. An isolated spectrum of amino protons from a specific tetrad-bound guanine can be extracted from the nuclear Overhauser effect spectroscopy spectrum based on the close proximity between the intra-residue imino and amino protons. We apply the method in different structural contexts of G-quadruplexes and their complexes. Our results highlight the role of stacking and hydrogen-bond interactions in restraining amino-group rotation. The measurement of the rotation rate of individual amino groups could give insight into the dynamic processes occurring at specific locations within G-quadruplex nucleic acids, providing valuable probes for local structure, dynamics, and ligand binding.