An L-DNA G-quadruplex: application for peroxidase DNAzyme

The clinical potential of l-oligonucleotides: challenges and opportunities

Chemically modified nucleotides are central to the development of biostable research tools and oligonucleotide therapeutics. In this context, l-oligonucleotides, the synthetic enantiomer of native d-nucleic acids, hold great promise. As enantiomers, l-oligonucleotides share the same physical and chemical properties as their native counterparts, yet their inverted l-(deoxy)ribose sugars afford them orthogonality towards the stereospecific environment of biology. Notably, l-oligonucleotides are highly resistant to degradation by cellular nucleases, providing them with superior biostability. As a result, l-oligonucleotides are being increasingly utilized for the development of diverse biomedical technologies, including molecular imaging tools, diagnostic biosensors, and aptamer-based therapeutics. Herein, we present recent such examples that highlight the clinical potential of l-oligonucleotides. Additionally, we provide our perspective on the remaining challenges and practical considerations currently associated with the use of l-oligonucleotides and explore potential solutions that will lead to the broader adoption of l-oligonucleotides in clinical applications.

The fluorescence regulation of a tri-functional oligonucleotide probe HEX-OND in detecting Pb(II), cysteine, and K(I) based on two G-quadruplex forms

A novel tri-functional probe HEX-OND was developed for detecting Pb(II), cysteine (Cys), and K(I) by fluorescence quenching, recovery, and amplification strategies respectively, based on Pb(II)-induced chair-type G-quadruplex (CGQ) and K(I)-induced parallel G-quadruplex (PGQ). The thermodynamic mechanism was illustrated as that HEX-OND transformed into CGQ by associating equimolar Pb(II) (K₁ = 1.10 ± 0.25 × 10⁶ L/mol), forcing (G)₂ spontaneously approaching and static-quenching HEX (5'-hexachlorofluorescein phosphoramidite) in the photo-induced electron transfer (PET) way by the van der Waals force and hydrogen bond (K₂ = 5.14 ± 1.65 × 10⁷ L/mol); the additional Cys recovered fluorescence in the molecular ratio of 2:1 via Pb(II)-precipitation induced CGQ destruction (K₃ = 3.03 ± 0.77 × 10⁹ L/mol); the equimolar K(I) induced HEX-OND transforming into PGQ (K₄ = 3.53 ± 0.30 × 10⁴ L/mol) and specifically associating with the equimolar N-methyl mesoporphyrin IX (NMM) by hydrophobic force (K₅ = 3.48 ± 1.08 × 10⁵ L/mol), leading to the fluorescence enhancement. Moreover, the practicability results showed that the detection limits reached a nanomolar level for Pb(II) and Cys and micromolar for K(I), with mere disturbances for 6, 10, and 5 kinds of other substances, respectively; no significant deviations of the real sample detection results were found between the well-understood methods with ours in detecting Pb(II) and Cys, and K(I) could be recognized and quantified even in the presence of Na(I) with 5000 and 600 fold respectively. The results demonstrated the triple-function, sensitivity, selectivity, and tremendous application feasibility of the current probe in sensing Pb(II), Cys, and K(I).

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.

Expanding the potential of G-quadruplex structures: formation of a heterochiral TBA analogue

In order to expand the potential applications of G-quadruplex structures, we explored the ability of heterochiral oligodeoxynucleotides based on the thrombin-binding aptamer (TBA) sequence to fold into similar complexes, with particular focus on their resistance in biological environments. A combination of CD and NMR techniques was used. Similarly to TBA, the ODN ggTTggtgtggTTgg (lower case letters indicate L residues) is able to fold into a chair-like antiparallel G-quadruplex structure, but has a slightly higher thermal stability. The discovery that heterochiral ODNs are able to form stable G-quadruplex structures opens up new possibilities for their development in several fields, as aptamers, sensors and, as recently shown, as catalysts for enantioselective reactions.