Fluorescence reporting of G-quadruplex structures and modulating their DNAzyme activity using polyethylenimine-pyrene conjugate

Molecular Architectonics-guided Design of Biomaterials

The quest for mastering the controlled engineering of dynamic molecular assemblies is the basis of molecular architectonics. The rational use of noncovalent interactions to programme the molecular assemblies allow the construction of diverse molecular and material architectures with novel functional properties and applications. Understanding and controlling the assembly of molecular systems are daunting tasks owing to the complex factors that govern at the molecular level. Molecular architectures depend on the design of functional molecular modules through the judicious selection of functional core and auxiliary units to guide the precise molecular assembly and co-assembly patterns. Biomolecules with built-in information for molecular recognition are the ultimate examples of evolutionary guided molecular recognition systems that define the structure and functions of living organisms. Explicit use of biomolecules as auxiliary units to command the molecular assemblies of functional molecules is an intriguing exercise in the scheme of molecular architectonics. In this minireview, we discuss the implementation of the principles of molecular architectonics for the development of novel biomaterials with functional properties and applications ranging from sensing, drug delivery to neurogeneration and tissue engineering. We present the molecular designs pioneered by our group owing to the requirement and scope of the article while acknowledging the designs pursued by several research groups that befit the concept.

Supramolecular spectral/visual detection of urinary polyamines through synergetic/competitive complexation with γ-CD and CB[7]

A supramolecular strategy for detecting the concentration of polyamines has been established through competitive/synergetic complexation among polyamines, CB[7], γ-CD, and pyrene derivatives, which allows for convenient, rapid, and high throughput spectral/visual detection of the concentration of urinary polyamines based on the switching on/off of the pyrene excimer fluorescence.

Threading Intercalator-Induced Nanocondensates and Role of Endogenous Metal Ions in Decondensation for DNA Delivery

The interplay of condensation and decondensation of DNA plays a crucial role in chromosome maintenance and gene expression. The molecular architectonics governing the chromatin condensation-decondensation cycle are worth studying, as DNA performs unique and distinct roles in each state and switches between two states without the loss of structural and functional integrity. This phenomenon has been adapted and implemented in transfection studies. Effective gene delivery into the cells to achieve respectable transfection efficiency has remained a challenge and emphasizes the need for understanding the steps involved in DNA delivery and transfection. Especially, recognizing the factors that effectively regulate DNA decondensation can provide logical solutions to the hurdles affecting the transfection efficiency. We designed a set of small molecule-based threading intercalation ligands as model condensing agents to study various factors influencing the DNA condensation and decondensation process. This study revealed condensation of DNA into nanocondensate by the threading intercalator and endogenous stimuli induced effective decondensation. Further, DNA nanocondensates are tracked using the intrinsic fluorescence in the lower pH of endocytic pathway and were evaluated as nonviral vectors for in cellulo delivery of plasmids. The correlation of decondensation of DNA nanocondensate with endogenous metal ions at their physiological concentrations provided valuable insights and implications for intracellular DNA delivery.

Recognition of G-quadruplex topology through hybrid binding with implications in cancer theranostics

The selective recognition and imaging of oncogene specific G-quadruplex (GQ) structures holds great promise in the development of diagnostic therapy (theranostics) for cancer and has been challenging due to their structural dynamics and diversity. We report selective recognition of GQ by a small molecule through unique hybrid loop stacking and groove binding mode with turn on far-red fluorescence response and anticancer activity demonstrating the potential implications for GQ-targeted cancer theranostics.

Methods: Biophysical investigation reveal the turn on far-red emission property of TGP18 for selective recognition of GQ. In cellulo studies including DNA damage and oxidative stress evaluation guided us to perform in vitro (3D spheroid) and in vivo (xenograft mice model) anti-cancer activity, and tumor tissue imaging to assess the theranostic potential of TGP18.

Results: Neocuproine-based far-red turn on fluorescence probe TGP18 shows GQ-to-duplex selectivity and specifically recognizes BCL-2 GQ with high affinity through a unique hybrid binding mode involving loop-stacking and groove interactions. Our study reveals that the selective recognition originating from the distinct loop structure of GQ that alters the overall probe interaction and binding affinity. TGP18 binding to anti-apoptotic BCL-2 GQ ablates the pro-survival function and elicit anti-cancer activity by inducing apoptosis in cancer cells. We deciphered that inhibition of BCL-2 transcription synergized with signaling cascade of nucleolar stress, DNA damage and oxidative stress in triggering apoptosis signaling pathway.

Conclusion: Intervention of GQ mediated lethality by TGP18 has translated into anti-cancer activity in both in vitro 3D spheroid culture and in vivo xenograft models of lung and breast cancer with superior efficacy for the former. In vivo therapeutic efficacy supplemented with tumor 3D spheroid and tissue imaging potential define the role of TGP18 in GQ-targeted cancer theranostics.

Photo-Induced Electron Transfer-Based Versatile Platform with G-Quadruplex/Hemin Complex as Quencher for Construction of DNA Logic Circuits

G-quadruplex has been developed as an innovator for analytical chemistry and biomedicine due to its vibrant binding activity, structural polymorphism, and critical roles in biological regulation. Herein, a simple but versatile platform was obtained by integrating split G-quadruplex and fluorophore into a molecular beacon, where the photoinduced electron transfer could occur when the fluorophore approached the preformed G-quadruplex/hemin complexes. Such design subtly combined the G4 disruption-induced fluorescent turn-on strategy and the photoinduced electron transfer property into one platform for constructing the logic circuits. On the basis of such a universal platform, a series of binary logic gates (OR, INHIBIT, AND, and XOR), a combinatorial gate (INHIBIT-OR), and even a complex logic operation for discrimination of multiples of three from natural numbers less than ten have been successfully achieved only by employing such platform as work unit and single-strand DNAs as inputs. The set-reset function of this platform could be realized by alternatively introducing blocking and releasing strands. In addition, this platform could operate in a biological matrix stably and precisely. Therefore, such a universal platform lays the foundation for complicating the logic systems, realizing the biocomputing and also points out a new direction for target detection.

Bicomponent β-sheet assembly of dipeptide fluorophores of opposite polarity and sensitive detection of nitro-explosives

Fluorescent hydrogels formed by the bicomponent β-sheet co-assembly of dipeptide–pyrene amphiphiles of opposite polarity provide a 3D microenvironment to detect toxic nitro-explosives.

A pyrene-based fluorescent sensor for ratiometric detection of heparin and its complex with heparin for reversed ratiometric detection of protamine in aqueous solution

An imidazolium-modified pyrene derivative, IPy, was used for ratiometric detection of heparin, and its complex with heparin was used for reversed ratiometric detection of protamine in both aqueous solution and serum samples. The cationic fluorescent probe could interact with anionic heparin via electrostatic interaction to bring about blue-to-green fluorescence changes as monomer emission significantly decreases and excimer increases. The binary combination of IPy and heparin could be further used for green-to-blue detection of protamine since heparin prefers to bind to protamine instead of the probe due to its stronger affinity with protamine. The cationic probe shows high sensitivity to heparin with a low detection limit of 8.5nM (153ng/mL) and its combination with heparin displays high sensitivity to protamine with a detection limit as low as 15.4nM (107.8ng/mL) according to the 3σ IUPAC criteria. Moreover, both sensing processes are fast and can be performed in serum solutions, indicating possibility for practical applications.