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The mechanism by which informational polymers first formed on the early earth is currently unknown. The RNA world hypothesis implies that RNA oligomers were produced prebiotically, before the emergence of enzymes, but the demonstration of such a process remains challenging. Alternatively, RNA may have been preceded by an earlier ancestral polymer, or proto-RNA, that had a greater propensity for self-assembly than RNA, with the eventual transition to functionally superior RNA being the result of chemical or biological evolution. We report a new class of nucleic acid analog, depsipeptide nucleic acid (DepsiPNA), which displays several properties that are attractive as a candidate for proto-RNA. The monomers of depsipeptide nucleic acids can form under plausibly prebiotic conditions. These monomers oligomerize spontaneously when dried from aqueous solutions to form nucleobase-functionalized depsipeptides. Once formed, these DepsiPNA oligomers are capable of complementary self-assembly and are resistant to hydrolysis in the assembled state. These results suggest that the initial formation of primitive, self-assembling, informational polymers on the early earth may have been relatively facile if the constraints of an RNA-first scenario are relaxed.

Aqueous solutions of equimolar mixtures of 2,4,6-triaminopyrimidine (TAP) and carboxylic acid substituted cyanuric acid (CyCo6 or R-4MeCyCo6) monomers self-assemble into gel-forming supramolecular polymers. Macroscopic fibers drawn from these mixtures were analyzed by X-ray diffraction to determine their molecular structures. Computational methods were used to explore the intrinsic intermolecular interactions that contribute to the structure and stability of these assemblies. Both polymers are formed by the stacking of hexameric rosettes, (TAP/CyCo6)3 or (TAP/R-4MeCyCo6)3, respectively, into long, stiff, twisted stacks of essentially planar rosettes. Chiral, left-handed supramolecular polymers with a helical twist angle of -26.7° per hexad are formed when the pure enantiomer R-4MeCyCo6 is used. These hexad stacks pack into bundles with a hexagonal crystalline lattice organization perpendicular to the axis of the macroscopic fiber. Polymers formed from TAP and CyCo6, both of which are achiral, assemble into macroscopic domains that are packed as a centered rectangular lattice. Within these domains, the individual polymers exist as either right-handed or left-handed helical stacks, with twist angles of +15° or -15° per hexad, respectively. The remarkable ability of TAP and cyanuric acid derivatives to self-assemble in water, and the structural features of their supramolecular polymers reported here, provide additional support for the proposal that these heterocycles could have served as recognition units for an early form of nucleic acids, before the emergence of RNA.

The cyanuric acid (CA) heterocycle forms supramolecular structures with adenine nucleobases/nucleosides and oligonucleotides, leading to speculation that they can act as forerunners to RNA. Herein, the assembly behavior of RNA containing CA and CA-ribose nucleoside was studied. Contrary to previous reports, CA in RNA and the CA-ribonucleoside resulted in destabilization of supramolecular assemblies, which led to a reevaluation of the CA-adenine hexameric rosette structure. An unprecedented noncovalent supramolecular helicene structure is proposed to account for the striking difference in behavior, which has implications for novel paradigms for reorganizing the structures of nucleic acids, the synthesis of long helicenes, and pre-RNA world paradigms. The results caution against extrapolating the self-assembly behavior of individual heterocycles from the level of monomers to oligomers because the base-paring properties of (non-)canonical nucleobases are impacted by the type of oligomeric backbone to which they are attached.

A goal of supramolecular chemistry is to create covalent polymers of precise composition and stereochemistry from complex mixtures by the reversible assembly of specific monomers prior to covalent bond formation. We illustrate the power of this approach with short oligomers of deoxyadenosine monophosphate ((dA)n3′p), n ≥ 3, which form supramolecular assemblies with cyanuric acid. The addition of a condensing agent to these assemblies results in their selective, non-enzymatic polymerization to form long polymers (e.g., (dA)1003′p). Significantly, mixtures of D- and L-(dA)53′p form homochiral covalent polymers, which demonstrates self-sorting of racemic monomers and covalent bond formation exclusively in homochiral assemblies.

Aqueous solutions of the achiral, monomeric, nucleobase mimics (2,4,6-triaminopyrimidine, TAP, and a cyanuric acid derivative, CyCo6) spontaneously assemble into macroscopic homochiral domains of supramolecular polymers. These assemblies exhibit a high degree of chiral amplification. Addition of a small quantity of one handedness of a chiral derivative of CyCo6 generates exclusively homochiral structures. This system exhibits the highest reported degree of chiral amplification for dynamic helical polymers or supramolecular helices. Significantly, homochiral polymers comprised of hexameric rosettes with structural features that resemble nucleic acids are formed from mixtures of cyanuric acid (Cy) and ribonucleotides (l-, d-pTARC) that arise spontaneously from the reaction of TAP with the sugars. These findings support the hypothesis that nucleic acid homochirality was a result of symmetry breaking at the supramolecular polymer level.

The mechanism by which genetic polymers spontaneously formed on the early Earth is currently unknown. The RNA World hypothesis implies that RNA oligomers were produced prebiotically, but the demonstration of this process has proven challenging. Alternatively, RNA may be the product of evolution and some, or all, of its chemical components may have been preceded by functionally analogous moieties that were more readily accessible under plausible early-Earth conditions. We report a new class of nucleic acid analog, depsipeptide nucleic acid, which displays several properties that make it an attractive candidate for the first informational polymer to arise on the Earth. The monomers of depsipeptide nucleic acids can form under plausibly prebiotic conditions. These monomers oligomerize spontaneously when dried from aqueous solutions to form nucleobase-functionalized depsipeptides. Once formed, these depsipeptide nucleic acid oligomers are capable of complementary self-assembly, and are resistant to hydrolysis in the assembled state. These results suggest that the initial formation of primitive, self-assembling, informational polymers may have been relatively facile.

Supramolecular polymers are increasingly important materials for applications that require the controlled assembly and disassembly of structures having well-defined shapes and properties. Subtle changes in molecular structure and solvent properties can profoundly affect these materials because of the relatively weak noncovalent interactions that govern their formation. We report the discovery that positively charged small molecules that are planar, or have planar elements, can be employed as noncovalent chain stoppers (NCSs) to control the length of supramolecular polymers in aqueous solution. The supramolecular polymers are composed of 2,4,6-triaminopyrimidine and a modified cyanuric acid, monomers that assemble through interactions that mimic the base pairs of DNA. These assemblies are equilibrium polymers, a type of supramolecular polymers that, in the absence of any chain stoppers, are extremely long (e.g., multiple microns in length). The lengths of these assemblies are controlled by a NCS in a concentration-dependent and compound-specific manner, giving rise to supramolecular polymers with low polydispersity. This behavior is attributed to the homogeneity of the NCS distribution within the system, and their “ideal-gas-like” number density fluctuations. These supramolecular polymers form physical hydrogel with viscoelastic properties that can be tuned by the addition of a NCS, thereby demonstrating the potential of this approach for controlling the dimensions of supramolecular polymers in water as well as the macroscopic properties of materials formed by such polymers.

The simple and reversible control of the degree of polymerization, and thereby the bulk material properties, of a supramolecular polymer is reported. Noncovalent capping agents (chain stoppers) modulate the length of supramolecular polymers by stacking on the surfaces of the polymer's ends. Methylene blue (MB) is a positively charged, planar polycyclic dye that acts as a chain stopper. It can be reversibly switched between its colored, planar, cationic state and a colorless, nonplanar, neutral state (leucomethylene blue, LMB) by reduction with ascorbic acid and then reoxidized to MB by O2. LMB does not act as a chain stopper. This behavior was utilized to reversibly trigger the gel to sol transformation of supramolecular polymers formed by the self-assembly of hexameric rosettes comprising 2,4,6-triaminopyrimidine and a hexanoic acid-substituted cyanuric acid (CyCo6) in aqueous media. The results of our experiments highlight the ability of this approach to reversibly switch between the gel and solution states of materials formed from supramolecular polymers and thereby control their bulk properties.

Herein, we report the synthesis of two amphiphilic porphyrins having pyridinium moieties and their anion recognition properties in aqueous medium. The study of their interactions with various anions reveals that these porphyrins exhibit unique and selective interactions with CN- ions when compared to the other anions. The addition of CN- ions to an aqueous solution of the butyl porphyrin resulted in a hypochromicity of ca. 78% at 419 nm with a concomitant band formation at 449 nm in the absorption spectrum. Similarly, we observed ca. 82% quenching in the emission intensity by the addition of 12.5 M of CN- ions in the fluorescence spectrum of the porphyrin mediated through aggregation. The limit of detection of CN- ions was found to be ca. 49 ppb and the nature of interactions has been studied through various microscopic and spectroscopic techniques. These studies have confirmed 1,4-addition of CN- ions to the pyridinium moiety of the porphyrin system, which led to the aggregation induced self-assembly resulting in the sensitive detection of CN- ions through changes in absorbance and fluorescence intensity in aqueous medium.

The free nucleobases and mononucleotides of RNA do not form Watson-Crick base pairs in water, a fact that presents several challenges for the prebiotic synthesis of RNA. 2,6-Diaminopurine and adenosine-5'-monophosphate (AMP) are shown to form supramolecular assemblies with cyanuric acid in water. These assemblies and their propensity to form liquid crystals suggest a possible means by which non-covalent structures might have originally selected the shape of the Watson-Crick base pairs.

With the objective of developing efficient sensitizers for therapeutic applications, we synthesized a water-soluble 5,10,15,20-tetrakis(3,4-dihydroxyphenyl)chlorin (TDC) and investigated its in vitro and in vivo biological efficacy, comparing it with the commercially available sensitizers. TDC showed high water solubility (6-fold) when compared with that of Foscan and exhibited excellent triplet-excited-state (84%) and singlet-oxygen (80%) yields. In vitro photobiological investigations in human-ovarian-cancer cell lines SKOV-3 showed high photocytotoxicity, negligible dark toxicity, rapid cellular uptake, and specific localization of TDC in neoplastic cells as assessed by flow-cytometric cell-cycle and propidium iodide staining analysis. The photodynamic effects of TDC include confirmed reactive-oxygen-species-induced mitochondrial damage leading to necrosis in SKOV-3 cell lines. The in vivo photodynamic activity in nude-mouse models demonstrated abrogation of tumor growth without any detectable pathology in the skin, liver, spleen, or kidney, thereby demonstrating TDC application as an efficient and safe photosensitizer.

Synthesis, photophysical and metal ion recognition properties of a series of amino acid-linked free-base and Zn-porphyrin derivatives (5-9) are reported. These porphyrin derivatives showed favorable photophysical properties including high molar extinction coefficients (>1 × 10(5) m(-1) cm(-1) for the Soret band), quantum yields of triplet excited states (63-94%) and singlet oxygen generation efficiencies (59-91%). Particularly, the Zn-porphyrin derivatives, 6 and 9 showed higher molar extinction coefficients, decreased fluorescence quantum yields, and higher triplet and singlet oxygen quantum yields compared to the corresponding free-base porphyrin derivatives. Further, the study of their interactions with various metal ions indicated that the proline-conjugated Zn-porphyrins (6 and 9) showed high selectivity toward Cu(2+) ions and signaled the recognition through changes in fluorescence intensity. Our results provide insights on the role of nature of amino acid and metallation in the design of the porphyrin systems for application as probes and sensitizers.

Novel biomimetic mononuclear complexes, [Fe()Cl2](+) () and [Cu()(H2O)](2+) () based on naphthalimide appended tripodal tetradentate ligand ( = 2,2',2''-(3,3',3''-(2,2',2''-nitrilotris(methylene)tris(1H-benzo[d]imidazole-2,1-diyl))tris(propane-3,1-diyl))tris(1H-benzo-[de]isoquinoline-1,3(2H)-dione)) have been synthesized and characterized by various analytical and spectral techniques. In addition, the structures of the ligand () and complex were established unambiguously through X-ray crystal structure analysis. Uniquely, the coordination with a metal ion modified the ligand scaffold to interact efficiently with ct-DNA (groove binding) as well as protein (hydrophobic and/or electrostatic interactions). We have determined the affinity of these complexes for DNA/protein and the values are found to be in the range, KDNA = 0.34-1.01 × 10(4) M(-1) and KBSA = 4.1-5.0 × 10(5) M(-1). Furthermore, the fluorescence quenching of BSA with complexes and occurs through a static mechanism and affects the conformation of BSA around the tryptophan residues. The in vitro biological studies of these systems employing HeLa cell lines indicated that both these complexes exhibited enhanced cytotoxicity (IC50 = 32 ± 0.19 and 10 ± 0.21 μM for complexes and , respectively), when compared to the ligand () (IC50 = 150 μM). Interestingly, both the complexes ( and ) were found to be non-toxic to normal H9C2 cell lines. The mechanism of in vitro biological activity of these complexes has been evaluated through a variety of techniques: acridine orange/ethidium bromide, DAPI staining studies, annexin V-FITC/PI and poly(ADP-ribose)-polymerase (PARP) cleavage, which confirmed the apoptotic mediated cell death. Our results demonstrate the importance of complexation of the naphthalimide ligand () as well as the potential of these biomimetic metal complexes as cytotoxic and anticancer agents.

A cationic tentacle porphyrin selectively recognises guanosine (G) based nucleotides and was effectively utilized as a fluorescence “turn-on” probe to discriminate GTP from ATP through fluorescence indicator displacement (FID) assay in an aqueous medium.

We have investigated the DNA binding interactions and in vitro photoactivated DNA damage induced by a neutral water soluble porphyrin derivative 5,10,15,20-tetrakis(2,4,6-trihydroxyphenyl)porphyrin (TTHPP) and its zinc derivative 5,10,15,20-tetrakis(2,4,6-trihydroxyphenyl)porphyrinato zinc(II) (Zn-TTHPP) upon visible light irradiation through various spectroscopic techniques and employing repair endonucleases. These porphyrin derivatives exhibited high affinity toward DNA through groove binding interactions as evidenced through the UV-vis absorption, emission, circular dichroism spectral and viscosity changes. Interestingly, the free base porphyrin derivative, TTHPP generated efficient singlet oxygen mediated DNA damage sensitive to formamidopyrimidine-DNA glycosylase (Fpg protein), when compared with its metal derivative and to the well-known photosensitizer, hematoporphyrin. These results provide direct evidence for the role of DNA binding mode as well as extent of interactions with DNA in the efficiency of photoactivated DNA damage induced by the neutral porphyrins, which are believed to be the ideal candidates for photodynamic therapeutic applications.

[reaction: see text] A novel donor-acceptor conjugate 1 was synthesized, and its interactions with various amino acids have been investigated as compared to the model system 2. The conjugate 1 unusually forms an intramolecular charge-transfer complex in the aqueous medium and undergoes selective binding interactions with tryptophan. The uniqueness of this system is that it selectively recognizes tryptophan among all other amino acids and involves synergistic effects of pi-stacking, electrostatic, and donor-acceptor interactions.

The Gram-negative Aggregatibacter actinomycetemcomitans and Fusobacterium nucleatum are major causative agents of aggressive periodontal disease. Due to increase in the number of antibiotic-resistant bacteria, antimicrobial Photodynamic therapy (aPDT) seems to be a plausible alternative. In this work, photosensitization was performed on Gram-positive and Gram-negative bacteria in pure culture using new-age cationic porphyrins, namely mesoimidazolium-substituted porphyrin derivative (ImP) and pyridinium-substituted porphyrin derivative (PyP). The photophysical properties of both the sensitizers including absorption, fluorescence emission, quantum yields of the triplet excited states and singlet oxygen generation efficiencies were evaluated in the context of aPDT application. The studied porphyrins exhibited high ability to accumulate into bacterial cells with complete penetration into early stage biofilms. As compared with ImP, PyP was found to be more effective for photoinactivation of bacterial strains associated with periodontitis, without any signs of dark toxicity, owing to its high photocytotoxicity.

We synthesized a novel water-soluble porphyrin THPP and its metalated derivative Zn-THPP having excellent triplet excited state quantum yields and singlet oxygen generation efficiency. When compared to U.S. Food and Drug Administration approved and clinically used sensitizer Photofrin, THPP showed ca. 2-3-fold higher in vitro photodynamic activity in different cell lines under identical conditions. The mechanism of the biological activity of these porphyrin systems has been evaluated through a variety of techniques: 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, comet assay, poly(ADP-ribose)polymerase (PARP) cleavage, CM-H(2)DCFDA assay, DNA fragmentation, flow cytometric analysis, fluorescence, and confocal microscopy, which confirm the apoptotic cell death through predominantly reactive oxygen species (ROS). Moreover, THPP showed rapid cellular uptake and are localized in the nucleus of the cells as compared to Hoechst dye and Photofrin, thereby demonstrating its use as an efficient sensitizer in photodynamic therapy and live cell NIR nucleus imaging applications.

Novel viologen linked pyrene conjugates permeate cells efficiently and exhibit spacer length dependent DNA damage and cytotoxicity upon photoexcitation.