Using full chloroplast genomes of 'red' and 'yellow' Bixa orellana (achiote) for kmer based identification and phylogenetic inference.

BACKGROUND: Full chloroplast genomes provide high resolution taxonomic discrimination between closely related plant species and are quickly replacing single and multi-locus barcoding regions as reference materials of choice for DNA based taxonomic annotation of plants. Bixa orellana, commonly known as "achiote" and "annatto" is a plant used for both human and animal foods and was thus identified for full chloroplast sequencing for the Center for Veterinary Medicine (CVM) Complete Chloroplast Animal Feed database. This work was conducted in collaboration with the Instituto de Medicina Tradicional (IMET) in Iquitos, Peru. There is a wide range of color variation in pods of Bixa orellana for which genetic loci that distinguish phenotypes have not yet been identified. Here we apply whole chloroplast genome sequencing of "red" and "yellow" individuals of Bixa orellana to provide high quality reference genomes to support kmer database development for use identifying this plant from complex mixtures using shotgun data. Additionally, we describe chloroplast gene content, synteny and phylogeny, and identify an indel and snp that may be associated with seed pod color. RESULTS: Fully assembled chloroplast genomes were produced for both red and yellow Bixa orellana accessions (158,918 and 158,823 bp respectively). Synteny and gene content was identical to the only other previously reported full chloroplast genome of Bixa orellana (NC_041550). We observed a 17 base pair deletion at position 58,399-58,415 in both accessions, relative to NC_041550 and a 6 bp deletion at position 75,531-75,526 and a snp at position 86,493 in red Bixa orellana. CONCLUSIONS: Our data provide high quality reference genomes of individuals of red and yellow Bixa orellana to support kmer based identity markers for use with shotgun sequencing approaches for rapid, precise identification of Bixa orellana from complex mixtures. Kmer based phylogeny of full chloroplast genomes supports monophylly of Bixaceae consistent with alignment based approaches. A potentially discriminatory indel and snp were identified that may be correlated with the red phenotype.

Advances in anion transport and supramolecular medicinal chemistry.

Advances in anion transport by synthetic supramolecular systems are discussed in this article. Developments in the design of discrete molecular carriers for anions and supramolecular anion channels are reviewed followed by an overview of the use of these systems in biological systems as putative treatments for diseases such as cystic fibrosis and cancer.

Oxidation of 8-thioguanosine gives redox-responsive hydrogels and reveals intermediates in a desulfurization pathway.

A disulfide made by oxidation of 8-thioguanosine is a supergelator. The hydrogels are redox-responsive, as they disassemble upon either reduction or oxidation of the S-S bond. We also identified this disulfide, and 2 other compounds, as intermediates in oxidative desulfurization of 8-thioG to guanosine.

Drawing with Iron on a Gel Containing a Supramolecular Siderophore.

Guanosine-5'-hydroxamic acid (3) forms hydrogels when mixed with guanosine (1) and KCl. The 5'-hydroxamic acid (HA) unit is pH-responsive and also chelates Fe3+ . When gels are prepared under basic conditions, the 5'-HA groups are deprotonated and the anionic hydrogel binds cationic thiazole orange (TO), signaled by enhanced fluorescence. The HA nucleoside 3, when immobilized in the G-quartet gel, acts as a supramolecular siderophore to form red complexes with Fe3+ . We patterned the hydrogel's surface with FeCl3 , by hand and by using a 3D printer. Patterns form instantly, are visible by eye, and can be erased using vitamin C. This hydrogel, combining self-assembled G-quartet and siderophore-Fe3+ motifs, is strong, can be molded into different shapes, and is stable on the bench or under salt water.

Self-Assembly of Metallo-Nucleoside Hydrogels for Injectable Materials That Promote Wound Closure.

Injectable hydrogels are increasingly being used as scaffolds for in situ tissue engineering and wound healing. Most of these injectable hydrogels are made from polymers, and there are fewer examples of such soft materials made via self-assembly of low-molecular weight gelators. We report the room-temperature synthesis of a functional hydrogel formed by mixing cytidine (C) with 0.5 equiv each of B(OH)3 and AgNO3. The structural basis for this supramolecular hydrogel (C-B-C·Ag+) involves orthogonal formation of cytidine borate diesters (C-B-C) and Ag+-stabilized C-C base pairs, namely, the C·Ag+·C dimer. The C-B-C·Ag+ hydrogels, which can have high water content (at least 99.6%), are stable (no degradation after 1 year in the light), stimuli-responsive, and self-supporting, with elastic moduli of up to 104 Pa. Incorporation of Ag+ ions into the gel matrix endows the C-B-C·Ag+ hydrogel with significant antibacterial capability. Importantly, the rapid switching between the sol and gel states for this supramolecular hydrogel, as a response to shear stress, enables 3D printing of a flexible medical patch made from the C-B-C·Ag+ hydrogel. The C-B-C·Ag+ hydrogel was used to promote the closure of burn wounds in a mouse model.

Playing supramolecular dominoes with light: building and breaking a photoreversible G-quadruplex made from guanosine, boric acid and an azobenzene.

Addition of azobenzene-derivative 1 in its E configuration to an aqueous solution containing various guanosine borate esters induces a helical G-quartet based self-organization, stabilized by intercalation of the dye. The process is driven, in a domino fashion, by the initial host-guest interaction between the dye and a specific guanosine borate diester, whose structure can be thus assigned. This inclusion complex templates the formation of G-quartets. The quartets, in turn, pile up to form a supramolecular G-quadruplex structure, in which other G species present in solution are progressively included. The G-quadruplex can be reversibly broken and reformed by photoisomerization of the dye. This hierarchical and photosensitive self-assembly is unprecedented for simple guanosine derivatives.

Templating and Catalyzing [2+2] Photocycloaddition in Solution Using a Dynamic G-Quadruplex.

We describe a templating/covalent capture strategy that enables photochemical formation of 8 cyclobutanes in one noncovalent assembly. This process was characterized by experiment and quantum mechanical/molecular mechanics (ONIOM) calculations. Thus, KI and 16 units of 5'-cinnamate guanosine form a G-quadruplex where C=C π bonds in neighboring G4 -quartets are separated by 3.3 Å, enabling [2+2] photocycloaddition in solution. This reaction is high-yielding (>90 %), regio- and diastereoselective. Since all components are in dynamic equilibrium this photocycloaddition is catalytic in K+ .

A G4·K+ hydrogel made from 5'-hydrazinoguanosine for remediation of α,ß-unsaturated carbonyls.

A G4·K+ hydrogel made from 5'-hydrazinoguanosine and KCl reacts with α,ß-unsaturated carbonyls of different electrophilicities (acrolein, methyl vinyl ketone and methyl acrylate) in water and the gas phase to form cyclic adducts. This aza-Michael addition/cyclization domino reaction by the 5'-hydrazino G4·K+ hydrogel has promise for environmental remediation of toxic α,ß-unsaturated carbonyls from water and the atmosphere.

Coherent phenomena in photosynthetic light harvesting: part two-observations in biological systems.

Considerable debate surrounds the question of whether or not quantum mechanics plays a significant, non-trivial role in photosynthetic light harvesting. Many have proposed that quantum superpositions and/or quantum transport phenomena may be responsible for the efficiency and robustness of energy transport present in biological systems. The critical experimental observations comprise the observation of coherent oscillations or "quantum beats" via femtosecond laser spectroscopy, which have been observed in many different light harvesting systems. Part Two of this review aims to provide an overview of experimental observations of energy transfer in the most studied light harvesting systems. Length scales, derived from crystallographic studies, are combined with energy and time scales of the beats observed via spectroscopy. A consensus is emerging that most long-lived (hundreds of femtoseconds) coherent phenomena are of vibrational or vibronic origin, where the latter may result in coherent excitation transport within a protein complex. In contrast, energy transport between proteins is likely to be incoherent in nature. The question of whether evolution has selected for these non-trivial quantum phenomena may be an unanswerable question, as dense packings of chromophores will lead to strong coupling and hence non-trivial quantum phenomena. As such, one cannot discern whether evolution has optimised light harvesting systems for high chromophore density or for the ensuing quantum effects as these are inextricably linked and cannot be switched off.

Coherent phenomena in photosynthetic light harvesting: part one-theory and spectroscopy.

The role of non-trivial quantum mechanical effects in biology has been the subject of intense scrutiny over the past decade. Much of the focus on potential "quantum biology" has been on energy transfer processes in photosynthetic light harvesting systems. Ultrafast laser spectroscopy of several light harvesting proteins has uncovered coherent oscillations dubbed "quantum beats" that persist for hundreds of femtoseconds and are putative signatures for quantum transport phenomena. This review describes the language and basic quantum mechanical phenomena that underpin quantum transport in open systems such as light harvesting and photosynthetic proteins, including the photosystem reaction centre. Coherent effects are discussed in detail, separating various meanings of the term, from delocalized excitations, or excitons, to entangled states and coherent transport. In particular, we focus on the time, energy and length scales of energy transport processes, as these are critical in understanding whether or not coherent processes are important. The role played by the protein in maintaining chromophore systems is analysed. Finally, the spectroscopic techniques that are used to probe energy transfer dynamics and that have uncovered the quantum beats are described with reference to coherent phenomena in light harvesting.

G4-quartet hydrogels from 5'-hydrazino-guanosine for the non-covalent and covalent remediation of contaminants from water.

The creation of supramolecular hydrogels from relatively simple building blocks demonstrates the power of molecular self-assembly to make functional materials. G4-quartet hydrogels are appealing for a number of applications, including the environmental remediation of pollutants in water. We find that the guanosine analog, 5'-deoxy-5'-hydrazinoguanosine (HG 2) self-assembles into a self-standing hydrogel in the presence of stoichiometric amounts (0.25 equiv.) of KCl. The higher water solubility of HG 2 (14.5 mM), compared to that of the parent compound G 1 (2.1 mM), likely contributes to its enhanced gelation. The structural basis for this HG 2·KCl hydrogel, confirmed by PXRD, IR and CD, is the G4·K+ quartet, which forms extended 1D ion-channel assemblies that entangle to give a stable and long-lived hydrogel. We also find that adding KCl to a saturated solution of HG 2 triggers the generation of colloidal G4·K+ assemblies in situ that selectively and efficiently binds the anionic dye naphthol blue black (NBB) over a cationic dye. In addition to this non-covalent electrostatic binding of anions, the nucleophilic 5'-hydrazino group in the HG 2·KCl hydrogel HG 2 enables the efficient absorption of propionaldehyde from both the gas phase and from water solution via the formation of covalent hydrazone linkages with the gel matrix.

A self-assembled peroxidase from 5'-GMP and heme.

Guanosine 5'-monophosphate (5'-GMP) and Fe(iii)-heme form a supramolecular catalyst with peroxidase activity. Catalysis, which depends on self-assembly of 5'-GMP into a G-quadruplex that binds hemin, can be modulated by nucleotide concentration, temperature and the identity of the nucleotide's sugar.

G-Quartet hydrogels for effective cell growth applications.

Functional G-quartet hydrogels formed from natural guanosine cross linked with benzene-1,4-diboronic acid and Mg2+ support cell growth with no visible signs of gel degradation.

Supramolecular hydrogels for environmental remediation: G4-quartet gels that selectively absorb anionic dyes from water.

Binary mixtures of guanosine (G 1) and 8-aminoguanosine (8AmG 2) form stable, transparent supramolecular hydrogels with stoichiometric concentrations of either K+ or Ba2+ salts. These hydrogels selectively bind anionic dyes.

Anion transport and supramolecular medicinal chemistry.

New approaches to the transmembrane transport of anions are discussed in this review. Advances in the design of small molecule anion carriers are reviewed in addition to advances in the design of synthetic anion channels. The application of anion transporters to the potential future treatment of disease is discussed in the context of recent findings on the selectivity of anion transporters.

Co-existence of Distinct Supramolecular Assemblies in Solution and in the Solid State.

The formation of distinct supramolecular assemblies, including a metastable species, is revealed for a lipophilic guanosine (G) derivative in solution and in the solid state. Structurally different G-quartet-based assemblies are formed in chloroform depending on the nature of the cation, anion and the salt concentration, as characterized by circular dichroism and time course diffusion-ordered NMR spectroscopy data. Intriguingly, even the presence of potassium ions that stabilize G-quartets in chloroform was insufficient to exclusively retain such assemblies in the solid state, leading to the formation of mixed quartet and ribbon-like assemblies as revealed by fast magic-angle spinning (MAS) NMR spectroscopy. Distinct N-H⋅⋅⋅N and N-H⋅⋅⋅O intermolecular hydrogen bonding interactions drive quartet and ribbon-like self-assembly resulting in markedly different 2D 1 H solid-state NMR spectra, thus facilitating a direct identification of mixed assemblies. A dissolution NMR experiment confirmed that the quartet and ribbon interconversion is reversible-further demonstrating the changes that occur in the self-assembly process of a lipophilic nucleoside upon a solid-state to solution-state transition and vice versa. A systematic study for complexation with different cations (K+ , Sr2+ ) and anions (picrate, ethanoate and iodide) emphasizes that the existence of a stable solution or solid-state structure may not reflect the stability of the same supramolecular entity in another phase.

Controlling molecularity and stability of hydrogen bonded G-quadruplexes by modulating the structure's periphery.

We report on self-assembly of guanosines with aromatic esters at their 5'-position. Depending on the basicity of the 5'-ester either discrete octamers G8·K(+)I(-) or hexadecamers G16·3K(+)3I(-) are formed. The thermodynamic and kinetic stabilities of the G-quadruplex can be controlled by interlayer hydrogen-bonding and by dispersion interactions on the assembly's periphery.

Supramolecular gels made from nucleobase, nucleoside and nucleotide analogs.

Supramolecular or molecular gels are attractive for various applications, including diagnostics, tissue scaffolding and targeted drug release. Gelators derived from natural products are of particular interest for biomedical purposes, as they are generally biocompatible and stimuli-responsive. The building blocks of nucleic acids (i.e. nucleobases, nucleosides, and nucleotides) are desirable candidates for supramolecular gelation as they readily engage in reversible, noncovalent interactions. In this review, we describe a number of organo- and hydrogels formed through the assembly of nucleosides, nucleotides, and their derivatives. While natural nucleosides and nucleotides generally require derivatization to induce gelation, guanosine and its corresponding nucleotides are well known gelators. This unique gelating ability is due to propensity of the guanine nucleobase to self-associate into stable higher-order assemblies, such as G-ribbons, G4-quartets, and G-quadruplexes.