Academic literature on the topic 'Adenine-sensing'

Riboswitches are natural biosensors that can regulate gene expression by sensing small molecules. Knowledge of the structural dynamics of riboswitches is crucial to elucidate their regulatory mechanism and develop RNA biosensors. In this work, we incorporated the fluorophore, Cy3, and its quencher, TQ3, into a full-length adenine riboswitch RNA and its isolated aptamer domain to monitor the dynamics of the RNAs in vitro and in cell. The adenine riboswitch was sensitive to Mg2+ concentrations and could be used as a biosensor to measure cellular Mg2+ concentrations. Additionally, the TQ3/Cy3-labeled adenine riboswitch yielded a Mg2+ concentration that was similar to that measured using a commercial assay kit. Furthermore, the fluorescence response to the adenine of the TQ3/Cy3-labeled riboswitch RNA was applied to determine the proportions of multiple RNA conformational changes in cells. The strategy developed in this work can be used to probe the dynamics of other RNAs in cells and may facilitate the developments of RNA biosensors, drugs and engineering.

The present thesis provides a systematic investigation of coordination polymers of 3d, rare-earth (4f) and main group element (Bi) using both rigid aromatic, flexible aliphatic linkers. Luminescent sensing behavior towards nitro aromatics, metal ions and ferroelectric behavior have been investigated using some of the prepared compounds. The possible usefulness of lone pair on the structure has been investigated using bismuth based coordination polymers. The thermal and optical behavior of lanthanide coordination polymers (Ce, Pr and Nd) have also been studied. Chapter 1 An Overview of Coordination Polymer (CP) Compounds This chapter presents a brief introduction to coordination polymer (CP) compounds. Starting from the brief historical background on coordination compounds, this chapter shed light on some earlier developments in this family of compounds by Yaghi, Robson and others. The usefulness of carboxylate and imidazolates in construction of some important coordination polymer compounds like MOF-5, HKUST-1, ZIFs, MIL-53, UiO-66, CD-MOF-1 etc has been described in detail along with its properties. The coordination polymers exhibit many important properties and some of the properties like sorption, separation, ionic conductivity, catalysis and ferroelectricity have been discussed briefly and summerized. Chapter 1 also provides the general synthetic and characterization approaches that have been employed during the present studies. Chapter 2 Part A: Adenine Based Coordination Polymers with Cyclohexane dicarboxylic acids This chapter presents the synthesis, structure and properties of four new coordination polymers [Zn4(C8H10O4)2.5(C5H4N5)3.2H2O].7H2O.2DMA (I), [Cd3(C8H10O4)2(C5H4N5)2.H2O] (II), [Cd(C8H11O4)2(C5H5N5)2.2H2O] (III), [Cd(C8H10O4)(C7H8N5O).H2O]. 4H2O (IV), (CHDA = cyclohexane dicarboxylic acid, ad = adenine, DMA = dimethylacetamide, 9-HEA = 9-hydroxyethyl adenine). The compound I and II forms three-dimensional structure having distinct arrangements of 1,4-CHDA and adenine units with Zn and Cd metals respectively. The molecular complex unit is observed in compound III with 1,2-CHDA and adenine. Compound IV forms two-dimensional structure with 9-HEA and 1,2-CHDA. The observation of base-pairing interactions in the above compounds is noteworthy. In compounds I, II and IV amino groups are appears to be free and utilized for the detection of nitro aromatic explosives through fluorescence quenching. The results revealed that the emission behavior of the present compounds is greatly influenced by the hydroxyl nitroaromatic analyses like indophenol, dinitrophenyl and trinitrophenols with very low detection limits. The compound I also exhibits considerable sensitivity towards metal ion detection, especially Fe2+/Fe3+, Cr3+, Ag+ and Hg2+ ions in solution. The presence of free nitrogen sites in compound II has been explored for the base catalyzed Knoevenagel condensation reaction, the quantitative yields are observed with various aldehyde substrates. Part B: Adenine Based Coordination Polymer with Oxydiacetic acid: [Cd2(C4H4O5)2(C5H5N5)].H2O.DMA The synthesis, structure and properties of a Cd based coordination polymer with oxydiacetic acid and adenine, [Cd2(C4H4O5)2(C5H5N5)].H2O. DMA is described. The compound has a two-dimensional structure formed by the connectivity involving Cd and oxydiacetic acid. The adenine ligand binds with the Cd metal center through the pyrimidine nitrogen and hangs in the inter layer spaces. The layers are stacked in a ABAB.... fashion and the inter layer spaces occupied by the dimethyl amine and water molecules. The water molecules are very labile and its removal can be accomplished by heating the sample at 100°C, which is also confirmed by the single crystal XRD, PXRD and IR studies. The availability of free amino groups of adenine molecule has been utilized for the detection of nitroaromatics, especially nitrophenols with good sensitivity. The amino group was also found to be useful in catalyzing Knoevenagel condensation reactions. Chapter 3: Rare-Earth Metal Carboxylates: Ln2(µ3-OH)(C4H4O5)2(C4H2O4)].2H2O [Ln=Ce, Pr and Nd] This chapter describes synthesis, structure and properties of series of rare-earth based compounds, [Ln2(µ3-OH)(C4H4O5)2(C4H2O4)].2H2O (Ln = Ce, Pr and Nd). The malic acid and fumaric acid form part of the structure. The lanthanide centers are connected by the malate units to form a two dimensional layers, which are pillared by fumarate units forming the three-dimensional structure. Overall, structure can be described as I2O1 type inorganic in two-dimension (Ln-O-Ln layers) and organic in one dimension. The extra framework water molecules form a dimer and occupy the channels. The robustness of the framework was reflected in terms of facile removal and reinsertion of the water molecules, which is also confirmed by single crystal XRD, variable temperature IR and cyclic TGA study. The presence of water dimers and weakly interacting water chain suggested the possibility of proton migration in these compounds. Proton conductivity studies reveal the conductivity values of ~2.85 x 10-6 Ω-1cm-1 at 98% relative humidity. The optical studies revealed an up-conversion behavior involving more than one photon for the neodymium compound. Chapter 4: Bismuth Carboxylates with Brucite and Fluorite Related Structures The synthesis, structure and properties of three new bismuth based coordination polymers have been described in this chapter. The compounds [C4N2H10][Bi(C7H4NO4)(C7H3NO4)].H2O (I), [Bi(C5H3N2O4) (C5H2N2O4)] (II) and [Bi(µ2-OH)(C7H3NO4)] (III) were isolated employing hydrothermal condition with three different heterocyclicdicarboxylic acids, 3,6-pyridinedicarboxylic acid, 4,5-imidazoledicarboxylic acid and 3,4-pyridinedicarboxylic acid respectively. The structures of all the compounds have linkages between Bi2O2 and the corresponding dicarboxylate forming a simple molecular unit in I, a bilayer arrangement in II and a three-dimensional extended structure in III. The topological arrangement of the nodal building units in the structures resembles brucite related layers in II and fluorite related arrangement in compound III. By utilizing the secondary interactions, the structure of III can be correlated to a Kagome related net. The observation of such classical inorganic related structures in the bismuth carboxylates is noteworthy. Heterogeneous catalytic studies indicate Lewis acidic nature in the bismuth center in all three compounds. Chapter 5: Solvent dependent Delamination, Restacking and Ferroelectric studies in a Two-Dimensional Compound [NH4][Ag3(C9H5NO4S)2(C13H14N2)2].8H2O This chapter describes synthesis, structure, water dependent delamination/restacking and ferroelectric behavior in a layered coordination polymer compound, [NH4][Ag3(C9H5NO4S)2(C13H14N2)2].8H2O. The compound has a two-dimensional structure with the water molecules occupying the inter-lamellar spaces. The lattice water molecules can be fully removed and reinserted, which accompany the crystalline-amorphous-crystalline transformation. This transformation resembles the collapse/delamination and re-stacking of the layers. This transformation has also been investigated by in-situ IR and PXRD studies. The presence of a natural dipole (anionic framework and cationic ammonium ions) along with the non-centrosymmetric space group gives rise to a room-temperature ferroelectric behavior to the compound with saturation polarization (Ps) of 1.95 μC/cm2 and remnant polarization of 0.63 μC/cm2. The temperature dependent dielectric measurements indicate that the ferroelectric-paraelectric transformation occurs at 320 K. The ferroelectric-paraelectric transformation also follows the crystalline-amorphous-crystalline transitions.

Surface stress changes associated with hybridization of surface immobilized DNA molecules are measured. A novel interferometry technique employing two adjacent micromachined cantilevers a sensing/reference pair is used to measure the surface stress development. Measurement approach relies on coating the sensing cantilever with single stranded DNA (30-mer Adenine (poly A)) and reference cantilever with hybridized DNA. The sensing/reference pair is exposed to varying concentrations of complimentary DNA strand (30-mer Thymine (Poly T)) and differential deflection of sensing cantilever with respect to reference is measured to determine the change in surface stress. Experimental results indicate that surface stress develops only on exposure to complimentary strands (specific binding) and is not affected by exposure to other single stranded DNA (non-specific binding). Varying the poly T concentration from 0.1 to 1.0 μM results in a linear increase of the surface stress changes from 40 to 110 mN/m during DNA hybridization. Surface stress development starts as soon as the complementary poly T is introduced in the fluid cell and reaches a stable value within 15 minutes of injection time.