The binding of a c-MYC promoter G-quadruplex to neurotransmitters: An analysis of G-quadruplex stabilization using DNA melting, fluorescence spectroscopy, surface-enhanced Raman scattering and molecular docking.

The interactions of several neurotransmitter and neural hormone molecules with the c-MYC G-quadruplex DNA sequence were analyzed using a combination of spectroscopic and computational techniques. The interactions between indole, catecholamine, and amino acid neurotransmitters and DNA sequences could potentially add to the understanding of the role of G-quadruplex structures play in various diseases. Also, the interaction of the DNA sequence derived from the nuclear hypersensitivity element (NHE) III1 region of c-MYC oncogene (Pu22), 5'-TGAGGGTGGGTAGGGTGGGTAA-3', has added significance in that these molecules may promote or inhibit the formation of G-quadruplex DNA which could lead to the development of promising drugs for anticancer therapy. The results showed that these molecules did not disrupt G-quadruplex formation even in the absence of quadruplex-stabilizing cations. There was also evidence of concentration-dependent binding and high binding affinities based on the Stern-Volmer model, and thermodynamically favorable interactions in the form of hydrogen-bonding and interactions involving the π system of the aromatic neurotransmitters.

Honey gold nanoparticles attenuate the secretion of IL-6 by LPS-activated macrophages.

Interleukin-6 (IL-6) is a pleiotropic cytokine that coordinates host immune responses to infection. Though essential to the acute phase response, prolonged IL-6-mediated recruitment of mononuclear cells has been implicated in chronic inflammatory diseases such as rheumatoid arthritis, psoriasis, and Crohn's disease. Accordingly, identifying novel therapeutics that diminish circulating IL-6 levels could benefit individuals suffering from chronic inflammation. In immunocompetent hosts, bacterial lipopolysaccharide (LPS) recognition by toll-like receptor 4 (TLR4) activates the transcription factor NF-κB, driving macrophage production of IL-6. Interestingly, both citrate-stabilized and 'green' synthesized gold nanoparticles (AuNPs) have been shown to modulate the cytokine responses of LPS-activated macrophages. Here we demonstrate that AuNPs, synthesized with commercial and locally sourced honey, downregulate LPS-induced macrophage secretion of IL-6. Compared to LPS-only controls, inhibition of IL-6 levels was observed for all three types of honey AuNPs. The effect was likely driven by honey AuNP-mediated perturbation of the TLR4/NF-κB signaling pathway, as evidenced by a reduction in the phosphorylation of IκB. Further investigation into the anti-inflammatory properties of honey AuNPs may yield novel therapeutics for the treatment of chronic inflammation.

Fluorescence quenching of various indoles by nickel complexes.

The interactions between two nickel complexes with the ligand N,N'-bis (2-pyridylmethylene)-1,3-diaminopropyl and the indoles melatonin, serotonin, tryptamine, and tryptophol were characterized using UV-vis and fluorescence spectroscopy. The fluorescence of all the indoles were quenched in the presence of the complex with a hydroxyl group, indicating that hydrogen-bonding is a necessary interaction for quenching to occur. Various quenching parameters were determined using Stern-Volmer analysis and the quenching was determined to be of a mixed nature with high static quenching values (1011-1013 M-1). Additional analysis using the finite sink approximation indicated that the bimolecular reactions were not diffusion-limited and had high activation energies (135-199 kJ mol-1).

Detection of quadruplex DNA by gold nanoparticles.

Gold nanoparticles have been used as a probe to detect low (<10 ppb) concentrations of quadruplex DNA. These nanoparticles display a tendency to form aggregates in the presence of certain quadruplex forms, as observed via enhanced plasmon resonance light scattering (PRLS) signals. These nanoparticles showed differing degrees of interactions with different types of quadruplex and mixed sequences but no interaction with duplex DNA. Enhancement of PRLS signals greater than 50% was observed at nanomolar DNA concentration, and a lower limit of detection of 2.1 nM was established for three different quadruplex DNA sequences, including the thrombin-inhibiting single-stranded 15 mer aptamer DNA, d(GGTTGGTGTGGTTGG), and the double-stranded 12 mer DNA, d(G4T4G4). Two different sample preparation protocols were used for the PRLS experiments, and they yielded similar results.

Quenching of tryptophan fluorescence in various proteins by a series of small nickel complexes.

A series of twelve anionic, cationic, and neutral nickel(II) complexes have been synthesized and characterized. The interaction of these complexes with bovine serum albumin (BSA), human serum albumin (HSA), lysozyme (Lyso), and tryptophan (Trp) has been studied using steady-state fluorescence spectroscopy. Dynamic and static quenching constants have been calculated, and the role played in quenching by the ligand and complex charge investigated. The nickel complexes showed selectivity towards the different proteins based on the environment surrounding the Trp residue(s). Only small neutral complexes with hydrophobic ligands effectively quenched protein fluorescence via static quenching, with association constants ranging from 10(2) M(-1) (free Trp) to 10(10) M(-1) (lysozyme), indicating a spontaneous and thermodynamically favorable interaction. The number of binding sites, on average, was determined to be one in BSA, HSA and free Trp, and two in lysozyme.

Competition between solvent quenching and indole quenching of 9-fluorenone: a spectroscopic and computational study.

The interaction between 9-fluorenone, various indoles and solvents has been studied using steady-state fluorescence spectroscopy and quantum chemical calculations. It was determined that polar protic solvents such as methanol and ethanol significantly quenched the fluorescence of 9-fluorenone but various indoles reversed the solvent quenching. The effect of various solvents on the 9-fluorenone carbonyl vibration was investigated using infrared spectroscopy. Ab initio calculations using Gaussian03 were also carried out in order to determine the minimum energy conformations of these systems along with binding energies.

Detection of quadruplex DNA by luminescence enhancement of lanthanide ions and energy transfer from lanthanide chelates.

Small amounts of quadruplex DNA have been detected using luminescence enhancement of aqueous lanthanide ions and energy transfer from lanthanide chelates. The 22mer human telomeric DNA, AGGG(TTAGGG)(3), was detected using europium ions at concentrations as low as 20 ppb DNA. Detection with terbium ions was not possible due to the inherent weak luminescence intensities of lanthanides. Two different terbium chelates were used to overcome this challenge. When quadruplex DNA was added to the chelates there was a change in the excited-state lifetime of the chelate with subsequent energy transfer to the DNA. Experiments showed an increase in the amount of energy transferred from the chelate to the human telomeric DNA and other quadruplex sequences increased as a function of DNA concentration.

Tryptophol cation conformations studied with ZEKE spectroscopy.

The relative energies of several conformations of the tryptophol cation are determined by zero kinetic energy (ZEKE) photoelectron spectroscopy and photoionization efficiency measurements. Recently published high-resolution electronic spectroscopy on the neutral species determined the absolute configuration of the different conformers in the S1 spectrum. These assignments are utilized in the photoelectron experiments by pumping through conformer specific S1 resonances yielding ZEKE spectra of the specific, assigned conformations. The adiabatic ionization of one specific conformation is definitively determined, and two others are estimated. The photoelectron spectra, coupled with calculations, reveal that structural changes upon ionization are dominated by interactions of the hydroxyl group with the changes of electronic structure in the aromatic system.

Multiphoton excited fabrication of collagen matrixes cross-linked by a modified benzophenone dimer: bioactivity and enzymatic degradation.

Multiphoton excited (MPE) photochemistry is used to fabricate model tissue engineering scaffolds directly from types I, II, and IV collagen. A modified benzophenone dimer (BPD) provides the photoactivation and becomes incorporated into the resulting collagen matrixes. Unlike xanthene photochemistries, the benzophenone dimer can be used in acidic environments, where most forms of collagen have the greatest solubility. The minimum feature sizes are investigated by using two- and three-photon excitation, where the latter provides for superior "resolution" and suggests that collagen structures can be fabricated on the size scales of focal contacts. The resulting structures display excellent retention of bioactivity as evidenced by highly specific cell adhesion as well as immunofluorescence labeling. Structural and chemical aspects of the collagen matrixes are probed through measuring the enzymatic degradation through specific and nonspecific proteases, as the resulting relative rates are consistent with the activity of these enzymes. The degradation rates can also be controlled through varying the cross-link density in the matrixes, which is achieved through tuning the exposure dose during the fabrication process. The degradation rates are also found to be consistent with swelling/shrinking measurements and thus the average mesh size of the matrixes. In all cases the enzymatic degradations are well-fit single exponentials, suggesting that the matrixes can be fabricated with a priori knowledge of their structural properties. These results coupled with the resulting bioactivity suggest that the multiphoton fabrication process may be a powerful tool for the creation of cell-sized tissue engineering scaffolds.

Multiphoton-excited microfabrication in live cells via Rose Bengal cross-linking of cytoplasmic proteins.

We demonstrate the use of multiphoton-excited photochemistry to cross-link three-dimensional matrices directly from cytoplasmic proteins in a live cell (starfish oocyte). Fluorescence recovery after photobleaching measurements were used to determine diffusion coefficients inside intracellular cross-linked structures, and it was found that the diffusion was approximately 3 to 4 orders of magnitude slower than in free solution and 2-3 orders of magnitude slower than in cytoplasm and that the value can be tuned by controlling the laser exposure. Complex structures can be fabricated to construct channels and compartments that could be used to isolate cellular processes, and the method should thus be applicable to a broad range of problems in cell biology.

Measurement of normal and anomalous diffusion of dyes within protein structures fabricated via multiphoton excited cross-linking.

We demonstrate microscale spatial and chemical control of diffusion within protein matrixes created through the use of nonlinear multiphoton excited photochemistry. The mobility of fluorescent dyes of different mass and composition within controlled cross-linked environments has been measured using two-photon excited fluorescence recovery after photobleaching (FRAP). The diffusion times for several rhodamine and sulforhodamine dyes within these fabricated structures were found to be approximately 3-4 orders of magnitude slower than in free solution. The precise diffusion times can be tuned by varying the laser exposure during the fabrication of the matrix, and the diffusion can be correlated with the mesh size determined by TEM and Flory-Rehner analysis. We find that the hydrophobic Texas Red dyes (sulforhodamines) exhibit diffusion that is highly anomalous, indicative of a strong interaction with the hydrophobic cross-linked protein matrix. These results suggests the use of these cross-linked protein matrixes as ideal model systems in which to systematically study anomalous diffusion. Finally, the diffusion can be tuned within a multilayered protein matrix, and this in conjunction with slow diffusion also suggests the use of these structures in controlled release applications.

Properties of crosslinked protein matrices for tissue engineering applications synthesized by multiphoton excitation.

We demonstrate the fabrication of model scaffolds and extracellular matrices using multiphoton excited photochemistry. This method is three-dimensional in nature and has excellent biocompatibility. Crosslinked matrices were fabricated from the proteins fibrinogen, fibronectin, and concanavalin A using two-photon rose bengal photoactivation and the relatives rates were determined. Immunofluorescence labeling of fibrinogen and fibronectin indicated retention of bioactivity following the multiphoton crosslinking process. Using the fluorescence recovery after photobleaching method, we measured the lateral mobility of fluorescent dyes of different mass and chemistry in order to model the behavior of therapeutic agents and bioactive molecules and found diffusion coefficients within these fabricated structures to be on the order of 10(-9)-10(-10) cm(2)/s, or approximately three to four orders of magnitude slower than in free solution. The precise diffusion coefficients can be smoothly tuned by varying the laser exposure during the fabrication of the matrix, which results in both an increase in crosslink density as well as protein concentration in the matrix. Terminal crosslink density is achieved at integrated high exposure dose and the relative fabrication rates were determined for these proteins. For all the proteins, the range of diffusion coefficients between the threshold for fabrication and the terminal limit is correlated with the change in matrix mesh size as determined by Flory-Rehner swelling analysis. Both normal Fickian as well as hindered anomalous diffusion is observed depending on specific molecular interactions of the tracer dyes and protein host. (c) 2004 Wiley Periodicals, Inc. J Biomed Mater Res 71A: 359-368, 2004.

Vibrational dynamics of 9-fluorenemethanol using infrared-ultraviolet double-resonance spectroscopy.

Vibrational spectroscopy of jet-cooled 9-fluorenemethanol and its clusters 9-fluorenemethanol-H2O, 9-fluorenemethanol-CH3OH, 9-fluorenemethanol-C2H5OH, and 9-fluorenemethanol-C3H7OH has been carried out using an IR-UV double-resonance method. The spectrum of the OH stretching vibration, v(OH), has been measured for the 9-fluorenemethanol monomer and for each of the clusters. Two conformers of 9-fluorenemethanol, symmetric (sym) and unsymmetric (unsym), have been identified using a combination of spectroscopy and quantum chemical calculations with B3LYP and HF methods using the 6-31G(d) basis set. Vibrational dynamics resulting from IR excitation has also been studied using the S0-S1 transition probed by a nanosecond-time-delayed UV laser. The data suggest that isomerization occurs as a result of the IR excitation, but the breadth of the probe spectra makes an unequivocal conclusion difficult. The effect of hydrogen bonding on the v(OH) of 9-fluorenemethanol has also been studied in clusters with water, methanol, ethanol, and propanol by measuring the IR spectra. Cluster dissociation dynamics have also been studied following IR excitation. It is observed that upon excitation of the cluster of a particular conformation the monomer product is generally produced in both conformer forms. Energetic considerations indicate that isomerization occurs before dissociation.

Enzymatic activity of alkaline phosphatase inside protein and polymer structures fabricated via multiphoton excitation.

We demonstrate micron scale control of bioactivity through the use of multiphoton excited photochemistry, where this technique has been used to cross-link three-dimensional matrixes of alkaline phosphatase, bovine serum albumin, and polyacrylamide and combinations therein. Using a fluorescence-based assay (ELF-97), the enzymatic activity has been studied using a Michaelis-Menten analysis, and we have measured the specificity constants kcat/KM for alkaline phosphatase in both the protein and polymer matrixes to be on the order of 10(5)-10(6) M(-1) s(-1)and are comparable to known literature values in other environments. It is found that the enzyme is simply entrapped in the polymer matrix, whereas it is completely covalently bound in the protein structures. The relative reaction rate of alkaline phosphatase bound to BSA with the ELF substrate was measured as a function of cross-link density and was found to decrease in the more tightly formed matrixes, indicating a decrease in the diffusion in the matrix.