A Pyrene Excimer Fluorescence (PEF) Study of the Interior of Amylopectin in Dilute Solution

Interactions between DNA and a Pyrene-Labeled Surfactant Probed by Pyrene Excimer Formation, Transmission Electron Microscopy, and Dynamic Light Scattering

The interactions between calf thymus DNA and a pyrene-labeled gemini surfactant termed PyO-3-12 were investigated by using dynamic light scattering (DLS), transmission electron microscopy (TEM), and pyrene excimer formation (PEF) between an excited and a ground-state pyrene. PyO-3-12 was prepared with two dimethylammonium bromide headgroups linked with a propyl spacer, with one ammonium bearing a dodecyl tail and the other bearing a 1-pyrenemethoxyhexyl pendent. The size and electrostatic properties of the colloidal species were characterized by DLS, and TEM was used to describe the overall dimensions and morphologies of the aggregates. PEF enabled the study of PyO-3-12 at the molecular level. The association of PyO-3-12 and DNA was studied in detail for two specific PyO-3-12 concentrations of 16 and 56 μM using a (∓) ratio equal to the [DNA]/[PyO-3-12] ratio with [DNA] expressed in terms of DNA base pairs, yielding a (∓) ratio ranging from 0.1 to 10. An increase in PyO-3-12 association upon adding DNA was detected through an increase in PEF. Analysis of the fluorescence decays indicated a progressive binding of PyO-3-12 to DNA until the equicharge point was reached after which all PyO-3-12 surfactants were bound to DNA. The formation of large colloidal aggregates was observed by DLS, which showed a spike in the hydrodynamic diameter (Dh) as the (∓) ratio approached unity. Analysis of the fluorescence spectra suggested that the excited pyrenyl labels experienced a more hydrophobic environment for the lipoplexes generated by the 56 μM PyO-3-12 solutions, which appeared smaller and more globular in the TEM images than the lipoplexes obtained with the lower 16 μM PyO-3-12 concentration. Together, these experiments suggest that the concentrations of the cationic gemini surfactants and DNA are important parameters for the morphology of lipoplexes with possible implications for their transfection efficiency.

Glycogen β-particles surface characterized by a combination of size exclusion chromatography and pyrene excimer fluorescence before and after β-amylolysis

Size exclusion chromatography (SEC) and pyrene excimer formation (PEF) experiments were conducted to characterize the local density profile inside a glycogen sample before (Glycogen) and after (Gly-β-LD) treatment with β-amylase. These experiments were conducted to assess whether the density at the periphery of the glycogen particles was very high to limit access to proteins involved in the metabolism of glycogen as predicted by the Tier model or low as suggested by the Gilbert model. SEC analysis indicated that the density inside the Glycogen and Gly-β-LD samples remained constant with particle size and was not affected by β-amylolysis. Analysis of the PEF experiments conducted on the Glycogen and Gly-β-LD samples labeled with 1-pyrenebutyric acid showed that the particles have a dense interior and loose corona. The conclusions reached by the SEC and PEF experiments agree with the Gilbert model and have implications for the association of glycogen β-particles into larger α-particles.

Flexibility of Poly(alkyl methacrylate)s Characterized by Their Persistence Length Determined through Pyrene Excimer Formation

A series of poly(alkyl methacrylate)s and poly(oligo(ethylene glycol) methyl ether methacrylate)s labeled with 1-pyrenebutanol were referred to as the PyC4-PCnMA samples with n = 1, 4, 6, 8, 12, and 18 and the PyC4-PEGnMA samples with n = 0-5, 9, 16, and 19, respectively. Pyrene excimer formation (PEF) upon the encounter between an excited and a ground-state pyrenyl labels was employed to determine their persistence length (lp) in o-xylene. The fluorescence decays of the PyC4-PCnMA and PyC4-PEGnMA samples were acquired and analyzed with the fluorescence blob model to yield the number (Nblob) of structural units in the volume probed by an excited pyrenyl label. Nblob was found to decrease with an increasing number (NS) of non-hydrogen atoms in the side chain, reaching a plateau for the PyC4-PEGnMA samples with a longer side chain (n = 16 and 19). The Nblob values were used to determine lp. The lp values for the PyC4-PCnMA and PyC4-PEGnMA samples increased linearly with increasing NS2 as predicted theoretically, which agreed with the lp values obtained by viscometry for a series of PCnMA samples. The good agreement between the lp values retrieved by PEF and viscometry served to validate the PEF-based methodology for determining lp for linear polymers.

Probing the inner local density of complex macromolecules by pyrene excimer formation

The direct relationship existing between the average rate constant 〈k〉 for pyrene excimer formation and the local concentration [Py]loc of ground-state pyrenyl labels covalently attached to a macromolecule was established for 55 pyrene-labeled macromolecules (PyLM). These PyLM belonged to three different families of macromolecules with the first representing short monodisperse linear chains end-labeled with pyrene (polystyrene, poly(ethylene oxide), and poly(N-isopropyl acrylamide)), the second representing long polydisperse linear chains randomly labeled with pyrene (poly(methyl acrylate), poly(methyl methacrylate), polystyrene, poly(butyl methacrylate), poly(methoxyethyl methacrylate), and poly(N-isopropyl acrylamide)), and the third being comprised of two series of pyrene end-labeled low generation dendrimers with a bis(hydroxymethyl)propionic acid or a polyamidoamine backbone. The assumption, that the polymeric segments probed by an excited pyrenyl label covalently attached to one of these macromolecules obeyed Gaussian statistics, enabled the calculation of their square root average squared end-to-end distance (LPy), which was applied to calculate [Py]loc. The log-log plots of 〈k〉 as a function of [Py]loc yielded straight lines with a slope of unity for all families of macromolecules studied in four different organic solvents demonstrating the validity and generality of the 〈k〉-vs.-[Py]loc relationship. Since an experimentalist knows how the the pyrenyl labels are covalently attached onto a macromolecule, [Py]loc offers a means to probe the local density of a macromolecule, which can be employed to characterize its conformation in solution. Consequently, the 〈k〉-vs.-[Py]loc relationship provides a novel experimental means to probe the conformation of macromolecules which should establish pyrene excimer formation as an appealing method for conformational studies of macromolecules in solution, which should nicely complement scattering techniques.

Interior of glycogen probed by pyrene excimer fluorescence

A glycogen sample from oyster (O) and another from corn (C) were fluorescently labeled with 1-pyrenebutyric acid to yield two series of pyrene-labeled glycogen samples (Py-Glycogen(O/C)). Analysis of the time-resolved fluorescence (TRF) measurements of the Py-Glycogen(O/C) dispersions in dimethyl sulfoxide yielded the maximum number (<N_blob^exp>) of anhydroglucose units (AGUs), that could separate two pyrene-labeled AGUs and still allow efficient pyrene excimer formation (PEF) between an excited and a ground-state pyrene. Molecular mechanics optimizations (MMOs) were conducted on a lattice of hexagonally close packed oligosaccharide helices to determine how the theoretical N_blob^theo varied as a function of the lattice density. Comparing <N_blob^exp> and <N_blob^theo>, obtained after integrating N_blob^theo along the local density profile ρ(r) across the glycogen particles, led to the conclusion that ρ(r) took a maximum value at the center of the glycogen particles contrary to expectations based on the Tier Model.

Cluster Size of Amylopectin and Nanosized Amylopectin Fragments Characterized by Pyrene Excimer Formation

Amylopectin from waxy corn and the three nanosized amylopectin fragments (NAFs)—NAF(56), NAF(20), and NAF(8)—from waxy corn starch with a hydrodynamic diameter of 227, 56, 20, and 8 nm, respectively, were randomly labeled with 1-pyrenebutyric acid. The efficiency of these pyrene-labeled amylopectin-based polysaccharides (Py-AbPS) for pyrene excimer formation (PEF) upon diffusive encounter between an excited and a ground-state pyrene increased with increasing concentration of unlabeled NAF(56) in Py-AbPS dispersions in DMSO. Fluorescence decay analysis of the Py-AbPS dispersions in DMSO prepared with increasing [NAF(56)] yielded the maximum number (N_blob^exp) of anhydroglucose units (AGUs) separating two pyrene-labeled AGUs while still allowing PEF. Comparison of N_blob^exp with N_blob^theo, obtained by conducting molecular mechanics optimizations on helical oligosaccharide constructs with HyperChem, led to a relationship between the interhelical distance (d_h-h) in a cluster of oligosaccharide helices, [NAF(56)], and the number of helices in a cluster. It was found that the AbPSs were composed of building blocks made of 3.5 (±0.9) helices that self-assembled into increasingly larger clusters with increasing [NAF(56)]. The ability of PEF-based experiments to yield the cluster size of AbPSs provides a new experimental means to probe the interior of AbPSs at the molecular level.

Unfolding of Helical Poly(L-Glutamic Acid) in N,N-Dimethylformamide Probed by Pyrene Excimer Fluorescence (PEF)

The denaturation undergone by α–helical poly(L-glutamic acid) (PLGA) in N,N-dimethylformamide upon addition of guanidine hydrochloride (GdHCl) was characterized by comparing the fluorescence of a series of PLGA constructs randomly labeled with the dye pyrene (Py-PLGA) to that of a series of Py-PDLGA samples prepared from a racemic mixture of D,L-glutamic acid. The process of pyrene excimer formation (PEF) was taken advantage of to probe changes in the conformation of α–helical Py-PLGA. Fluorescence Blob Model (FBM) analysis of the fluorescence decays of the Py-PLGA and Py-PDLGA constructs yielded the average number (<N_blob>) of glutamic acids located inside a blob, which represented the volume probed by an excited pyrenyl label. <N_blob> remained constant for randomly coiled Py-PDLGA but decreased from ~20 to ~10 glutamic acids for the Py-PLGA samples as GdHCl was added to the solution. The decrease in <N_blob> reflected the decrease in the local density of PLGA as the α–helix unraveled in solution. The changes in <N_blob> with GdHCl concentration was used to determine the change in Gibbs energy required to denature the PLGA α–helix in DMF. The relationship between <N_blob> and the local density of macromolecules can now be applied to characterize the conformation of macromolecules in solution.

Interior of Amylopectin and Nano-Sized Amylopectin Fragments Probed by Viscometry, Dynamic Light Scattering, and Pyrene Excimer Fluorescence

Nano-sized amylopectin fragments (NAFs), prepared by extrusion of waxy corn starch, were investigated by viscometry, dynamic light scattering (DLS), and pyrene excimer fluorescence (PEF). NAF57, with a hydrodynamic diameter of 57 nm, was treated with nitric acid to yield three degraded NAFs, which appeared to share the same interior and structural features as amylopectin based on their measured intrinsic viscosity and hydrodynamic diameter. This conclusion was further supported by comparing the efficiency of forming excimer between an excited and a ground-state pyrenyl label covalently attached to the NAFs (Py-NAFs) using their I_E/I_M ratio of the fluorescence intensity of the excimer (I_E) to that of the monomer (I_M). The overlapping trends obtained for all Py-NAFs and the pyrene-labeled amylopectin samples by plotting the I_E/I_M ratio as a function of pyrene content provided further evidence that the interior of NAFs and amylopectin shared the same structural features and contained a similar amount of free volume as predicted by the Solution-Cluster (Sol-CL) model. The presence of free volume was validated by adding linear poly(ethylene glycol) (PEG) chains that could not penetrate the interior of Py-NAFs, thus subjecting the Py-NAFs to increased osmotic pressure, which induced their compression and resulted in an increase in I_E/I_M.