Arborescent Poly(l-glutamic acid)s as Standards To Study the Dense Interior of Polypeptide Mesoglobules by Pyrene Excimer Fluorescence

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.

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.

Direct Measure of the Local Concentration of Pyrenyl Groups in Pyrene-Labeled Dendrons Derived from the Rate of Fluorescence Collisional Quenching

The model-free analysis (MFA) was applied to measure the average rate constant (<k>) for pyrene excimer formation (PEF) in a series of pyrene-labeled dendrons referred to as Py_x-G(N), where x (= 2^N) is the number of pyrenyl labels born by a dendron of generation N ranging from 1 to 6. <k> was measured in four different solvents, namely tetrahydrofuran (THF), toluene, N,N-dimethylformamide (DMF), and dimethylsulfoxide (DMSO). <k> was found to increase linearly with increasing local pyrene concentration ([Py]_loc), where [Py]_loc had been determined mathematically for the Py_x-G(N) dendrons. The slope of each straight line changed with the nature of the solvent and represented k_diff, the bimolecular rate constant for PEF. k_diff depended on the solvent viscosity (η) and the probability (p) for PEF upon encounter between an excited and a ground-state pyrene. In a same solvent, k_diff for the Py_x-G(N) dendrons was about 360 ± 30 times smaller than k_diff obtained for ethyl 4-(1-pyrene)butyrate (PyBE), a pyrene model compound similar to the pyrene derivative used to label the dendrons. The massive decrease in k_diff observed for the Py_x-G(N) samples reflected the massive loss in mobility experienced by the pyrenyl labels after being covalently attached onto a macromolecule compared to freely diffusing PyBE. Interestingly, the k_diff values obtained for the Py_x-G(N) dendrons and the PyBE model compound followed similar trends as a function of solvent, indicating that the difference in behavior between the k_diff values obtained in different solvents were merely due to the changes in the η and p values between the solvents. Normalizing the <k> values obtained with the Py_x-G(N) dendrons by the k_diff values obtained for PyBE in the same solvents accounted for changes in η and p, resulting in a master curve upon plotting <k>/(f_diff × k_diff) as a function of [Py]_loc, where f_diff was introduced to account for some pyrene aggregation in the higher generation dendron (Py₆₄-G(6)). This result demonstrates that <k> represents a direct measure of [Py]_loc in pyrene-labeled macromolecules.

Effect of Structure on Polypeptide Blobs: A Model Study Using Poly(l-lysine)

The conformation of a series of pyrene-labeled poly(l-lysine)s (Py-PLLs) in 60:40 and 90:10 (v/v) acetonitrile:water mixtures was determined by comparing the results obtained from the fluorescence blob model (FBM) analysis of their fluorescence decays with those obtained from molecular mechanics optimizations (MMOs). PLL aggregates formed in both solutions as demonstrated by FRET experiments between naphthalene- and pyrene-labeled PLLs. Addition of an excess of unlabeled PLL allowed the conformational study of isolated Py-PLL embedded in a matrix of unlabeled PLLs. By varying the acetonitrile (ACN) content of the solution from 60 to 90 vol % ACN, Py-PLL was found to undergo a conformational change from a random coil to an α-helix. The conformational change induced an increase in the maximum number of lysines (N_blob) separating two pyrene-labeled lysines that could still form an excimer between an excited- and a ground-state pyrene. N_blob obtained from the FBM analysis increased from 15.2 ± 2.1 to 25.2 ± 1.2 lysines as PLL changed its conformation from a random coil to an α-helix. AFM revealed that the α-helical PLLs organized themselves into structured bundles ∼22 nm in diameter. The FBM analysis of the decays acquired with a solution of aggregated Py-PLLs in a 90:10 ACN:water mixture yielded a larger N_blob value of 36.6 ± 3.4. The increase in N_blob indicated that the Py-PLL constructs could now interact with one another in the helical bundles. This increase in N_blob was then used in conjunction with MMOs to determine an interhelical spacing of 2.9 ± 0.1 nm for Py-PLLs in a bundle. This interhelical spacing resulted in a local density of 0.25 ± 0.01 g·cm^-3 for the bundles of PLL α-helices, which was a reasonable density for a protein in solution. This study describes an experimental means to probe the number of amino acids that interact with each other as the conformation of a polypeptide evolves from that of a random coil to that of an α-helix to finally that of a bundle of α-helices.