Sulayman A. Oladepo

UV Resonance Raman Investigations of Peptide and Protein Structure and Dynamics

A study was conducted to demonstrate ultraviolet resonance Raman (UVRR) investigations of peptide and protein structure and dynamics. The tuning of the excitation wavelengths allowed the probing of different chromophoric segments of a macromolecule. Another advantage of deep UV Raman measurements was that there was no interference from molecular relaxed fluorescence, as those chromophores that had their first transition below 260 nm were highly flexible and possessed small fluorescence quantum yields. UVRR was also used in pump-probe measurements to give kinetic information on fast biological processes. It was a powerful technique for studying static protein structure and for studying protein dynamics, such as in protein folding. The rapid development of UVRR was aided by the latest advancements in lasers, optics, and detectors.

Silica-coated super paramagnetic iron oxide nanoparticles (SPION) as biocompatible contrast agent in biomedical photoacoustics

In this study, we report for the first time the use of silica-coated superparamagnetic iron oxide nanoparticles (SPION) as contrast agents in biomedical photoacoustic imaging. Using frequency-domain photoacoustic correlation (the photoacoustic radar), we investigated the effects of nanoparticle size, concentration and biological media (e.g. serum, sheep blood) on the photoacoustic response in turbid media. Maximum detection depth and the minimum measurable SPION concentration were determined experimentally. The nanoparticle-induced optical contrast ex vivo in dense muscular tissues (avian pectus and murine quadricept) was evaluated and the strong potential of silica-coated SPION as a possible photoacoustic contrast agents was demonstrated.

pH-dependent UV resonance Raman spectra of cytosine and uracil.

Cytosine is a nucleobase found in both DNA and RNA, while uracil is found only in RNA. Uracil has abstractable protons at N3 and N1. Cytosine has only one abstractable proton at N1 but can also accept a proton at N3. The pKa values of these protons are well-known, but the effect of the change in protonation on the rest of the molecule is not well understood and is very important in base stacking, base pairing, and protein-nucleic acid interactions. In this paper, UV resonance Raman (UVRR) spectroscopy is used to probe the structures of both cytosine and uracil at varying pH to determine the structural changes that take place. The results show that cytosine has increased electronic delocalization when moving to either basic or acidic environments, whereas uracil shows no significant change in acidic environment but increases its electronic delocalization in basic environment.

Initial excited-state structural dynamics of 9-methyladenine from UV resonance Raman spectroscopy.

The photophysics and photochemistry of nucleobases are the factors governing the photostability of DNA and RNA, since they are the UV chromophores in nucleic acids. Because the formation of photoproducts involves structural changes in the excited electronic state, we study here the initial excited-state structural dynamics of 9-methyladenine (9-MeA) by using UV resonance Raman (UVRR) spectroscopy. UV resonance Raman intensities are sensitive to the initial excited-state structural dynamics of molecules. Therefore, information about the initial structural changes in the excited-state of a given molecule can be obtained from its UVRR intensities. The resonance Raman spectra of 9-MeA at wavelengths throughout its 262 nm absorption band were measured, and a self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum was performed using a time-dependent wave packet formalism. We found that the initial structural dynamics of this molecule primarily lie along the N3C4, C4C5, C5C6, C5N7, N7C8, and C8N9 stretching vibrations and CH(3) deformation vibrations. These results are discussed in the context of photochemistry and other deactivation processes.

Self-quenching smart probes as a platform for the detection of sequence-specific UV-induced DNA photodamage

Molecular beacons (MBs) are sensitive probes for many DNA sequence-specific applications, such as DNA damage detection, but suffer from technical and cost limitations. We have designed smart probes with self-quenching properties as an alternative to molecular beacons to monitor sequence-specific UV-induced photodamage of oligonucleotides. These probes have similar stem-loop structural characteristics as molecular beacons, but quenching is achieved instead via photoinduced intramolecular electron transfer by neighboring guanosine residues. Our results indicate that the probes are sensitive enough to detect nanomolar target concentrations and are specific enough to discriminate single-base damage. When the probes were used to monitor UV-induced photodamage in oligonucleotide sequences that differ by a single-base mismatch, the photodamage time constant was higher for the perfectly complementary target sequences than for the mismatch sequences, indicating that these probes are specific for each target sequence. In addition, time constants obtained for oligonucleotide target sequences with both stem and loop base mismatches are lower than those with only loop mismatches, suggesting that these sequences are also specifically distinguished by the smart probes. These probes thus constitute robust, sensitive, specific, and cheaper alternatives to MBs for sequence-specific DNA damage detection.

Macro-Raman spectroscopy for bulk composition and homogeneity analysis of multi-component pharmaceutical powders

&NA; A new macro‐Raman system equipped with a motorized translational sample stage and low‐frequency shift capabilities was developed for bulk composition and homogeneity analysis of multi‐component pharmaceutical powders. Different sampling methods including single spot and scanning measurement were compared. It was found that increasing sample volumes significantly improved the precision of quantitative composition analysis, especially for poorly mixed powders. The multi‐pass cavity of the macro‐Raman system increased effective sample volumes by 20 times from the sample volume defined by the collection optics, i.e., from 0.02 &mgr;L to about 0.4 &mgr;L. A stochastic model simulating the random sampling process of polydisperse microparticles was used to predict the sampling errors for a specific sample volume. Comparison of fluticasone propionate mass fractions of the commercial products Flixotide® 250 and Seretide® 500 simulated for different sampling volumes with experimentally measured compositions verified that the effective sample volume of a single point macro‐Raman measurement in the multi‐pass cavity of this instrument was between 0.3 &mgr;L and 0.5 &mgr;L. The macro‐Raman system was also successfully used for blend uniformity analysis. It was concluded that demixing occurred in the binary mixture of L‐leucine and D‐mannitol from the observation that the sampling errors indicated by the standard deviations of measured leucine mass fractions increased during mixing, and the standard deviation values were all larger than the theoretical lower limit determined by the simulation. Since sample volume was shown to have a significant impact on measured homogeneity characteristics, it was concluded that powder homogeneity analysis results, i.e., the mean of individual test results and absolute and relative standard deviations, must be presented together with the effective sample volumes of the applied testing techniques for any measurement of powder homogeneity to be fully meaningful. Graphical abstract Figure. No caption available. HighlightsMacro‐Raman systems are suitable for bulk composition and blend uniformity analysis.Two methods of evaluating macro‐Raman effective sample volumes were proposed.Uniformity analysis results strongly rely on the effectively tested sample volumes.

Excited-State Structural Dynamics of Nucleic Acids and TheirComponents

Nucleic acids are the very essence of life, containing the genetic potential of all organisms. However, the sheer size of nucleic acids makes them susceptible to a variety of environmental insults. Of these, ultraviolet-induced damage to nucleic acids has received extensive attention due to its role in disease. The primary step in ultraviolet-induced damage is the absorption of light and the subsequent electronic and structural dynamics on the excited-state potential energy surface. In this chapter, we will review the use of Raman and resonance Raman spectroscopy as a means of obtaining excited-state structural dynamics. Specifically, the application of Raman and resonance Raman spectroscopy to determine the excited-state structural dynamics of nucleic acids and their components will be discussed

The Effect of Tryptophan on UV-induced DNA Photodamage

Trp–DNA adducts resulting from UV irradiation of pyrimidine bases and nucleotides in the presence of tryptophan (Trp) have been the subject of previous research. However, the relative yield of the adducts compared with the UV screening effect of Trp has not been previously considered. To determine whether Trp–DNA adduct formation or absorption “screening” by Trp is the predominant process when DNA solutions are irradiated with UV light in the presence of Trp, we irradiated Trp‐containing DNA oligonucleotide solutions with UVC light and incubated aliquots of those solutions with molecular beacons (MBs) to detect the damage. We observed a rapid decay of fluorescence of the MBs for pure DNA solutions, thereby indicating damage. However, in the presence of Trp, the fluorescence decay is prolonged, with time constants that increase exponentially with Trp concentration. The results are discussed in terms of a beneficial in vivo cellular protection rather than harmful adduct formation and suggest a net sacrificial absorption of UV light by Trp which actually protects the DNA from UV damage.