Polymorphic potential of SRF binding site of gene promoter: study.

Recently published observations have highlighted the presence of cruciform structures within the genome, suggesting their potential significance in the rapid recognition of the target sequence for transcription factor binding. In this study, we investigate the organization and stability of the (coding) strand within the Serum Response Element of the gene promoter ( SRE), specifically focusing on segments spanning 12 to 36 nucleotides, centered around the CArG-box. Through a thorough examination of UV absorption patterns with varying temperatures, we identified the emergence of a remarkably stable structure, which we conclusively characterized as a hairpin using complementary H NMR experiments.

Detection of Guanine Quadruplexes by Raman Optical Activity and Quantum-Chemical Interpretation of the Spectra.

Quadruplexes formed by guanine derivatives or guanine-rich nucleic acids are involved in metabolism and genetic storage of many living organisms, they are used in DNA nanotechnologies or as biosensors. Since many quadruplex geometries are possible the determination of their structures in aqueous solutions is difficult. Raman optical activity (ROA) can make it easier: For guanosine monophosphate (GMP), we observed a distinct change of the spectra upon its condensation and quadruplex formation.

Probing solution conformations of l-DOPA: Integration of experiment and simulation via vibrational optical activity.

l-DOPA plays a critical role as a precursor to dopamine and is a standard treatment for Parkinson's disease. Recent research has highlighted the potential therapeutic advantages of deuterated l-DOPA analogs having a longer biological half-life. For their spectroscopic characterization, the in-detail characterization of l-DOPA itself is necessary.

Structure of Zinc and Nickel Histidine Complexes in Solution Revealed by Molecular Dynamics and Raman Optical Activity.

The histidine residue has an exceptional affinity for metals, but solution structure of its complexes are difficult to study. For zinc and nickel complexes, Raman and Raman optical activity (ROA) spectroscopy methods to investigate the link between spectral shapes and the geometry were used. The spectra were recorded and interpreted on the basis of ionic equilibria, molecular dynamics, ab initio molecular dynamics, and density functional theory.

Effects of sulfation and the environment on the structure of chondroitin sulfate studied via Raman optical activity.

Glycosaminoglycans are linear carbohydrate polymers with essential roles in many biological processes. Chondroitin sulfate (CS) is one of them, omnipresent in living organisms as an important structural component of cartilage. It provides much of its resistance to compression.

Absolute Configuration Determination of a Taxol Precursor Based on Raman Optical Activity Spectra.

Enantiomeric purity of drugs is essential for their biological activity. In the present study, we investigate the performance of Raman optical activity (ROA) spectroscopy in distinguishing four possible stereoisomers of the synthetic precursor used for the production of taxol from baccatin III. Taxol is one of the best-selling medicaments used in the treatment of ovarian, lung, and breast cancers and Kaposi's sarcoma.

Organization of the MADS box from human SRF revealed by tyrosine perturbation.

MADS box family transcription factors are involved in signal transduction and development control through DNA specific sequence recognition. The DNA binding domain of these proteins contains a conservative 55-60 amino acid sequence which defines the membership of this large family. Here we present a thorough study of the MADS segment of serum response factor (MADS(SRF)).

Electronic circular dichroism of the chiral rigid tricyclic dilactam with nonplanar tertiary amide groups.

Electronic circular dichroism (ECD) of the spirocyclic dilactam 5,8-diazatricyclo[6,3,0,0(1,5)]undecane-4,9-dione has been measured in the extended wavelength range (170-260 nm) utilizing far-UV CD instrumentation including synchrotron radiation light source. The data of this model of two nonplanar tertiary amide groups interacting within the rigid chiral environment provided new information particularly about the shorter wavelength π-π* transition region below 190 nm. The interpretation using TDDFT calculations confirmed that effects of amide nonplanarity follow our previous observations on monolactams as far as amide n-π* transitions are concerned.

Protonation effect of tyrosine in a segment of the SRF transcription factor: a combined optical spectroscopy, molecular dynamics, and density functional theory calculation study.

The high sensitivity to pH of a short segment (an octamer) of serum response factor (SRF), an important member of the MADS box family of transcription factors, was investigated by Raman scattering, infrared and circular dichroism spectroscopies. Molecular dynamics (MD) and density functional theory (DFT) calculations enabled interpretation of spectral changes in close detail. Although there was a negligible difference between spectra in acidic and neutral environments, the spectrum in basic pH was substantially different.

Nonplanar tertiary amides in rigid chiral tricyclic dilactams. Peptide group distortions and vibrational optical activity.

We investigate amide nonplanarity in vibrational optical activity (VOA) spectra of tricyclic spirodilactams 5,8-diazatricyclo[6,3,0,0(1,5)]undecan-4,9-dione (I) and its 6,6',7,7'-tetradeuterio derivative (II). These rigid molecules constrain amide groups to nonplanar geometries with twisted pyramidal arrangements of bonds to amide nitrogen atoms. We have collected a full range vibrational circular dichroism (VCD) and Raman optical activity (ROA) spectra including signals of C-H and C-D stretching vibrations.

CH Stretching Region: Computational Modeling of Vibrational Optical Activity.

Most organic compounds provide vibrational spectra within the CH stretching region, yet the signal is difficult to interpret because of multiple difficulties in experiment and modeling. To better understand various factors involved, the ability of several harmonic and anharmonic computational approaches to describe these vibrations was explored for α-pinene, fenchone, and camphor as test compounds. Raman, Raman optical activity (ROA), infrared absorption (IR), and vibrational circular dichroism (VCD) spectra were measured and compared to quantum chemical computations.

Tracking of the polyproline folding by density functional computations and Raman optical activity spectra.

Polyprolines offer many opportunities to study factors influencing peptide and protein folding and structure. Longer chains can adopt two well-defined forms (PPI and PPII), but shorter peptides are quite flexible. To understand in detail the dependence of the secondary structure on the length and the interplay between the side chain and main chain conformation, zwitterionic (Pro)(N) models (with N = 2, 3, 4, 6, 9, 12 and longer inhomogeneous chains) were studied by a combination of the Raman and Raman optical activity (ROA) spectroscopy with the density functional theory (DFT).

Photoinduced processes in hydrogen bonded system: photodissociation of imidazole clusters.

The photodissociation of imidazole in hydrogen bonded clusters has been studied at photodissociation wavelengths 243 and 193 nm. Imidazole clusters of different mean cluster sizes n approximately 3 and 6 have been produced in expansions with He and Ar carrier gases, and the mean cluster sizes were determined by mass spectrometric and crossed beam scattering experiments. Simultaneously, the (C(3)N(2)H(4))(n) clusters were studied by ab initio calculations for n up to 4 molecules, confirming the hydrogen bond N-H.

Fragmentation dynamics of size-selected pyrrole clusters prepared by electron impact ionization: forming a solvated dimer ion core.

Structure and dynamics of size-selected charged pyrrole clusters have been studied by means of molecular beam scattering experiments and ab initio calculations. Small neutral Pyn clusters were produced in Py/He mixture expansions, and the scattering experiment with a secondary beam of He-atoms was exploited to select the neutral clusters of different sizes. The complete size-selected fragmentation patterns for the neutral dimer to the tetramer after an electron impact ionization at 70 eV were obtained from the measurements of the angular and velocity distributions at different fragment masses.

Experimental and theoretical study of the pyrrole cluster photochemistry: closing the pisigma* dissociation pathway by complexation.

Photolysis of size selected pyrrole clusters has been investigated and compared to the photolysis of an isolated pyrrole molecule. Experimentally, size distributions of different mean cluster sizes (n=3 and n>>5) have been prepared in supersonic expansions and the clusters were photolyzed at 243 and 193 nm. The kinetic energy distributions of the H photofragments have been measured.