Investigation of restriction endonuclease EcoRII complex with DNA in solution by FTIR spectroscopy

The X-ray structure of type IIE EcoRII restriction endonuclease has been solved but the structure of the R.EcoRII-DNA complex is still unknown. We report here on the structure of the pre-reactive R.EcoRII-DNA-Ca²⁺ complex in solution examined by FTIR spectroscopy. The secondary structure of R.EcoRII as well as the structure of the target DNA in the R.EcoRII-DNA-Ca²⁺ complex was characterized. It was shown that the R.EcoRII-DNA-Ca²⁺ complex formation is accompanied by changes in the spectrum of both DNA bases and DNA sugar-phosphate backbone that suggest contacts of the enzyme with different groups of atoms in DNA. The change of the R.EcoRII secondary structure in the R.EcoRII-DNA-Ca²⁺ complex is also observed.     

A study on the anisole-water complex by molecular beam-electronic spectroscopy and molecular mechanics calculations

An experimental and theoretical study is made on the anisole-water complex. It is the first van der Waals complex studied by high resolution electronic spectroscopy in which the water is seen acting as an acid. Vibronically and rotationally resolved electronic spectroscopy experiments and molecular mechanics calculations are used to elucidate the structure of the complex in the ground and first electronic excited state. Some internal dynamics in the system is revealed by high resolution spectroscopy.     

Probing the kinetics in supramolecular chemistry and molecular assembly by microfluidic-NMR spectroscopy

Microfluidic-NMR spectroscopy has been extended to study the kinetics in supramolecular chemistry and molecular assembly. Kinetics of a multicomponent host-guest supramolecular system containing viologen derivatives, β-cyclodextrins and cucurbit [7]urils are studied by a PMMA based microfluidic chip combined with a dedicated transmission line probe for NMR detection. By combining microfluidic technology with NMR spectroscopy, the amount of material required for a full kinetic study could be minimized. This is crucial in supramolecular chemistry, which often involves highly sophisticated and synthetically costly building blocks. The small size of the microfluidic structure is crucial in bringing the time scale for kinetic monitoring down to seconds. At the same time, the transmission line NMR probe provides sufficient sensitivity to work at low (2 mM) concentrations.     

Investigation of the interaction of DNA and neutral red by fluorescence spectroscopic analysis

The binding characteristics of neutral red (NR) with DNA were investigated by fluorescence spectrometry. Chemometrics approach as singular value decomposition (SVD) was used to evaluate the number of spectral species in the drug-DNA binding process, and then the intrinsic binding constant of 1.6 × 104 in base pairs and the binding site number of 0.97 were obtained from the Scatchard plot.     

States of molecular assembly and physical properties of crystalline long-chain compounds studied by vibrational spectroscopy

Various types of molecular assembly of long-chain compounds in solid states were investigated by means of infrared absorption, Raman and Brillouin spectroscopic methods. As for the polymorphism in even-numbered n-fatty acids, three monoclinic modifications, B, C, and E, all consisting of the orthorhombic polyethylene sublattice, give rise to their characteristic infrared and Raman spectra. A dynamical equilibrium between cis and trans conformations of the hydrogen-bonded carboxyl groups in modification C, which is related to the high-temperature stable character of this phase, is reflected to a dramatic change with temperature in the low-frequency Raman spectra. A new type of reversible solid state phase transition was found between two A-type (triclinic) modifications of myristic, palmitic, and stearic acids. The γ→α phase transition of oleic acid was found to be caused by a conformational disordering of polymethylene chains at the lamellar interfacial region. Two basic polytype structures, Mon and Orth II, of stearic acid B were investigated, and it was found that the low-frequency phonon frequencies (below 50 cm⁻¹) were strongly influenced by the polytype structure. Based on the spectroscopic considerations, Orth II was predicted as the thermodynamically stable phase around room temperature compared with Mon, and the stability is responsible for the vibrational free energy term. Some experimental findings which support this prediction were obtained. The values of the stiffness tensor elements of Mon and Orth II, measured by Brillouin scattering, indicate that the mechanical behavior of bulk crystals is very dependent on the polytype structure. The relationship between the mobility of chain molecules and the width of the spectral bands was investigated in a quantitative manner for the case of n-alkane molecules entrapped in the urea inclusion adducts. The changes in the half-width for the polarization components of various Raman bands on the transition from the orthorhombic to the hexagonal phase are interpreted in terms of the correlation functions of the Raman tensor related to the rotational motion of the alkane molecules around the chain axes.     

Investigation of molecular motions of crosslinked polyepichlorohydrin by nuclear magnetic resonance spectroscopy

The molecular motion of crosslinked polyepichlorohydrin (PECH) is studied qualitatively by NMR techniques. The results of temperature dependence of ¹H T₂ and T₁ indicate that the crosslinking (crosslink density < 3%) restricts molecular motions of the polymer even far above its T_g. The ¹H T₁ minimum, corresponding to the large-scale chain-motion of crosslinked PECH, shifts to higher temperatures with increasing crosslink density. ¹H T₂ data also show that the crosslinking hinders free chain motions of the polymer above its T_g. The ¹³C T₁ relaxation time is sensitive to such motional changes as well. ¹³C linewidths of crosslinked PECHs vary with the crosslink density in both the swollen state and the solid state. The mechanism of ¹³C linewidth broadening of crosslinked polymers is discussed in detail. In the case of PECH, the linewidth broadening is caused by changing molecular environment due to crosslinking (such as presence of various chemical shift structures and freezing effects in conformational environment as chain mobility decreases), rather than increasing correlation times, which shorten the relaxation time (T₂) of polymer chains. © 1994 John Wiley & Sons, Inc.     

Investigation of the interaction of DNA and neutral red by?uorescence spectroscopic analysis

The binding characteristics of neutral red (NR) with DNA were investigated by fluorescence spectrometry. Chemometrics approach as singular value decomposition (SVD) was used to evaluate the number of spectral species in the drug-DNA binding process, and then the intrinsic binding constant of 1.6 104 in base pairs and the binding site number of 0.97 were obtained from the Scatchard plot.     

Controlled assembly of mesoscale structures using DNA as molecular bridges

Mesoscale polyhedral structures from binary mixtures of microspheres of specific size ratios were prepared by using DNA as a molecular bridge. Carboxy-modified polystyrene beads were decorated with fluorescently labeled single-stranded DNA via carboxydiimide chemistry. Fluorescent resonance electron transfer in a confocal microscopy setting was utilized to corroborate DNA hybridization. Tetrahedrons were made by combining DNA-containing 0.818 and 0.211 mum beads, while octahedrons were obtained by bridging 0.818 and 0.364 mum beads. Confocal data in the reflection mode and SEM provide evidence for the formation of mesoscale building blocks.     

Internal rotation in enaminonitriles: Investigation by dynamic NMR spectroscopy and molecular modeling

Rotational isomerism in enaminonitriles was studied using dynamic NMR spectroscopy and molecular modeling. It was found that the barrier to rotation about C_vinyl-NH bond was higher for enaminonitriles derived from aliphatic amines than that of enaminonitriles derived from aromatic amines. It was also found that the rotational isomerism about the C_ar-C_vinyl bond also exists in enaminonitriles.     

Resonance Raman spectroscopy of the neutral radical Trp306 in DNA photolyase

The resonance Raman spectrum of the tryptophan neutral radical in a protein, Escherichia coli photolyase, is reported for the first time. The data compare very well to a solution study and computational predictions, and tentative assignments are made for the observed vibrations. This important new result demonstrates the potential of time-resolved resonance Raman spectroscopy as a powerful tool to investigate these radicals in protein electron-transfer processes and in enzymatic reactions in real time.     

Rotational spectroscopy and molecular structure of the 1,1-difluoroethylene-acetylene complex

Fourier transform microwave, rotational spectra in the 6-21 GHz region are obtained for the complex formed between 1,1-difluoroethylene and acetylene, including the normal isotopomer and each singly substituted (13)C species along with complexes derived from commercially available isotopic varieties of acetylene (HCCD, DCCD, and H(13)C(13)CH). Although two possible planar structures are consistent with the rotational constants derived from analysis of the spectra, ab initio calculations, as well as chemical intuition, support only one of the two as the structure of the complex. Nuclear quadrupole coupling constants for D-containing species show no evidence of electric field gradient perturbation and are consistent with the structures obtained from inertial data. The primary interaction between the two molecules is a 2.646(11) A hydrogen bond with acetylene as the donor and a 1,1-difluoroethylene fluorine as the acceptor that forms a 122.41(79) degrees C-Fcdots, three dots, centeredH angle. A secondary interaction between the acetylenic bond and the difluoroethylene hydrogen atom cis to the acceptor fluorine atom causes the hydrogen bond to deviate 53.25(24) degrees from linearity. Structural comparisons with the related complex, 1,1-difluoroethylene-hydrogen chloride [Z. Kisiel et al., J. Chem. Soc., Faraday Trans. 88, 3385 (1992)], suggest that the hydrogen bond in the acetylene complex is weaker, whereas comparisons with vinyl fluoride-acetylene [G. C. Cole and A. C. Legon, Chem. Phys. Lett. 369, 31 (2003)] indicate that the fluorine atoms in 1,1-difluoroethylene are less basic than the one in vinyl fluoride.     

Rotational spectroscopy and molecular structure of the 1,1,2-trifluoroethylene-acetylene complex

Guided by ab initio calculations, Fourier transform microwave rotational spectra in the 6-22 GHz region are obtained for the complex formed between 1,1,2-trifluoroethylene and acetylene, including the normal isotopomer, three of four singly substituted (13)C species obtained in natural abundance, and using commercially available isotopic varieties of acetylene, species containing HCCD and H(13)C(13)CH. Although the ab initio calculations suggest two possible low energy planar arrangements for the molecules in the complex, only a single, unique structure is obtained from a combined analysis of the rotational constants derived from the spectra and atomic positions determined using Kraitchman [Am. J. Phys. 21, 17 (1953)] substitution coordinates. This structure is similar to that obtained for the CF(2)CHF[Single Bond]HF complex [H. O. Leung and M. D. Marshall, J. Chem. Phys. 126, 114310 (2007)] in which both the primary and secondary interactions occur between the HCCH molecule and a F atom and a H atom bonded to the same carbon of CF(2)CHF. The 2.748(15) A hydrogen bond has acetylene as the donor and 1,1,2-trifluoroethylene as the acceptor and forms a 104.49(15) degrees C[Single Bond]Fcdots, three dots, centeredH angle. The 2.8694(9) A secondary interaction between the pi bond of acetylene and the H atom geminal to the acceptor F atom causes the hydrogen bond to deviate 69.24(67) degrees from linearity. This large deviation from linearity and the similarity of the two intermolecular bond lengths suggest that the two interactions are becoming comparable in importance.     

Duocarmycins binding to DNA investigated by molecular simulation

Duocarmycins are a potent class of antitumor agents, whose activity arises through their covalent binding to adenine nucleobases of DNA.(1-3) Here, we perform molecular dynamics (MD) and hybrid Car-Parinello QM/MM simulations to investigate aspects of duocarmycin binding to the d(pGpApCpTpApApTpTpGpApC) oligonucleotide. We focus on the derivatives (+)-duocarmycin SA (DSA) and (+)-duocarmycin SI (DSI), for which structural information of the covalent complex with the oligonucleotide is available, as well as on the related, but less reactive, NBOC-duocarmycin SA (NBOC-DSA), interacting with the same oligonucleotide. Comparison is made with adenine alkylation reaction in water performed by the smallest of these compounds (NBOC-DSA). The MD calculations suggest that, in noncovalent complexes, (i) drug binding causes a partial dehydration of the minor groove, without inducing a significant conformational changes, and (ii) DSA and DSI occupy a more favorable position for nucleophilic attack than NBOC-DSA, consistently with the lower reactivity of the latter. The QM/MM calculations, which are used to investigate the first step of the alkylation reaction, turn out to provide strongly underestimated free energy barriers. Within these approximations, our calculations suggest that an important ingredient for the experimentally observed DNA catalytic power is the polarization of the drug by the biomolecular scaffold.     

De novo design and molecular assembly of a transmembrane diporphyrin-binding protein complex

The de novo design of membrane proteins remains difficult despite recent advances in understanding the factors that drive membrane protein folding and association. We have designed a membrane protein PRIME (PoRphyrins In MEmbrane) that positions two non-natural iron diphenylporphyrins (Fe(III)DPP's) sufficiently close to provide a multicentered pathway for transmembrane electron transfer. Computational methods previously used for the design of multiporphyrin water-soluble helical proteins were extended to this membrane target. Four helices were arranged in a D(2)-symmetrical bundle to bind two Fe(II/III) diphenylporphyrins in a bis-His geometry further stabilized by second-shell hydrogen bonds. UV-vis absorbance, CD spectroscopy, analytical ultracentrifugation, redox potentiometry, and EPR demonstrate that PRIME binds the cofactor with high affinity and specificity in the expected geometry.     

Effect of oligonucleotide length on the assembly of DNA materials: molecular dynamics simulations of layer-by-layer DNA films

DNA strand length has been found to be an important factor in many DNA-based nanoscale systems. Here, we apply molecular dynamics simulations in a synergistic effort with layer-by-layer experimental data to understand the effect of DNA strand length on the assembly of DNA films. The results indicate that short (less than 10 bases) and long (more than 30 bases) single-stranded DNAs do not exhibit optimal film growth, and this can be associated with the limited accessibility of the bases on the surface due to formation of self-protected interactions that prevent efficient hybridization. Interestingly, the presence of a duplex attached to a single strand significantly alters the persistence length of the polyT strands. Our study suggests that restrained polyT, compared to labile suspensions of free polyT, are more capable of hybridization and hence DNA-based assembly.     

Protein assembly directed by synthetic molecular recognition motifs

Tris-functionalized cyanuric acid (TCA) and melamine (TM) selectively recognize each other in aqueous solution with 1 : 1 stoichiometry. We have coupled biotin to TCA and TM to allow pseudo-tetrahedral display of TCA and TM on streptavidin through biotin-ligand binding. Synthetic cyanuric acid/melamine recognition is found to drive selective protein-protein assembly.