Polymorphism of the d(CCCGCGGG)2 double helix studied by FT-i.r. spectroscopy

Plasmid DNA Complexes in Powder Form Studied by Spectroscopic and Diffraction Methods

Currently, new functional materials are being created with a strong emphasis on their ecological aspect. Materials and devices based on DNA biopolymers, being environmentally friendly, are therefore very interesting from the point of view of applications. In this paper, we present the results of research on complexes in the powder form based on plasmid DNA (pDNA) and three surfactants with aliphatic chains containing 16 carbon atoms (cetyltrimethylammonium chloride, benzyldimethylhexadecylammonium chloride and hexadecylpyridinium chloride). The X-ray diffraction results indicate a local hexagonal packing of DNA helices in plasmid DNA complexes, resembling the packing for corresponding complexes based on linear DNA. Based on the Fourier-transform infrared spectroscopy results, the DNA conformation in all three complexes was determined as predominantly of A-type. The two relaxation processes revealed by dielectric spectroscopy for all the studied complexes are connected with two different contributions to total conductivity (crystallite part and grain boundaries). The crystallite part (grain interior) was interpreted as an oscillation of the polar surfactant head groups and is dependent on the conformation of the surfactant chain. The influence of the DNA type on the properties of the complexes is discussed, taking into account our previous results for complexes based on linear DNA. We showed that the type of DNA has an impact on the properties of the complexes, which has not been demonstrated so far. It was also found that the layer of pDNA-surfactant complexes can be used as a layer with variable specific electric conductivity by selecting the frequency, which is interesting from an application point of view.

Experimental detection of conformational transitions between forms of DNA: problems and prospects

Under different conditions, the DNA double helix can take different geometric forms. Of the large number of its conformations, in addition to the "canonical" B form, the A, C, and Z forms are widely known, and the D, Hoogsteen, and X forms are less known. DNA locally takes the A, C, and Z forms in the cell, in complexes with proteins. We compare different methods for detecting non-canonical DNA conformations: X-ray, IR, and Raman spectroscopy, linear and circular dichroism in both the infrared and ultraviolet regions, as well as NMR (measurement of chemical shifts and their anisotropy, scalar and residual dipolar couplings and inter-proton distances from NOESY (nuclear Overhauser effect spectroscopy) data). We discuss the difficulties in applying these methods, the problems of theoretical interpretation of the experimental results, and the prospects for reliable identification of non-canonical DNA conformations.

Assessing B-Z DNA Transitions in Solutions via Infrared Spectroscopy

Z-DNA refers to the left-handed double-helix DNA that has attracted much attention because of its association with some specific biological functions. However, because of its low content and unstable conformation, Z-DNA is normally difficult to observe or identify. Up to now, there has been a lack of unified or standard analytical methods among diverse techniques for probing Z-DNA and its transformation conveniently. In this work, NaCl, MgCl₂, and ethanol were utilized to induce d(GC)₈ from B-DNA to Z-DNA in vitro, and Fourier transform infrared (FTIR) spectroscopy was employed to monitor the transformation of Z-DNA under different induction conditions. The structural changes during the transformation process were carefully examined, and the DNA chirality alterations were validated by the circular dichroism (CD) measurements. The Z-DNA characteristic signals in the 1450 cm^-1-900 cm^-1 region of the d(GC)₈ infrared (IR) spectrum were observed, which include the peaks at 1320 cm^-1, 1125 cm^-1 and 925 cm^-1, respectively. The intensity ratios of A₁₃₂₀/A₉₇₀, A₁₁₂₅/A₉₇₀, and A₉₂₅/A₉₇₀ increased with Z-DNA content in the transition process. Furthermore, compared with the CD spectra, the IR spectra showed higher sensitivity to Z-DNA, providing more information about the molecular structure change of DNA. Therefore, this study has established a more reliable FTIR analytical approach to assess BZ DNA conformational changes in solutions, which may help the understanding of the Z-DNA transition mechanism and promote the study of Z-DNA functions in biological systems.

Application of FTIR Spectroscopy to Detect Changes in Skeletal Muscle Composition Due to Obesity with Insulin Resistance and STZ-Induced Diabetes

Age, obesity, and diabetes mellitus are pathophysiologically interconnected factors that significantly contribute to the global burden of non-communicable diseases. These metabolic conditions are associated with impaired insulin function, which disrupts the metabolism of carbohydrates, lipids, and proteins and can lead to structural and functional changes in skeletal muscle. Therefore, the alterations in the macromolecular composition of skeletal muscle may provide an indication of the underlying mechanisms of insulin-related disorders. The aim of this study was to investigate the potential of Fourier transform infrared (FTIR) spectroscopy to reveal the changes in macromolecular composition in weight-bearing and non-weight-bearing muscles of old, obese, insulin-resistant, and young streptozotocin (STZ)-induced diabetic mice. The efficiency of FTIR spectroscopy was evaluated by comparison with the results of gold-standard histochemical techniques. The differences in biomolecular phenotypes and the alterations in muscle composition in relation to their functional properties observed from FTIR spectra suggest that FTIR spectroscopy can detect most of the changes observed in muscle tissue by histochemical analyses and more. Therefore, it could be used as an effective alternative because it allows for the complete characterization of macromolecular composition in a single, relatively simple experiment, avoiding some obvious drawbacks of histochemical methods.

Remodeling Chromatin Induces Z-DNA Conformation Detected through Fourier Transform Infrared Spectroscopy

The SWI/SNF complex is a highly conserved chromatin remodeling complex and can hydrolyze ATP by its catalytic subunit BRG1 or BRM to reconstruct the chromatin. To investigate whether this ATP-dependent chromatin remodeling could affect the DNA conformation, we therefore regulated (knocked down or overexpressed) BRG1/BRM in the cells and applied Fourier transform infrared (FTIR) spectroscopy to probe DNA conformational changes. As a result, we found that BRG1/BRM was indeed associated with the DNA conformational changes, in which knockdown of BRG1/BRM reduced Z-DNA conformation, while overexpression of BRG1/BRM enhanced Z-DNA conformation. This Z-DNA conformational transformation was also verified using the Z-DNA-binding proteins. Therefore, this work has provided a direct analytical tool to probe Z-DNA transformation upon ATP-dependent chromatin remodeling.

Assessment of Genetic Relationships between Streptocarpus x hybridus V. Parents and F1 Progenies Using SRAP Markers and FT-IR Spectroscopy

The genetic relationship among three Streptocarpus parents and twelve F1 hybrids was assessed using sequence-related amplified polymorphism (SRAP) molecular markers and Fourier-transform infrared (FT-IR) spectroscopy. Both methods were able to discriminate F1 hybrids and parents as revealed by cluster analysis. For hybrid identification, the type III SRAP marker was the most effective due to the presence of male-specific bands in the hybrids. Different behaviors in the biochemical variability of DNA samples have been observed by FT-IR spectral analysis, which might be attributed to the inherent nature of the genomic DNA from parents and their F1 progenies. Mantel test was also carried out to compare morphological, SRAP, and FT-IR results based on genetic distances. The highest correlation coefficient was found between morphological and SRAP marker distances (R = 0.607; p ≤ 0.022). A lower correlation was observed between the morphological and FT-IR distance matrix (R = 0.231; p ≤0.008). Moreover, a positive correlation was found between the distances generated with SRAP and FT-IR analyses (R = 0.026) but was not statistically significant. These findings show that both SRAP and FT-IR techniques combined with morphological descriptions can be used effectively for nonconventional breeding programs for Streptocarpus to obtain new and valuable varieties.

Robust IR-based detection of stable and fractionally populated G-C+ and A-T Hoogsteen base pairs in duplex DNA

Noncanonical G-C+ and A-T Hoogsteen base pairs can form in duplex DNA and play roles in recognition, damage repair, and replication. Identifying Hoogsteen base pairs in DNA duplexes remains challenging due to difficulties in resolving syn versus antipurine bases with X-ray crystallography; and size limitations and line broadening can make them difficult to characterize by NMR spectroscopy. Here, we show how infrared (IR) spectroscopy can identify G-C+ and A-T Hoogsteen base pairs in duplex DNA across a range of different structural contexts. The utility of IR-based detection of Hoogsteen base pairs is demonstrated by characterizing the first example of adjacent A-T and G-C+ Hoogsteen base pairs in a DNA duplex where severe broadening complicates detection with NMR.

Enantioselective recognition mechanism of ofloxacin via Cu(II)-modulated DNA

The specific interactions of Cu(2+) with self-complementary DNA sequences involving d[G4C4(GC)2G4C4], d[(GC)10], and d[(AT)10], as well as the chiral recognition mechanism of ofloxacin enantiomers via the Cu(II)-modulated DNAs, were investigated using characterizations of circular dichroism, gel electrophoresis, FT-IR spectroscopy, UV melting measurement, electron paramagnetic resonance, and HPLC. The Cu(II)-coordinated GC-rich DNAs exhibit amplified enantioselectivity toward the S-enantiomer of ofloxacin. Especially in the case of d[G4C4(GC)2G4C4], ofloxacin enantiomers intercalate into the two adjacent guanine bases through the minor groove mediated by Cu(2+), which leads to a more favorable binding between S-ofloxacin and DNA. The highest ee value of ofloxacin enantiomers in the permeate after being adsorbed by the Cu(II)-DNA complex is obtained as 49.2% in the R-enantiomer at the [Cu(2+)]/[base] molar ratio of 0.25, while at the [Cu(2+)]/[base] molar ratio of 0.05 the highest ee value of ofloxacin enantiomers in the retentate reaches 26.3% in the S-enantiomer. This work illustrates a novel promising route to construct DNA-based chiral selectors toward certain drug enantiomers through the programmable enantioselective recognition on the basis of DNA chirality and the specific binding of transition metal ions.

Strain dependent UV degradation of Escherichia coli DNA monitored by Fourier transform infrared spectroscopy

In this work we present a method for detection of DNA isolated from nonpathogenic Escherichia coli strains, respectively. Untreated and UV irradiated bacterial DNAs were analyzed by FT-IR spectroscopy, to investigate their screening characteristic features and their structural radiotolerance at 253.7nm. FT-IR spectra, providing a high molecular structural information, have been analyzed in the wavenumber range 800-1800cm(-1). FT-IR signatures, spectroscopic band assignments and structural interpretations of these DNAs are reported. Also, UV damage at the DNA molecular level is of interest. Strain dependent UV degradation of DNA from E. coli has been observed. Particularly, alterations in nucleic acid bases, base pairing and base stacking have been found. Also changes in the DNA conformation and deoxyribose were detected. Based on this work, specific E. coli DNA-ligand interactions, drug development and vaccine design for a better understanding of the infection mechanism caused by an interference between pathogenic and nonpathogenic bacteria and for a better control of disease, respectively, might be further investigated using Fourier transform infrared spectroscopy. Besides, understanding the pathways for UV damaged DNA response, like nucleic acids repair mechanisms is appreciated.

Ordered self-assembled locked nucleic acid (LNA) structures on gold(111) surface with enhanced single base mismatch recognition capability

Locked nucleic acid (LNA) is a conformationally restricted nucleic acid analogue, which is potentially a better alternative than DNA for application in the nucleic acid based biosensor technologies, due to its efficient and sequence-specific DNA/RNA detection capability and lack of molecule-surface interaction on solid surfaces, compared to DNA. We report, for the first time, a straightforward way (based on simple immersion method) of generating an ordered self-assembled LNA monolayer, which is bioactive, onto a gold(111) surface. This layer is capable of giving rise to a stronger DNA recognition signal (4-4.5 times) than its DNA counterpart, and importantly, it can differentiate between a fully complementary DNA target and that having a single base mismatch, where the mismatch discrimination ratio is almost two times compared to the ratio relevant in case of DNA-based detection. We have presented high-resolution atomic force microscopy (AFM) topographs of the well-defined one-dimensional LNA molecular ordering (few hundred nanometers long) and of the two-dimensional ordered assembly formed over a large area (7 μm × 7 μm) due to parallel positioning of the one-dimensional ordered arrangements. The effects of different parameters such as LNA concentration and incubation time on LNA self-assembly have been investigated. Further, reflection absorption infrared (RAIR) spectroscopy has been applied to obtain information about the orientation of the surface-immobilized LNA molecules for the first time. It has been found that the LNA molecules undergo an orientational transition from the "lying down" to the "upright" configuration in a time scale of few hours.

Conformational transitions of glycine induced by vibrational excitation of the O-H stretch

Vibrational energy flow and conformational transitions following excitation of the OH stretching mode of the most stable conformer of glycine are studied by classical trajectories. "On the fly" simulations with the PM3 semiempirical electronic structure method for the potential surface are used. Initial conditions are selected to correspond to the ν=1 excitation of the OH stretch. The main findings are: (1) An an equilibrium-like ratio is established between the populations of the 3 lowest-lying conformers after about 10 picoseconds. (2) There is a high probability throughout the 150 ps of the simulations for finding the molecule in geometries far from the equilibrium structures of the lowest-energy conformers. (3) Energy from the initial excited OH (ν=1) stretch flows preferentially to 5 other vibrational modes, including the bending motion of the H atom. (4) RRK theory yields conformational transition rates that deviate substantially from the classical trajectory results. Possible implication of these results for vibrational energy flow and conformational transitions in small biological molecules are discussed.

Theoretical spectroscopy of floppy peptides at room temperature. A DFTMD perspective: gas and aqueous phase

Theoretical spectroscopy is mandatory for a precise understanding and assignment of experimental spectra recorded at finite temperature. We review here room temperature DFT-based molecular dynamics simulations for the purpose of interpreting finite temperature infrared spectra of peptides of increasing size and complexity, in terms of temperature-dependent conformational dynamics and flexibility, and vibrational anharmonicities (potential energy surface anharmonicities, vibrational mode couplings and dipole anharmonicities). We take examples from our research projects in order to illustrate the main key-points and strengths of dynamical spectra modeling in that context. The calculations are presented in relation to room temperature gas phase IR-MPD experiments and room temperature liquid phase IR absorption experiments. These illustrations of floppy polypeptides have been chosen in order to convey the following ideas: temperature-dependent spectra modeling is pivotal for a precise understanding of gas phase spectra recorded at room temperature, including conformational dynamics and vibrational anharmonicities; harmonic spectroscopy (as commonly performed in the literature) can be misleading and even erroneous for a proper interpretation of spectra recorded at finite temperature; taking into account vibrational anharmonicities is pivotal for a proper interplay between theory and experiments; amide I-III bands are not necessarily the most relevant fingerprints for unraveling the local structures of peptides and more complex systems; liquid phase simulations have unraveled relationships between the zwitterionic properties of the peptide bonds and infrared signatures. The review presents a state-of-the-art account of the domain and offers perspectives and new developments for future still more challenging applications.

Alanine polypeptide structural fingerprints at room temperature: what can be gained from non-harmonic Car-Parrinello molecular dynamics simulations

Structural infrared fingerprints of neutral gas phase alanine peptides of increasing size and complexity (dipeptide, octapeptide, and beta-strand peptide) are characterized through DFT-based Car-Parrinello molecular dynamics simulations. Harmonic and nonharmonic vibrational signatures are calculated from the time correlation of the dipole moment of the gas phase peptide in a direct way (without any approximation) respectively from low temperature (20 K) and room temperature (300 K) molecular dynamics. Our main purpose is to answer the two following questions: (i) Is the direct inclusion of temperature for the calculation of infrared spectra mandatory for the comprehension of the vibrational signatures experimentally recorded at room temperature? (ii) To what extent is the amide I, II, and III domain sensitive enough to the local structure of the peptides, to provide vibrational signatures that can be definitely used to assess the peptide conformation at 300 K?

Characterization of an RNA bulge structure by Fourier transform infrared spectroscopy

There may be several advantages associated with an antisense oligonucleotide that induces a bulged structure into its RNA target molecule. Many structures of RNA bulges are elucidated from single-stranded RNA models. However, a two-component system is the minimum requirement for a realistic antisense model. We have used Fourier transform infrared spectroscopy to investigate a single-stranded RNA oligonucleotide with known NMR solution structure, constructed to model a five nucleotide bulge, and its two-component oligonucleotide counterpart. The infrared spectra show A-helical base-paired stems and non-base-paired loops in both systems. The nucleosides are mainly in an anti-conformation. Both N-type and S-type of sugar puckers can be inferred from the infrared region sensitive to sugar conformations. The S-type of sugar pucker is likely to be associated with the nucleotides in the bulge. The FTIR results display an overall structural similarity between the two model systems.

A library of IR bands of nucleic acids in solution

This review presents a compilation and discussion of infrared (IR) bands characteristic of nucleic acids in various conformations. The entire spectral range 1800-800 cm(-1) relevant for DNA/RNA in aqueous solution has been subdivided into four sections. Each section contains descriptions of bands appearing from group specific parts of nucleic acid structure, such as nucleobase, base-sugar, sugar-phosphate and sugar moiety. The approach allows comparisons of information obtained from one spectral region with another. The IR band library should facilitate detailed and unambiguous assignment of structural changes, ligand binding, etc. in nucleic acids from IR spectra. is aimed at highlighting specific features that are useful for following major changes in nucleic acid structures. also concerns some recent results, where IR spectroscopy has been used to obtain semi-quantitative information on coexisting modes of sugar pucker in oligonucleotides.

Structural effects of cytosine methylation on DNA sugar pucker studied by FTIR

This FTIR investigation concerns structural consequences of 5-methylation of cytosine in a DNA decamer in solution. Methylation of DNA is an important functional signal in transcription, but its effect on DNA structure is variable and not fully understood. Here, single and multiple 5-methylcytosine substitutions are introduced into the self-complementary sequence d(CCGGCGCCGG)(2). No major structural effect of methylation on the DNA duplex in solution is seen in the IR spectra: The overall B-form character of the backbone and S-type of sugar puckering are maintained in all the studied sequences, in agreement with previous literature. However, certain significant effects are detected in the IR regions sensitive to sugar pucker and glycosidic torsional angle. A single or multiple 5-methylcytosine substitution in d(CCGGCGCCGG)(2) leads to a doublet splitting of the S-type 840-820 cm(-1) sugar conformational band. The results suggest the coexistence of two different major sugar puckers within the S-conformational family, with an increased relative contribution of the C2'-endo type of sugar in the methylated sequences. In addition, a partial or full downshift of the guanosine/anti marker band at 1,375 cm(-1) in the methylated sequences reflects a change in the value of the dihedral angle chi of guanosine upon methylation. The IR spectra are interpreted in terms of localized transitions between the BI and BII subconformational states of the B-DNA backbone caused by the methylation. An increased amount of the BII subconformer in the methylated sequences should give rise to a structurally more rigid conformation, in agreement with earlier observations on DNA backbone dynamics and bending flexibility in methylated DNA.

A and Z canonical conformations in d(CnGCGn) crystals characterized by microFTIR and microRaman spectroscopies

Two crystals d(C2GCG2) and d(C5GCG5) have been studied under microscope by Fourier transform ir spectroscopy and Raman spectroscopy. The x-ray diffraction study of the latter crystal had shown that the d(C5GCG5) sequence is the first DNA dodecamer known to adopt a canonical A conformation [N. Verdaguer, J. Aymami, D. Fernandez-Forner, I. Fita, M. Coll, T. Huynh-Dinh, J. Igolen, and J. A. Subirana (1991) Journal of Molecular Biology, Vol. 221, pp. 623-635]. Characteristic ir marker bands and Raman marker peaks of the A conformation have thus been obtained and are compared with previously proposed assignments correlated to fiber diffraction x-ray results obtained on polymers. The d(C2GCG2) sequence crystal had previously been studied in an intermediate form between B and Z [L. Urpi, J. P. Ridoux, J. Liquier, N. Verdagner, I. Fita, J. A. Subirana, F. Iglesias, T. Huynh-Dinh, J. Igolen, and E. Taillandier (1989) Nucleic Acids Research, Vol. 17, pp. 6669-6679]. In this paper we present results obtained from a crystal with this oligonucleotide in Z conformation. The effect of the crystallization conditions on the geometry of the obtained oligomer helix is discussed. The influence of the addition, to the central tetramer CGCG, of dCn stretches (at the 5' end) and dGn stretches (at the 3' end) of different lengths, on the conformational flexibility of the nucleic acid, is considered.