Effects of hydrogen bonding on the UV resonance Raman bands of the adenine ring and its C8-deuterated analog

Local and cooperative structural transitions of double-stranded DNA in choline-based deep eutectic solvents

The possibility of using deep eutectic solvents (DESs) as co-solvents for stabilizing and preserving the native structure of DNA provides an attractive opportunity in the field of DNA biotechnology. The rationale of this work is a systematic investigation of the effect of hydrated choline-based DES on the structural stability of a 30-base-pair double-stranded DNA model via a combination of spectroscopic experiments and MD simulations. UV absorption and CD experiments provide evidence of a significant contribution of DESs to the stabilization of the double-stranded canonical (B-form) DNA structure. Multi-wavelength synchrotron UV Resonance Raman (UVRR) measurements indicate that the hydration shell of adenine-thymine pairs is strongly perturbed in the presence of DESs and that the preferential interaction between H-bond sites of guanine residues and DESs is significantly involved in the stabilization of the dsDNA. Finally, MD calculations show that the minor groove of DNA is significantly selective for the choline part of the investigated DESs compared to the major groove. This finding is likely to have a significant impact not only in terms of thermal stability but also in the modulation of ligand-DNA interactions.

Hexahelicene DNA-binding: Minor groove selectivity, semi-intercalation and chiral recognition

In this contribution, we focused on a fundamental study targeting the interaction of water-soluble [6]helicene derivative 1 (1-butyl-3-(2-methyl[6]helicenyl)-imidazolium bromide) with double-stranded (ds) DNA. A synthetic 30-base pair duplex, plasmid, chromosomal calf thymus and salmon DNA were investigated using electrochemistry, electrophoresis and spectroscopic tools supported by molecular dynamics (MD) and quantum mechanical approaches. Both experimental and theoretical work revealed the minor groove binding of 1 to the dsDNA. Both the positively charged imidazole ring and hydrophobic part of the side chain contributed to the accommodation of 1 into the dsDNA structure. Neither intercalation into the duplex DNA nor the stable binding of 1 to single-stranded DNA were found in topoisomerase relaxation experiments with structural components of 1, i.e. [6]helicene (2) and 1-butyl-3-methylimidazolium bromide (3), nor by theoretical calculations. Finally, the binding of optically pure enantiomers (P)-1 and (M)-1 was studied using circular dichroism spectroscopy, isothermal titration calorimetry and UV Resonance Raman (UVRR) methods. Using MD and quantum mechanical methods, minor groove and semi-intercalation were proposed for compound 1 as the predominant binding modes. From the UVRR findings, we also can conclude that 1 tends to preferentially interact with adenine and guanine residues in the structure of dsDNA.

Insight into the thermal stability of DNA in hydrated ionic liquids from multi-wavelength UV resonance Raman experiments

The utility of ionic liquids (ILs) as alternative solvents for stabilizing and preserving the native structure of DNA over the long term may be envisaged for biotechnological and biomedical applications in the near future. The delicate balance between the stabilizing and destabilizing effects of IL-mediated interactions with the structure of DNA is complex and is still not well understood. This work reports a fundamental study dealing with the effect exerted by cations and anions in imidazolium-based ILs on the thermal structural stability of large nucleic acid molecules. Multi-wavelength UV resonance Raman spectroscopy is used for selectively detecting heat-induced structural transitions of DNA localized on specific base tracts. Our study reveals the establishment of preferential interactions between the imidazolium cations of ILs and the guanine bases in the DNA groove that lead to more effective stacking between the guanine bases even at high temperatures. Interestingly, we observe that this trend for ILs sharing the same chloride anion is further enhanced as the alkyl chain on the imidazolium cation gets shorter. The results from the present investigation lead to a more comprehensive view of the IL-mediated interactions with A-T and G-C base pairs during thermal unfolding.

Proton Transfer Accompanied by the Oxidation of Adenosine

Despite numerous experimental and theoretical studies, the proton transfer accompanying the oxidation of 2'-deoxyadenosine 5'-monophosphate 2'-deoxyadenosine 5'-monophosphate (5'-dAMP, A) is still under debate. To address this issue, we have investigated the oxidation of A in acidic and neutral solutions by using transient absorption (TA) and time-resolved resonance Raman (TR³ ) spectroscopic methods in combination with pulse radiolysis. The steady-state Raman signal of A was significantly affected by the solution pH, but not by the concentration of adenosine (2-50 mm). More specifically, the A in acidic and neutral solutions exists in its protonated (AH⁺ (N1+H⁺ )) and neutral (A) forms, respectively. On the one hand, the TA spectral changes observed at neutral pH revealed that the radical cation (A^.+ ) generated by pulse radiolysis is rapidly converted into A^. (N6-H) through the loss of an imino proton from N6. In contrast, at acidic pH (<4), AH^.2+ (N1+H⁺ ) generated by pulse radiolysis of AH⁺ (N1+H⁺ ) does not undergo the deprotonation process owing to the pK_a value of AH^.2+ (N1+H⁺ ), which is higher than the solution pH. Furthermore, the results presented in this study have demonstrated that A, AH⁺ (N1+H⁺ ), and their radical species exist as monomers in the concentration range of 2-50 mm. Compared with the Raman bands of AH⁺ (N1+H⁺ ), the TR³ bands of AH^.2+ (N1+H⁺ ) are significantly down-shifted, indicating a decrease in the bond order of the pyrimidine and imidazole rings due to the resonance structure of AH^.2+ (N1+H⁺ ). Meanwhile, A^. (N6-H) does not show a Raman band corresponding to the pyrimidine+NH₂ scissoring vibration due to diprotonation at the N6 position. These results support the final products generated by the oxidation of adenosine in acidic and neutral solutions being AH^.2+ (N1+H⁺ ) and A^. (N6-H), respectively.

Ultrafast structural dynamics of photoexcited adenine

Ultraviolet Resonance Raman (UVRR) spectroscopy derives distinct electronic properties of adenine in the L_a (260 nm) and B_b (210 nm) excited states.

Fast Optical Chemical and Structural Classification of RNA

As more biological activities of ribonucleic acids continue to emerge, the development of efficient analytical tools for RNA identification and characterization is necessary to acquire an in-depth understanding of their functions and chemical properties. Herein, we demonstrate the capacity of label-free direct surface-enhanced Raman scattering (SERS) analysis to access highly specific structural information on RNAs at the ultrasensitive level. This includes the recognition of distinctive vibrational features of RNAs organized into a variety of conformations (micro-, fully complementary duplex-, small interfering- and short hairpin-RNAs) or characterized by subtle chemical differences (single-base variances, nucleobase modifications and backbone composition). This method represents a key advance in the ribonucleic acid analysis and will have a direct impact in a wide range of different fields, including medical diagnosis, drug design, and biotechnology, by enabling the rapid, high-throughput, simple, and low-cost identification and classification of structurally similar RNAs.

Raman characterization of Avocado Sunblotch viroid and its response to external perturbations and self-cleavage

Background

Viroids are the smallest pathogens of plants. To date the structural and conformational details of the cleavage of Avocado sunblotch viroid (ASBVd) and the catalytic role of Mg²⁺ ions in efficient self-cleavage are of crucial interest.

Results

We report the first Raman characterization of the structure and activity of ASBVd, for plus and minus viroid strands. Both strands exhibit a typical A-type RNA conformation with an ordered double-helical content and a C3′-endo/anti sugar pucker configuration, although small but specific differences are found in the sugar puckering and base-stacking regions. The ASBVd(-) is shown to self-cleave 3.5 times more actively than ASBVd(+). Deuteration and temperature increase perturb differently the double-helical content and the phosphodiester conformation, as revealed by corresponding characteristic Raman spectral changes. Our data suggest that the structure rigidity and stability are higher and the D₂O accessibility to H-bonding network is lower for ASBVd(+) than for ASBVd(-). Remarkably, the Mg²⁺-activated self-cleavage of the viroid does not induce any significant alterations of the secondary viroid structure, as evidenced from the absence of intensity changes of Raman marker bands that, however exhibit small but noticeable frequency downshifts suggesting several minor changes in phosphodioxy, internal loops and hairpins of the cleaved viroids.

Conclusions

Our results demonstrate the sensitivity of Raman spectroscopy in monitoring structural and conformational changes of the viroid and constitute the basis for further studies of its interactions with therapeutic agents and cell membranes.

Molecular Imprinting of Tri-O-Acetyladenosine for the Synthetic Imitation of an ATP-Binding Cleft in Protein Kinases

A number of diseases, including cancer, diabetes, and inflammation, are linked to deregulation of cell signaling pathways controlled by protein kinases. Inhibition of the kinases involved can interrupt aberrant signaling and have a specific therapeutic effect. Protein kinases are recognized as validated therapeutic targets for the treatment of a number of diseases and there are considerable efforts to discover new kinase inhibitors suitable for drug development. The main goal of this study was to fabricate the synthetic imitations of the adenosine triphosphate (ATP) binding cleft in protein kinases and thus produce polymers suitable for screening and isolation of new protein kinase ATP-mimetic inhibitors from different sources. Such polymers were created by the imprinting of tri-O-acetyladenosine in acrylic polymer matrix with the use of methacrylic acid (MAA) or 3-vinylbenzoic acid (VBA) as a functional monomer and ethylene glycol dimethacrylate as a cross-linking agent. The imprints prepared with the use of VBA demonstrate substantially better binding efficiency than that with MAA and particularly high affinity to the initial template (K_d as low as 1.2 μM), sufficient concentration of binding sites N (up to 32 μmol g^-1 ), and pronounced specificity (imprinting factor up to 11). Under flow conditions, the fabricated polymers also demonstrate high capacity and template affinity. The produced imprints reproduce spatially noncovalent interactions present in the ATP binding site of protein kinases and can be anticipated as approximate synthetic imitations of the binding cleft.

The dependence of thymine and thymidine Raman spectra on solvent

Recent work has focused on developing Raman spectroscopy as a noninvasive probe of DNA interactions with solvents, intercalants, proteins, and other ligands. Here, we report the Raman spectra of thymine in eight solvents and thymidine in nine solvents obtained with visible excitation. Raman spectra under acidic, neutral, and basic conditions were also obtained of both thymine and thymidine. Changes in both the frequencies and intensities of several of the vibrational bands in the 800–1800 cm–1 region are observed. No evidence of deprotonation in the different solvents is observed for either thymine or thymidine. Correlations of the observed frequency shifts of specific vibrational modes with characteristic properties of the solvent for both thymine and thymidine show a significant correlation with acceptor and donor numbers, measures of the hydrogen-bonding ability of the solvent, in both thymine and thymidine. These results are interpreted in terms of hydrogen-bonding interactions between the N-H protons of the thymine base and lone pairs of electrons on the solvent molecules and between the solvent hydrogens and lone pairs on C=O sites. The solvent-dependent intensity in vibrational bands of thymine between 1500 and 1800 cm–1 indicates a strong interaction between thymine and solvent at the C=O and N-H sites that leads to separation of the C=O stretches from the C=C stretch. The intensity variations with solvent were much smaller for thymidine than for thymine, perhaps as a result of replacing the N1 proton by the sugar. These results suggest that Raman spectroscopy is uniquely sensitive to specific interactions of thymine and thymidine with their environment.Key words: Raman spectroscopy, thymine, thymidine, solvent effects, hydrogen bonding.

Binding modes of cyclic AMP and environments of tryptophan residues in 1:1 and 1:2 complexes of cyclic AMP receptor protein and cyclic AMP

Cyclic AMP (cAMP) receptor protein (CRP) forms 1:1 and 1:2 complexes with cAMP, and the former complex is considered to be the most active form of CRP in binding to specific DNA sequences and in modulating gene transcription by RNA polymerases. We examine the cAMP binding modes and structural changes of CRP upon cAMP binding by UV resonance Raman spectroscopy. The Raman spectra of CRP-(cAMP)(1) and CRP-(cAMP)(2) extracted from those of CRP-cAMP mixtures at varied mixing ratios clearly show that the hydrogen bonding state and the conformation of cAMP in both complexes in solution are very similar to those found in the X-ray crystal structure of CRP-(cAMP)(2), which is evidence that the cAMP binding mode does not differ between the two complexes. The environmental hydrophobicity of Trp85 monitored by UV resonance Raman intensity shows a significant decrease upon binding of the first cAMP molecule, whereas no further change occurs in the second cAMP binding step. The environmental change of Trp85 suggests an opening of the cleft between the N-terminal cAMP and C-terminal DNA binding domains in the process of CRP activation by binding of a single cAMP molecule.

Temperature dependence of the Raman spectrum of DNA. II. Raman signatures of premelting and melting transitions of poly(dA).poly(dT) and comparison with poly(dA-dT).poly(dA-dT)

The temperature dependence of the Raman spectrum of poly(dA).poly(dT) (dA: deoxyadenosine; dT: thymidine), a model for DNA containing consecutive adenine.thymine (A.T) pairs, has been analyzed using a spectrometer of high spectral precision and sensitivity. Three temperature intervals are distinguished: (a) premelting (10 < t < 70 degrees C), in which the native double helix is structurally altered but not dissociated into single strands; (b) melting (70 < t < 80 degrees C), in which the duplex is dissociated into single strands; and (c) postmelting (80 < t degrees C), in which no significant structural change can be detected. The distinctive Raman difference signatures observed between 10 and 70 degrees C and between 70 and 80 degrees C are interpreted in terms of the structural changes specific to premelting and melting transitions, respectively. Premelting alters the low-temperature conformation of the deoxyribose-phosphate backbone and eliminates base hydrogen bonding that is distinct from canonical Watson-Crick hydrogen bonding; these premelting perturbations occur without disruption of base stacking. Conversely, melting eliminates canonical Watson-Crick pairing and base stacking. The results are compared with those reported previously on poly(dA-dT).poly(dA-dT), the DNA structure consisting of alternating A.T and T.A pairs (L. Movileanu, J. M. Benevides, and G. J. Thomas, Jr. Journal of Raman Spectroscopy, 1999, Vol. 30, pp. 637-649). Poly(dA).poly(dT) and poly(dA-dT).poly(dA-dT) exhibit strikingly dissimilar temperature-dependent Raman profiles prior to the onset of melting. However, the two duplexes exhibit very similar melting transitions, including the same Raman indicators of ruptured Watson-Crick pairing, base unstacking and collapse of backbone order. A detailed analysis of the data provides a comprehensive Raman assignment scheme for adenosine and thymidine residues of B-DNA, delineates Raman markers diagnostic of consecutive A.T and alternating A.T/T.A tracts of DNA, and identifies the distinct Raman difference signatures for premelting and melting transitions in the two types of sequences.