Drastic stability change of X-X mismatch in d(CXG) trinucleotide repeat disorders under molecular crowding condition.

The trinucleotide repeat d(CXG) (X = A, C, G or T) is the most common sequence causing repeat expansion disorders. The formation of non-canonical structures, such as hairpin structures with X-X mismatches, has been proposed to affect gene expression and regulation, which are important in pathological studies of these devastating neurological diseases. However, little information is available regarding the thermodynamics of the repeat sequence under crowded cellular conditions where many non-canonical structures such as G-quadruplexes are highly stabilized, while duplexes are destabilised. In this study, we investigated the different stabilities of X-X mismatches in the context of internal d(CXG) self-complementary sequences in an environment with a high concentration of cosolutes to mimic the crowding conditions in cells. The stabilities of full-matched duplexes and duplexes with A-A, G-G, and T-T mismatched base pairs under molecular crowding conditions were notably decreased compared to under dilute conditions. However, the stability of the DNA duplex with a C-C mismatch base pair was only slightly destabilised. Investigating different stabilities of X-X mismatches in d(CXG) sequences is important for improving our understanding of the formation and transition of multiple non-canonical structures in trinucleotide repeat diseases, and may provide insights for pathological studies and drug development.

DNA sensor's selectivity enhancement and protection from contaminating nucleases due to a hydrated ionic liquid.

The thermodynamic stability of certain mismatched base pairs has made the development of DNA sequence sensing systems challenging. Thus, the stability of fully matched and mismatched DNA oligonucleotides in the hydrated ionic liquid choline dihydrogen phosphate (choline dhp) was investigated. Mismatched base pairs were significantly destabilized in choline dhp relative to those in aqueous buffer. A molecular beacon that forms a triplex with a conserved HIV-1 sequence was then designed and tested in choline dhp. The molecular beacon specifically detected the target duplex via triplex formation at concentrations as low as 1 pmol per 10 µL with 10,000-fold sequence selectivity. Moreover, the molecular beacon was protected from a contaminating nuclease in choline dhp, and DNAs in aqueous solutions were not sufficiently stable for practical use.

i-Motifs are more stable than G-quadruplexes in a hydrated ionic liquid.

Thermodynamic analyses and molecular dynamics calculations demonstrated that i-motifs in a hydrated ionic liquid of choline dihydrogen phosphate (choline dhp) were more stable than G-quadruplexes due to choline ion binding to loop regions in the i-motifs. Interestingly, the i-motifs formed even at physiological pH in the choline dhp-containing solution.

Organelle-mimicking liposome dissociates G-quadruplexes and facilitates transcription.

Important biological reactions involving nucleic acids occur near the surface of membranes such as the nuclear membrane (NM) and rough endoplasmic reticulum (ER); however, the interactions between biomembranes and nucleic acids are poorly understood. We report here that transcription was facilitated in solution with liposomes, which mimic a biomembrane surface, relative to the reaction in a homogeneous aqueous solution when the template was able to form a G-quadruplex. The G-quadruplex is known to be an inhibitor of transcription, but the stability of the G-quadruplex was decreased at the liposome surface because of unfavourable enthalpy. The destabilization of the G-quadruplex was greater at the surface of NM- and ER-mimicking liposomes than at the surfaces of liposomes designed to mimic other organelles. Thermodynamic analyses revealed that the G-rich oligonucleotides adopted an extended structure at the liposome surface, whereas in solution the compact G-quadruplex was formed. Our data suggest that changes in structure and stability of nucleic acids regulate biological reactions at membrane surfaces.

Dangling ends perturb the stability of RNA duplexes responsive to surrounding conditions.

Unpaired terminal nucleotides (dangling ends) occur in various biologically important RNA structures. We studied the thermal stability of RNA duplexes with dangling ends under conditions that mimic those in cells. Dangling ends of one or two nucleotides stabilized a duplex up to approximately 2.7 kcal mol(-1) in the absence of cosolutes. RNA duplexes with dangling purine nucleotides were more stable than those with pyrimidine nucleotides. Interestingly, in the presence of various cosolutes, RNA duplexes with purine dangling ends were significantly destabilized, although those with pyrimidine dangling ends were destabilized slightly. For example, in 30 wt % poly(ethylene glycol), stabilization resulting from adenine dangling ends was reduced by 1.4 kcal mol(-1) . Our quantitative analyses also showed that the number of water molecules bound to the dangling ends in an aqueous solution was independent of the nucleotide type but dependent on the stability of the dangling-end region. It has been considered that dangling ends stabilize helices; however, our results suggest that the stabilization is responsive to the surrounding conditions.

Facile room temperature synthesis of lanthanum oxalate nanorods and their interaction with antioxidative naphthalimide derivative.

Polycrystalline lanthanum oxalate (LaOX) nanorods (NRs) were succesfully synthesized using reverse micellar (RM) method. The study espouses the versatility of the reverse micellar method forming monodisperse, stable nanorods at room temperature. The as-synthesized LaOX nanorods were characterised by different techniques. Result shows that the nanorods of LaOX with aspect ratio 10.2:1 have preferred growth direction of (020). The pure phase synthesis of the nanorods was confirmed from Fourier transformed infrared (FTIR) and X-ray diffraction (XRD) analysis. The thermo gravimetric analysis (TGA) and differential thermal analysis (DTA) of the as-synthesized nanorods were perfomed to observe their thermal degradation. Synthesized nanorods are fluorescent having emission maximum at 329 nm. Fluorescence resonance energy transfer (FRET) phenomenon has been observed between LaOX nanorods (energy donor) and naphthalimide (NAP) derivative (energy acceptor) and this mechanism can be helpful for sensing of NAP or NAP like molecules used as antioxidative in living systems.

DNA tetraplex structure formation from human telomeric repeat motif (TTAGGG):(CCCTAA) in nanocavity water pools of reverse micelles.

In an equimolar ratio the human telomeric oligonucleotides d[AGGG(TTAGGG)(3)] and d[(CCCTAA)(3)CCCT] formed mixed structures of duplex and tetraplex in bis(2-ethylhexyl)sulfosuccinate reverse micelles; only the duplex was observed in aqueous buffer. This finding suggests that heterogeneous confined media in the cell nucleus might induce a significant fraction of the telomeric region of genomic DNA to adopt non-canonical tetraplex structure.

Conformational flexibility influences degree of hydration of nucleic acid hybrids.

Four nucleic acid duplexes-DNA/RNA hybrid, RNA/DNA hybrid, RNA duplex, and DNA duplex-were studied under molecular crowding conditions of osmolytes. Destabilization of duplexes (ΔΔG°(25)) indicated that the ΔΔG°(25) values of hybrids were intermediate between those of DNA and RNA duplexes. In the presence of polyethylene glycol 200, the ΔΔG°(25) values were estimated to be +3.0, +3.5, +3.5, and +4.1 kcal mol(-1) for the DNA duplex, DNA/RNA hybrid, RNA/DNA hybrid, and RNA duplex, respectively. Differences in the number of water molecules taken up (-Δn(w)) upon duplex formations between 0 and 37 °C (Δ(-Δn(w))) were estimated to be 44.8 and 59.7 per duplex structure for the DNA/RNA and RNA/DNA hybrids, respectively. While the Δ(-Δn(w)) value for the DNA/RNA hybrid was intermediate between those of the DNA (26.1) and RNA (59.2) duplexes, the value for RNA/DNA hybrid was close to that of RNA duplex. These differences in the thermodynamic parameters and hydration are probably a consequence of the enhanced global flexibility of the RNA/DNA hybrid structure relative to the DNA/RNA hybrid structure observed in molecular dynamics simulations. This molecular crowding study provides information not only on hydration but also on the flexibility of the conformation of nucleic acid duplexes.

Thermodynamic stability of Hoogsteen and Watson-Crick base pairs in the presence of histone H3-mimicking peptide.

We found that Hoogsteen base pairs were stabilized by molecular crowding and a histone H3-mimicking peptide, which was not observed for Watson-Crick base pairs. Our findings demonstrate that the type of DNA base pair is critical for the interaction between DNA and histones.

Deciphering the fluorescence resonance energy transfer signature of 3-pyrazolyl 2-pyrazoline in transport proteinous environment.

In the present investigation, an attempt has been made to study the interaction of newly synthesized bioactive compound 3-pyrazolyl 2-pyrazoline (PZ) with model transport proteins, bovine serum albumin (BSA), and human serum albumin (HSA) employing steady state and time-resolved fluorescence technique. We have focused on fluorescence resonance energy transfer (FRET) between excited tryptophan in transport proteins to transport-proteins-bound PZ. An efficient Forster-type resonance energy transfer from the tryptophan residues to PZ indicates that PZ binds in the vicinity of the tryptophan residue. Binding of protein to that bioactive compound without changing conformation of primary and secondary structure of protein has been monitored using circular dichroism (CD) study.

Spectroscopic investigation of 3-pyrazolyl 2-pyrazoline derivative in homogeneous solvents.

How solvent conditions such as solvent polarity and hydrogen-bonding affect the fluorescence of a newly synthesized 3-pyrazolyl 2-pyrazoline derivative (Pyz) having pharmaceutical activity has been explored. The solvatochromic effect of Pyz is due to a change in dipole moment of the compound in the excited state. The relaxation of S1 state is perturbed in hydrogen-bonding solvents. The fluorescence properties of the systems are strongly dependent on the polarity of the media. The non-radiative relaxation process is facilitated by an increase in the polarity of the media. The photophysical response of Pyz in different solvents has been explained considering solute-solvent interactions.

Modulated photophysics of 3-pyrazolyl-2-pyrazoline derivative entrapped in micellar assembly.

The photophysical behavior of 3-pyrazolyl-2-pyrazoline derivative (PZ), a newly synthesized biologically active compound has been studied in micellar solutions of anionic sodium dodecyl sulfate (SDS), cationic cetyl trimethylammonium bromide (CTAB) and nonionic p- tert-octylphenoxy polyoxyethanol (Triton X-100, TX-100) micelle using steady state and time-resolved fluorescence spectroscopy technique. Influence of the micelles on the photophysics of PZ has also been investigated using different approaches. The location of the fluorophore PZ in the micelle has been identified by cetyl pyridinium chloride (CpCl) induced fluorescence quenching and micropolarity surrounding that fluorophore in micellar solution. The effect of urea on the steady state fluorescence and relaxation dynamics of the micelle bound probe has also been observed. The results have been interpreted in terms of the model that urea displaces water molecules from the micellar interface and the consequent destabilization leads to the expulsion of the probe molecules from the interfacial region. An attempt has been made to determine probe sensing microviscosities for these micellar microenvironments in the light of average reorientation times of the probe PZ.

Synthesis and characterization of nanodispersed molecular aggregates of Prussian blue in aerosol OT reverse micelle.

Prussian Blue (PB) nanomolecular aggregates were prepared in a well-characterized, monodispersed biomimicking nanocavities formed by Aerosol OT (AOT) reverse micelle in H2O/AOT/heptane at different omega ([H2O]/[Surfactant]) employing coprecipitation technique. The formed nanomolecular aggregates of PB have been characterized by the UV-visible, Fourier Transformed Infrared (FTIR) spectroscopy as well as by Transmission Electron Microscopy (TEM) and Cyclic Voltammetric methods. Visible and FTIR spectroscopic measurements confirm the formation of PB nano aggregates. Experimental results reveal that the molar extinction coefficient of PB nanomolecular aggregates is different for two different regimes of omega of reverse micelles. TEM measurements show that the size of these reverse micellar entrapped nano aggregrates varied with hydration (omega). Studies on these nano sized particles indicate that Fe is present in a single mixed valence state along the Fe-C-N-Fe skeleton in PB and the half wave potential (E1/2) becomes more positive with increase in the size of the nano aggregates.

Spectroscopic studies of 2-(2-bromo-ethyl)-6-nitro-benzo[de]isoquinolene-1,3-dione in water/alkanol mixed solvents and nonionic micelle of Igepal CO series.

Spectroscopic studies of newly synthesized bioactive compound 2-(2-bromo-ethyl)-6-nitro-benzo[de]isoquinolene-1,3-dione (BNBIO) have been carried out in polar aprotic solvent, viz. acetonitrile, tetrahydrofuran, 1,4-dioxan, ethylene glycol, dimethyl formamide, and polar protic solvent, viz. methanol, ethanol, propanol, water. Variation in absorbance of BNBIO in water-methanol, water-ethanol and water-propanol mixtures at their different compositions have been observed. Absorption behaviour of the dye has been studied in poly(oxyethylene) nonylphenol surfactants Igepal CO 630, Igepal CO 720 and Igepal CO 890 containing same hydrophobic tail and different numbers of poly(oxyethylene) groups. Experimental results of the BNBIO nonionic micelles have been explained in terms of 1:1 electron donor-acceptor (EDA) complexation and the complexation equilibrium becomes suppressed with increasing number of poly(oxyethylene) residue on the Igepal surfactant. Variation in binding constant of dye-micelle complexation has been rationalized considering a competitive equilibrium process between the BNBIO-water interactions.