Femtosecond studies of protein-DNA binding and dynamics: histone I

A novel molecular reporter for probing protein DNA recognition: An optical spectroscopic and molecular modeling study

A novel benzo[a]phenoxazine-based fluorescent dye LV2 has been employed as a molecular reporter to probe recognition of a linker histone protein H1 by calf-thymus DNA (DNA). Fluorescence lifetime of LV2 buried in the globular domain of H1 (∼2.1 ns) or in the minor groove of DNA (∼0.93 ns) increases significantly to 2.65 ns upon interaction of the cationic protein with DNA indicating formation of the H1-DNA complex. The rotational relaxation time of the fluorophore buried in the globular domain of H1 increases significantly from 2.2 ns to 8.54 ns in the presence of DNA manifesting the recognition of H1 by DNA leading to formation of the H1-DNA complex. Molecular docking and molecular dynamics (MD) simulations have shown that binding of LV2 is energetically most favourable in the interface of the H1-DNA complex than in the globular domain of H1 or in the minor groove of DNA. As a consequence, orientational relaxation of the LV2 is significantly hindered in the protein-DNA interface compared to H1 or DNA giving rise to a much longer rotational relaxation time (8.54 ns) in the H1-DNA complex relative to that in pure H1 (2.2 ns) or DNA (5.7 ns). Thus, via a significant change of fluorescence lifetime and rotational relaxation time, the benzo[a]phenoxazine-based fluorescent dye buried within the globular domain of the cationic protein, or within the minor groove of DNA, reports on recognition of H1 by DNA.

Structural Dynamics of Lipid Bilayer Membranes Explored by Magnetic Field Effect Based Fluorescence Microscopy

Lipid bilayer membranes are known to exist as heterogeneous and dynamic structures where the molecules are always moving and fluctuating under physiological conditions. Magnetic field effects (MFEs) studied herein are phenomena in which the exciplex emission from an electron donor-acceptor dyad increases or decreases by applying an external magnetic field. The characteristic dependence of MFEs on the viscosity and polarity of the surrounding medium has been applied to investigate the local environments around the probe molecule. In this study, a novel MFE-based fluorescence microscopy technique was developed to explore the structural dynamics of lipid bilayer membranes. The vesicle formation during the membrane deformation was selectively visualized through the MFEs, thus allowing the extraction of information on the cellular dynamics at high temporal and spatial resolutions. This highly versatile and powerful technique is applicable to a wide range of areas, such as biology and material science.

How Does Nanoconfinement within a Reverse Micelle Influence the Interaction of Phenazinium-Based Photosensitizers with DNA?

The major focus of the present work lies in exploring the influence of nanoconfinement within aerosol-OT (AOT) reverse micelles on the binding interaction of two phenazinium-based photosensitizers, namely, phenosafranin (PSF) and safranin-O (SO), with the DNA duplex. Circular dichroism and dynamic light-scattering studies reveal the condensation of DNA within the reverse micellar interior (transformation of the B-form of native DNA to ψ-form). Our results unveil a remarkable effect of the degree of hydration of the reverse micellar core on the stability of the stacking interaction (intercalation) of the drugs (PSF and SO) into DNA; increasing size of the water nanopool (that is, w ₀) accompanies decreasing curvature of the DNA duplex structure with the consequent effect of increasing stabilization of the drug:DNA intercalation. The marked differences in the dynamical aspects of the interaction scenario following encapsulation within the reverse micellar core and the subsequent dependence on the size of the water nanopool are also meticulously explored. The differential degrees of steric interactions offered by the drug molecules (presence of methyl substitutions on the planar phenazinium ring in SO) are also found to affect the extent of intercalation of the drugs to DNA. In this context, it is imperative to state that the water pool of the reverse micellar core is often argued to approach bulk-like properties of water with increasing micellar size (typically w ₀ ≥ 10), so that deviation from the bulk water properties is likely to be minimized in large reverse micelles (w ₀ ≥ 10). On the contrary, our results (particularly quantitative elucidation of micropolarity and dynamical aspects of the interaction) explicitly demonstrate that the bulk-like behavior of the nanoconfined water is not truly achieved even in large reverse micelles.

Effect of T·T Mismatch on DNA Dynamics Probed by Minor Groove Binders: Comparison of Dynamic Stokes Shifts of Hoechst and DAPI

Recognition of DNA base mismatches and their subsequent repair by enzymes is vital for genomic stability. However, it is difficult to comprehend such a process in which enzymes sense and repair different types of mismatches with different ability. It has been suggested that the differential structural changes of mismatched bases act as cues to the repair enzymes, although the effect of such DNA structural changes on surrounding water and ion dynamics is inevitable due to strong electrostatic coupling among them. Thus, collective dynamics of DNA, water, and ions near the mismatch site is believed to be important for mismatch recognition and repair mechanism. Here we show that introduction of a T·T mismatch in the minor groove of DNA induces dispersed (collective) power-law solvation dynamics (of exponent ∼0.24), measured by monitoring the time-resolved fluorescence Stokes shifts (TRFSS) of two popular minor groove binders (Hoechst 33258 and DAPI) over five decades of time from 100 fs to 10 ns. The same ligands however sense different dynamics (power-law of exponent ∼0.15 or power-law multiplied with biexponential relaxation) in the minor groove of normal-DNA. The similar fluorescence anisotropy decays of ligands measured in normal- and T·T-DNA suggest that Stokes shift dynamics and their changes in T·T-DNA purely originate from the solvation process, and not from any internal rotational motion of probe-ligands. The dispersed power-law solvation dynamics seen in T·T-DNA indicate that the ligands do not sense any particular (exponential) relaxation specific to T·T wobbling and/or other conformational changes. This could be the reason why T·T mismatch is recognized by enzymes with lower efficiency compared to purine-pyrimidine and purine-purine mismatches.

A sensitive fluorescent probe for the polar solvation dynamics at protein–surfactant interfaces

Relaxation dynamics at the surface of biologically important macromolecules is important taking into account their functionality in molecular recognition.

Effects of protein-DNA complex formation on the intermolecular vibrational density of states of interfacial water

Single-stranded DNAs (ss-DNAs) are formed as intermediates during DNA metabolic processes. ss-DNA binding (SSB) proteins specifically bind to the single-stranded segments of the DNA and protect it from being degraded. We have performed room temperature molecular dynamics simulations of the aqueous solution of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element (FUSE) binding protein (FBP) complexed with two ss-DNA oligomers. Efforts have been made to explore the influence of complex formation on low-frequency vibrational density of states of the surface water molecules. It is revealed that increased back scattering of water confined around the complexed structures leads to significant blue shifts of the band corresponding to the O···O···O bending or restricted transverse motions of water, the effect being more for the bridged water molecules. Importantly, it is demonstrated that the formation of such complexed structures of a similar type may often influence the transverse and longitudinal degrees of freedom of the surrounding water molecules in a nonuniform manner.

Dynamical perspective of protein-DNA interaction

The interactions between protein-DNA are essential for various biological activities. In this review, we provide an overview of protein-DNA interactions that emphasizes the importance of dynamical aspects. We divide protein-DNA interactions into two categories: nonspecific and specific and both the categories would be discussed highlighting some of our relevant work. In the case of nonspecific protein-DNA interaction, solvation studies (picosecond and femtosecond-resolved) explore the role environmental dynamics and change in the micropolarity around DNA molecules upon complexation with histone protein (H1). While exploring the specific protein-DNA interaction at λ-repressor-operator sites interaction, particularly OR1 and OR2, it was observed that the interfacial water dynamics is minimally perturbed upon interaction with DNA, suggesting the labile interface in the protein-DNA complex. Förster resonance energy transfer (FRET) study revealed that the structure of the protein is more compact in repressor-OR2 complex than in the repressor-OR1 complex. Fluorescence anisotropy studies indicated enhanced flexibility of the C-terminal domain of the repressor at fast timescales after complex formation with OR1. The enhanced flexibility and different conformation of the C-terminal domain of the repressor upon complexation with OR1 DNA compared to OR2 DNA were found to have pronounced effect on the rate of photoinduced electron transfer.

Dynamics and mechanisms of DNA repair by photolyase

Photolyases, a class of flavoproteins, use blue light to repair two types of ultraviolet-induced DNA damage, a cyclobutane pyrimidine dimer (CPD) and a pyrimidine-pyrimidone (6-4) photoproduct (6-4PP). In this perspective, we review the recent progress in the repair dynamics and mechanisms of both types of DNA restoration by photolyases. We first report the spectroscopic characterization of flavin in various redox states and the active-site solvation dynamics in photolyases. We then systematically summarize the detailed repair dynamics of damaged DNA by photolyases and a biomimetic system through resolving all elementary steps on ultrafast timescales, including multiple intermolecular electron- and proton-transfer reactions and bond-breaking and -making processes. We determined the unique electron tunneling pathways, identified the key functional residues and revealed the molecular origin of high repair efficiency, and thus elucidate the molecular mechanisms and repair photocycles at the most fundamental level. We finally conclude that the active sites of photolyases, unlike the aqueous solution for the biomimetic system, provide a unique electrostatic environment and local flexibility and thus a dedicated synergy for all elementary dynamics to maximize the repair efficiency. This repair photomachine is the first enzyme that the entire functional evolution is completely mapped out in real time.

Ultrafast water dynamics at the interface of the polymerase-DNA binding complex

DNA polymerases slide on DNA during replication, and the interface must be mobile for various conformational changes. The role of lubricant interfacial water is not understood. In this report, we systematically characterize the water dynamics at the interface and in the active site of a tight binding polymerase (pol β) in its binary complex and ternary state using tryptophan as a local optical probe. Using femtosecond spectroscopy, we observed that upon DNA recognition the surface hydration water is significantly confined and becomes bound water at the interface, but the dynamics are still ultrafast and occur on the picosecond time scale. These interfacial water molecules are not trapped but are mobile in the heterogeneous binding nanospace. Combining our findings with our previous observation of ultrafast water motions at the interface of a loose binding polymerase (Dpo4), we conclude that the binding interface is dynamic and the water molecules in various binding clefts, channels, and caves are mobile and even fluid with different levels of mobility for loose or tight binding polymerases. Such a dynamic interface should be general to all DNA polymerase complexes to ensure the biological function of DNA synthesis.

Direct probing of solvent accessibility and mobility at the binding interface of polymerase (Dpo4)-DNA complex

Water plays essential structural and dynamical roles in protein-DNA recognition through contributing to enthalpic or entropic stabilization of binding complex and by mediating intermolecular interactions and fluctuations for biological function. These interfacial water molecules are confined by the binding partners in nanospace, but in many cases they are highly mobile and exchange with outside bulk solution. Here, we report our studies of the interfacial water dynamics in the binary and ternary complexes of a polymerase (Dpo4) with DNA and an incoming nucleotide using a site-specific tryptophan probe with femtosecond resolution. By systematic comparison of the interfacial water motions and local side chain fluctuations in the apo, binary, and ternary states of Dpo4, we observed that the DNA binding interface and active site are dynamically solvent accessible and the interfacial water dynamics are similar to the surface hydration water fluctuations on picosecond time scales. Our molecular dynamics simulations also show the binding interface full of water molecules and nonspecific weak interactions. Such a fluid binding interface facilitates the polymerase sliding on DNA for fast translocation whereas the spacious and mobile hydrated active site contributes to the low fidelity of the lesion-bypass Y-family DNA polymerase.

Conformational fluctuations of a protein-DNA complex and the structure and ordering of water around it

Protein-DNA binding is an important process responsible for the regulation of genetic activities in living organisms. The most crucial issue in this problem is how the protein recognizes the DNA and identifies its target base sequences. Water molecules present around the protein and DNA are also expected to play an important role in mediating the recognition process and controlling the structure of the complex. We have performed atomistic molecular dynamics simulations of an aqueous solution of the protein-DNA complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. The conformational fluctuations of the protein and DNA and the microscopic structure and ordering of water around them in the complex have been explored. In agreement with experimental studies, the calculations reveal conformational immobilization of the terminal segments of the protein on complexation. Importantly, it is discovered that both structural adaptations of the protein and DNA, and the subsequent correlation between them to bind, contribute to the net entropy loss associated with the complex formation. Further, it is found that water molecules around the DNA are more structured with significantly higher density and ordering than that around the protein in the complex.

Dynamic properties of water around a protein-DNA complex from molecular dynamics simulations

Formation of protein-DNA complex is an important step in regulation of genes in living organisms. One important issue in this problem is the role played by water in mediating the protein-DNA interactions. In this work, we have carried out atomistic molecular dynamics simulations to explore the heterogeneous dynamics of water molecules present in different regions around a complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. It is demonstrated that such heterogeneous water motions around the complex are correlated with the relaxation time scales of hydrogen bonds formed by those water molecules with the protein and DNA. The calculations reveal the existence of a fraction of extraordinarily restricted water molecules forming a highly rigid thin layer in between the binding motifs of the protein and DNA. It is further proved that higher rigidity of water layers around the complex originates from more frequent reformations of broken water-water hydrogen bonds. Importantly, it is found that the formation of the complex affects the transverse and longitudinal degrees of freedom of surrounding water molecules in a nonuniform manner.

Interaction of an antituberculosis drug with nano-sized cationic micelle: Förster resonance energy transfer from dansyl to rifampicin in the microenvironment

In this contribution, we report studies on the interaction of an antituberculosis drug rifampicin (RF) in a macromolecular assembly of CTAB with an extrinsic fluorescent probe, dansyl chloride (DC). The absorption spectrum of the drug RF has been employed to study Förster resonance energy transfer (FRET) from DC, bound to the CTAB micelle using picosecond resolved fluorescence spectroscopy. We have applied a kinetic model developed by Tachiya to understand the kinetics of energy transfer and the distribution of acceptor (RF) molecules around the donor (DC) molecules in the micellar surface with increasing quencher concentration. The mean number of RF molecules associated with the micelle increases from 0.24 at 20 μm RF concentration to 1.5 at 190 μm RF concentration and consequently the quenching rate constant (k(q)) due to the acceptor (RF) molecules increases from 0.23 to 0.75 ns(-1) at 20 and 190 μm RF concentration, respectively. However, the mean number of the quencher molecule and the quenching rate constant does not change significantly beyond a certain RF concentration (150 μm), which is consistent with the results obtained from time resolved FRET analysis. Moreover, we have explored the diffusion controlled FRET between DC and RF, using microfluidics setup, which reveals that the reaction pathway follows one-step process.

Fluorescence lifetime probe for solvent microviscosity utilizing anilinonaphthalene sulfonate

The correlation between the fluorescent dynamics of excited anilinonaphthalene sulfonate (ANS) and the microviscosity of solvent molecules surrounding ANS is investigated by time-resolved fluorescence spectroscopy. ANS has been widely used to probe the local hydrophobicity due to the drastic change in its intensity. It is revealed that the fluorescence lifetime from the charge transfer (CT) state of ANS sensitively reflects the microviscosity. The higher sensitivity of 2,6-ANS than of 1,8-ANS demonstrates that the spatial freedom of the rotating phenylamino group in the photoexcited ANS is an important factor that determines the sensitivity. As an application, the measurements of the microviscosity of water in biologically important systems, such as hyaluronan, gellan gum, and gelatin aqueous solutions are also presented. The present results suggest that the fluorescence lifetime of ANS enables the estimation of the solvent microviscosity and provide a useful probe molecule for fluorescence lifetime imaging microscopy.

Ultrafast solvation dynamics at binding and active sites of photolyases

Dynamic solvation at binding and active sites is critical to protein recognition and enzyme catalysis. We report here the complete characterization of ultrafast solvation dynamics at the recognition site of photoantenna molecule and at the active site of cofactor/substrate in enzyme photolyase by examining femtosecond-resolved fluorescence dynamics and the entire emission spectra. With direct use of intrinsic antenna and cofactor chromophores, we observed the local environment relaxation on the time scales from a few picoseconds to nearly a nanosecond. Unlike conventional solvation where the Stokes shift is apparent, we observed obvious spectral shape changes with the minor, small, and large spectral shifts in three function sites. These emission profile changes directly reflect the modulation of chromophore's excited states by locally constrained protein and trapped-water collective motions. Such heterogeneous dynamics continuously tune local configurations to optimize photolyase's function through resonance energy transfer from the antenna to the cofactor for energy efficiency and then electron transfer between the cofactor and the substrate for repair of damaged DNA. Such unusual solvation and synergetic dynamics should be general in function sites of proteins.

Specific interactions of clausin, a new lantibiotic, with lipid precursors of the bacterial cell wall

We investigated the specificity of interaction of a new type A lantibiotic, clausin, isolated from Bacillus clausii, with lipid intermediates of bacterial envelope biosynthesis pathways. Isothermal calorimetry and steady-state fluorescence anisotropy (with dansylated derivatives) identified peptidoglycan lipids I and II, embedded in dodecylphosphocholine micelles, as potential targets. Complex formation with dissociation constants of approximately 0.3 muM and stoichiometry of approximately 2:1 peptides/lipid intermediate was observed. The interaction is enthalpy-driven. For the first time, to our knowledge, we evidenced the interaction between a lantibiotic and C(55)-PP-GlcNAc, a lipid intermediate in the biosynthesis of other bacterial cell wall polymers, including teichoic acids. The pyrophosphate moiety of these lipid intermediates was crucial for the interaction because a strong binding with undecaprenyl pyrophosphate, accounting for 80% of the free energy of binding, was observed. No binding occurred with the undecaprenyl phosphate derivative. The pentapeptide and the N-acetylated sugar moieties strengthened the interaction, but their contributions were weaker than that of the pyrophosphate group. The lantibiotic decreased the mobility of the pentapeptide. Clausin did not interact with the water-soluble UDP-MurNAc- and pyrophosphoryl-MurNAc-pentapeptides, pointing out the importance of the hydrocarbon chain of the lipid target.

Protein hydration dynamics and molecular mechanism of coupled water-protein fluctuations

Protein surface hydration is fundamental to its structural stability and flexibility, and water-protein fluctuations are essential to biological function. Here, we report a systematic global mapping of water motions in the hydration layer around a model protein of apomyoglobin in both native and molten globule states. With site-directed mutagenesis, we use intrinsic tryptophan as a local optical probe to scan the protein surface one at a time with single-site specificity. With femtosecond resolution, we examined 16 mutants in two states and observed two types of water-network relaxation with distinct energy and time distributions. The first water motion results from the local collective hydrogen-bond network relaxation and occurs in a few picoseconds. The initial hindered motions, observed in bulk water in femtoseconds, are highly suppressed and drastically slow down due to structured water-network collectivity in the layer. The second water-network relaxation unambiguously results from the lateral cooperative rearrangements in the inner hydration shell and occurs in tens to hundreds of picoseconds. Significantly, this longtime dynamics is the coupled interfacial water-protein motions and is the direct measurement of such cooperative fluctuations. These local protein motions, although highly constrained, are necessary to assist the longtime water-network relaxation. A series of correlations of hydrating water dynamics and coupled fluctuations with local protein's chemical and structural properties were observed. These results are significant and reveal various water behaviors in the hydration layer with wide heterogeneity. We defined a solvation speed and an angular speed to quantify the water-network rigidity and local protein flexibility, respectively. We also observed that the dynamic hydration layer extends to more than 10 A. Finally, from native to molten globule states, the hydration water networks loosen up, and the protein locally becomes more flexible with larger global plasticity and partial unfolding.

Relaxation dynamics of nucleosomal DNA

Recent experimental and theoretical evidence demonstrates that proteins and water in the hydration layer can follow complex stretched exponential or power law relaxation dynamics. Here, we report on a 50 ns all atom molecular dynamics (MD) simulation of the yeast nucleosome, where the interactions between DNA, histones, surrounding water and ions are explicitly included. DNA interacts with the histone core in 14 locations, approximately every 10.4 base pairs. We demonstrate that all sites of interaction exhibit anomalously slow power law relaxation, extending up to 10 ns, while fast exponential relaxation dynamics of hundreds of picoseconds applies to DNA regions outside these locations. The appearance of 1/f(alpha) noise or pink noise in DNA dynamics is ubiquitous. For histone-bound nucleotide dynamics alpha --> 1 and is a signature of complexity of the protein-DNA interactions. For control purposes two additional DNA simulations free of protein are conducted. Both utilize the same sequence of DNA, as found the in the nucleosome. In one simulation the initial conformation of the double helix is a straight B-form. In the other, the initial conformation is super helical. Neither of these simulations exhibits the variation of alpha as a function of position, the measure of power law for dynamical behavior, which we observe in the nucleosome simulation. The unique correspondence (high alpha to DNA-histone interaction sites, low alpha to free DNA sites), suggests that alpha may be an important and new quantification of protein-DNA interactions for future experiments.

Sequence dependent femtosecond-resolved hydration dynamics in the minor groove of DNA and histone-DNA complexes

Understanding the sequence dependent molecular recognition of DNA is crucial for the rational design of many drugs. Femtosecond resolved studies on the hydration dynamics of the dodecamer duplexes having sequences (CGCGAATTCGCG)2 and (CGCAAATTTGCG)2, and their complexes with the nucleic protein histone 1 (H1) reveal significant correlation of the molecular recognition of the DNA and DNA-protein complexes with the dynamics of hydration. The different molecular recognition of DNA and DNA-protein complexes is also borne out by circular dichroism (CD) and fluorescence detected CD measurements.

A versatile fiber-optic coupled system for sensitive optical spectroscopy in strong ambient light

In this work we describe design and use of a fiber-optic based optical system for the spectroscopic studies on the samples under the presence of strong ambient light. The system is tested to monitor absorption, emission, and picosecond-resolved fluorescence transients simultaneously with a time interval of 500 ms for several hours on a biologically important sample (vitamin B2) under strong UV light. An efficient stray-light rejection ratio of the setup is achieved by the confocal geometry of the excitation and detection channels. It is demonstrated using this setup that even low optical signal from a liquid sample under strong UV-exposure for the picosecond-resolved fluorescence transient measurement can reliably be detected by ultrasensitive microchannel plate photomultiplier tube solid state detector. The kinetics of photodeterioration of vitamin B2 measured using our setup is consistent with that reported in the literature. Our present studies also justify the usage of tungsten light than the fluorescent light for the healthy preservation of food with vitamin B2.

Nonspecific protein-DNA interactions: complexation of alpha-chymotrypsin with a genomic DNA

In this contribution, we report studies on nonspecific protein-DNA interactions of an enzyme protein bovine pancreatic alpha-chymotrypsin (CHT) with genomic DNA (from salmon testes) using two biologically common fluorescent probes: 1-anilinonaphthalene-8-sulfonate (ANS) and 2,6-p-toluidinonaphthalene sulfonate (TNS). TNS molecules that are nonspecifically bound to positively charged basic residues at the surface sites, not in the hydrophobic cavities of the protein, are preferentially displaced upon complexation of TNS-labeled CHT with DNA. The time-resolved fluorescence anisotropy of TNS molecules bound to hydrophobic cavities/clefts of CHT reveals that global tumbling motion of the protein is almost frozen in the protein-DNA complex. A control study on TNS-labeled human serum albumin (HSA) upon interaction with DNA clearly indicates that the ligands in the deep pockets of the protein cannot be displaced by interaction with DNA. We have also found that ANS, which binds to a specific surface site of CHT, is not displaced by DNA. The intactness of the ANS binding in CHT upon complexation with DNA offers the opportunity to measure the distance between the ANS binding site and the contact point of the ethidium bromide (EB)-labeled DNA using the Förster resonance energy transfer (FRET) technique. Enzymatic activity studies on CHT on a substrate (Ala-Ala-Phe 7-amido-4-methyl coumarin) reveal that the active site of the enzyme remains open for the substrate even in the protein-DNA complex. Circular dichroism (CD) studies on CHT upon complexation with DNA confirm the structural integrity of CHT in the complex. Our studies have attempted to explore an application of nonspecific protein-DNA interactions in the characterization of ligand binding of a protein in solution.

Aggregated CdS Quantum Dots: Host of Biomolecular Ligands

In this contribution, we have studied structural and photophysical properties of aggregated CdS quantum dots (QDs) capped with 2-mercaptoethanol in aqueous medium. The hydrodynamic diameter of the nanostructures in aqueous solution was found to be approximately 160 nm with the dynamic light scattering (DLS) technique, which is in close agreement with atomic force microscopy (AFM) studies (diameter approximately 150 nm). However, the UV-vis absorption spectroscopy, powder X-ray diffraction (XRD), and transmission electron microscopy (TEM) studies confirm the average particle size (QD) in the nanoaggregate to be 4.0 +/- 0.5 nm. The steady-state and time-resolved photoluminescence studies on the QDs further confirm preservation of electronic band structure of the QDs in the nanoaggregate. To study the nature of the nanoaggregate we have used small fluorescent probes, which are widely used as biomolecular ligands (2,6-p-toluidinonaphthalene sulfonate (TNS) and Oxazine 1), and found the pores of the aggregate to be hydrophobic in nature. The significantly large spectral overlap of the host quantum dots (donor) with that of the guest fluorescent probe Oxazine 1 (acceptor) allows us to carry out Förster resonance energy transfer (FRET) studies to estimate average donor-acceptor distance in the nanostructure, found to be approximately 25 Angstrom. The quantum dot aggregate and the characterization techniques reported here could have implications in the future application of the QD-nanoaggregate as host of small ligand molecules of biological interest.

Spectrofluorimetric characterization of mixed nanoaggregates comprising a double-chain cationic surfactant and a cationic or non-ionic single-chain surfactant

A series of mixed vesicle and pre-vesicle nanoaggregates, comprising a cationic double-chain surfactant (di-decyldimethylammonium bromide, di-C(10)DMAB, or di-dodecyldimethylammonium bromide, di-C(12)DMAB), and a cationic (dodecylethyldimethylammonium bromide, C(12)EDMAB) or non-ionic (octyl-beta-D-glucopyranoside, OBG) single-chain surfactant have been characterized by means of steady-state fluorescence spectroscopy. For that purpose, the fluorescent emission of two probes, one anionic (TNS) and the other non-ionic (PRODAN), which is known to be sensitive to the polarity, rigidity, and/or microviscosity of the environment within which the probes are housed, has been measured in the presence of the above-mentioned mixed aggregates. The results of this analysis yield interesting information about the characteristics of the vesicle surface and bilayer, as well as about the existence of clusters and/or nanoaggregates prior to the formation of vesicles.

Detection of the Local Structural Changes in the Dimer Interface of BamHI Initiated by DNA Binding and Dissociation Using a Solvatochromic Fluorophore

To detect the local structural change in an interface between proteins induced by the substrate binding and dissociation, a solvatochromic fluorescent N(beta)-L-alanyl-5-(N,N-dimethylamino)-naphthalene-1-sulfonamide (DanAla) was introduced into 132 position of the dimer interface in BamHI. Before addition of the substrate, the fluorescence from the normal planer excited state of DanAla moiety was observed as a main emission, and thereby the DanAla in the dimer interface is located in the hydrophobic microenvironment. The incubation with the substrate for 20 min induced the gradual increase in fluorescence intensity around 430 nm. The fact reflects that the polarity is reduced by the slight structural change initiated by the formation of the complex with the substrate. Furthermore, the incubation for more than 20 min caused the slight decrease in fluorescence around 430 nm and an appearance of fluorescence (560 nm) due to twisted intramolecular charge transfer (TICT) excited state. Therefore, the DanAla is exposed to comparative polar environment after the dissociation of the substrate. The fluorescence lifetime as a minor component, which is attributed to the TICT excited state, was reduced by addition of the substrate. The results provide that the hydrophobicity in the dimer interface is increased by the substrate binding. Interestingly, we found that the structure of an initial form is different from that of a refolded form after the dissociation of the substrate using a spectral subtraction technique. We have achieved detection of the changing structure induced by the substrate binding and dissociation using a steady-state and time-resolved fluorescence.

Direct observation of protein folding in nanoenvironments using a molecular ruler

We observe folding of horse heart cytochrome c in various environments including nano-compartments (micelles and reverse micelles). Using picosecond-resolved Förster resonance energy transfer (FRET) dynamics of an extrinsic covalently attached probe dansyl (donor) at the surface of the protein to a heme group (acceptor) embedded inside the protein, we measured angstrom-resolved donor-acceptor distances in the environments. The overall structural perturbations of the protein revealed from the FRET experiments are in close agreement with our circular dichroism (CD) and dynamic light scattering (DLS) studies on the protein in a variety of solution conditions. The change of segmental motion of the protein due to imposed restriction in the nano-compartments compared to that in bulk buffer is also revealed by temporal fluorescence anisotropy of the dansyl probe.

Electrochemical, microscopic, and spectroscopic characterization of prevesicle nanostructures and vesicles on mixed cationic surfactant systems

Several experimental techniques (conductivity, zeta potential, transmission electronic microscopy, and steady-state fluorescence spectroscopy) have been used to study the formation of mixed colloidal aggregates consisting of a cationic double-chain surfactant, di-dodecyldimethylammonium bromide (di-C12DMAB), and a single-chain alkyltrimethylammonium bromide with 10 and/or 14 carbon atoms (decyltrimethylammonium bromide, C10TAB, and/or tetradecyltrimethylammonium bromide, C14TAB). Special interest has been devoted to the prevesicle domain, within which the formation of aggregated nanostructures was first reported in our laboratory. For that purpose, studies have been carried out on the very dilute region by means of conductivity experiments, confirming the existence of two critical aggregation concentrations in that concentration domain: the so-called mixed critical aggregate concentration, CAC, and the mixed critical vesicle concentration, CVC. By carrying out TEM experiments on negatively stained samples, we were surprised to find a number of aggregates without a clear aggregation pattern and with a variety of sizes and shapes at concentrations below CAC, where only monomers were expected. However, the nanoaggregates found at concentrations between CAC and CVC, also by TEM microscopy, show a clear and ordered "fingerprint"-like aggregation pattern similar to the liquid-crystalline phases reported for DNA-liposome complexes and/or DNA packed with viral capsids. Finally, at total surfactant concentrations above CVC, the aggregates were confirmed, by means of cryo-TEM micrographs and zeta potential measurements, to be essentially unilamellar spherical vesicles with a medium polydispersity and a net-averaged surface density charge of around 12 x 10(-3) C m(-2). The fluorescence emission of two probes, TNS (anionic) and PRODAN (nonionic), allows for the analysis of the micropolarity and microviscosity of the different microenvironments present in aqueous surfactant solutions where the above-mentioned vesicle and prevesicle aggregates are present.

Femtochemistry of orange II in solution and in chemical and biological nanocavities

In this work, we report on studies of the nature of the dynamics and hydrophobic binding in cyclodextrins and human serum albumin protein complexes with orange II. With femtosecond time resolution, we examined the proton-transfer and trans-cis isomerization reactions of the ligand in these nanocavities and in pure solvents. Because of confinement at the ground state, the orientational motion in the formed phototautomer is restricted, leading to a rich dynamics. Therefore, the emission lifetimes span a large window of tens to hundreds of picoseconds in the cavities. Possible H-bond interactions between the guest and cyclodextrin do not affect the caged dynamics. For the protein-ligand complexes, slow diffusional motion ( approximately 630 ps) observed in the anisotropy decay indicates that the binding structure is not completely rigid, and the embedded guest is not frozen with the hydrophobic pocket. The ultrafast isomerization and decays are explained in terms of coupling motions between N-N and C-N stretching modes of the formed tautomer. We discuss the role of confinement on the trans-cis isomerization with the cavities and its relationships to frequency and time domains of nanostructure emission.