Magnetron-sputtered Polytetrafluoroethylene-stabilized Silver Nanoisland Surface for Surface-Enhanced Fluorescence.

Surface-enhanced fluorescence (SEF) requires the absorption/emission band of the fluorophore, the localized surface plasmon resonance (LSPR) of the nanostructure and the excitation wavelength to fall in the same (or very close) spectral range. In this paper, we monitor the SEF intensity and lifetime dependence of riboflavin (vitamin B2) adsorbed on a spacer-modified Ag substrate with respect to the thickness of the spacer. The substrates were formed by silver nanoislands deposited onto magnetron-sputtered polytetrafluoroethylene (ms-PTFE). The spacer was formed by the ms-PTFE layer with the thickness ranging from ~5 to 25 nm. The riboflavin dissolved in dimethylsulfoxide (DMSO) at a 10 µM concentration forms, at the ms-PTFE surface, a homogeneous layer of adsorbed molecules corresponding to a monomolecular layer. The microspectroscopic measurements of the adsorbed layer were performed through a sessile droplet; our study has shown the advantages and limitations of this approach. Time-resolved fluorescence enabled us to determine the enhanced fluorescence quantum yield due to the shortening of the radiative decay in the vicinity of the plasmonic surface. For the 5 nm ms-PTFE layer possessing the largest (estimated 4×) fluorescence enhancement, the quantum yield was increased 2.3×.

Anisotropic Optical Response of Silver Nanorod Arrays: Surface Enhanced Raman Scattering Polarization and Angular Dependences Confronted with Ellipsometric Parameters.

Silver nanorod arrays prepared by oblique angle deposition (AgOADs) represent versatile, simple and inexpensive substrates for high sensitivity surface enhanced Raman scattering (SERS) applications. Their anisotropic nature suggests that their optical responses such as the SERS signal, the depolarization ratio, reflectivity and ellipsometric parameters critically depend on the states of polarization, nanorod angular arrangement and specific illumination-observation geometry. SERS polarization and angular dependences of AgOADs were measured using methylene blue (MB) molecule. Our study constitutes, to our knowledge, the most detailed investigation of such characteristics of plasmonic nanostructures to date. This is due to the 90°-scattering geometry used in which two out of three Euler angles determining the nanorod spatial orientation and four polarization combinations can be varied simultaneously. We attributed the anisotropic optical response to anisotropic (pseudo)refractive index caused by different periodicity of our structures in different directions since the plasmonic properties were found rather isotropic. For the first time we demonstrate very good correspondence between SERS intensities and ellipsometric parameters for all measured configurations as compared on the basis of the surface selection rules. Obtained results enable quantitative analysis of MB Raman tensor elements, indicating that the molecules adsorb predominantly with the symmetry axis perpendicular to the surface.

Testing gold nanostructures fabricated by hole-mask colloidal lithography as potential substrates for SERS sensors: sensitivity, signal variability, and the aspect of adsorbate deposition.

Gold nanoplasmonic substrates with high sensitivity and spectral reproducibility are key components of molecular sensors based on surface-enhanced Raman scattering (SERS). In this work, we used a confocal Raman microscope and several types of gold nanostructures (arrays of nanodiscs, nanocones and nanodisc dimers) prepared by hole-mask colloidal lithography (HCL) to determine the sources of variability in SERS measurements. We demonstrate that significant variations in the SERS signal can originate from the method of deposition of analyte molecules onto a SERS substrate. While the method based on incubation of SERS substrates in a solution containing the analyte yields a SERS signal with low variability, the droplet deposition method produces a SERS signal with rather high variability. Variability of the SERS signal of a single nanoparticle was determined from the statistical analysis of the SERS signal in short-range Raman maps recorded using different sized laser spots produced by means of different objectives. We show that the number of nanoparticles located within the laser spot can be a source of substantial SERS signal variability, especially for high-magnification objectives. We demonstrate that SERS substrates prepared by HCL exhibit high SERS enhancement and excellent homogeneity (about 20% relative standard deviation from short-range maps). The nanocone arrays are shown to provide the highest SERS enhancement, the lowest relative level of fluorescence background, and also slightly better homogeneity when compared with arrays of nanodisc dimers or single nanodiscs.

DNA Electric Charge Oscillations Govern Protein-DNA Recognition.

The transcriptional activity of the serum response factor (SRF) protein is triggered by its binding to a 10-base-pair DNA consensus sequence designated the CArG box, which is the core sequence of the serum response element (SRE). Sequence-specific recognition of the CArG box by a core domain of 100 amino acid residues of SRF (core-SRF) was asserted to depend almost exclusively on the intrinsic SRE conformation and on the degree of protein-induced SRE bending. Nevertheless, this paradigm was invalidated by a temperature-dependent Raman spectroscopy study of 20-mer oligonucleotides involved in bonding interactions with core-SRF that reproduced both wild type and mutated c-fos SREs. Indeed, the SRE moieties that are complexed with core-SRF exhibit permanent interconversion dynamics between bent and linear conformers. Thus, sequence-specific recognition of the CArG box by core-SRF cannot be explained only in terms of the three-dimensional structure of the SRE. A particular dynamic pairing process discriminates between the wild type and mutated complexes. Specific oscillations of the phosphate charge network of the SRE govern the recognition between both partners rather than an intrinsic set of conformations of the SRE.

Organization of the MADS box from human SRF revealed by tyrosine perturbation.

MADS box family transcription factors are involved in signal transduction and development control through DNA specific sequence recognition. The DNA binding domain of these proteins contains a conservative 55-60 amino acid sequence which defines the membership of this large family. Here we present a thorough study of the MADS segment of serum response factor (MADS(SRF)). Fluorescence, UV-absorption, and Raman spectroscopy studies were performed in order to disclose its behavior and basic functional properties in an aqueous environment. The secondary structure of MADS(SRF) estimated by analysis of Raman spectra and supported by CD has revealed only the C-terminal part as homologous with those of free core-SRF, while the N-terminal part has lost the stable α-helical structure found in both the free core-SRF and its specific complex with DNA. The three tyrosine residues of the MADS(SRF) were used as spectroscopic inner probes. The effect of environmental conditions, especially pH variations and addition of variously charged quenchers, on their spectra was examined. Two-component fluorescence quenching was revealed using factor analysis and corresponding Stern-Volmer constants determined. Factor analysis of absorbance and fluorescence pH titration led to determination of three dissociation constants pKa1 = 6.4 ± 0.2, pKa2 = 7.3 ± 0.2, and pKa3 = 9.6 ± 0.6. Critical comparison of all experiments identified the deprotonation of His193 hydrogen bonded to Tyr195 as a candidate for pKa1 (and that of Tyr158 as a candidate for pKa2). Within MADS(SRF), His193 is a key intermediary between the N-terminal primary DNA binding element and the hydrophobic C-terminal protein dimerization element.

5'-O-Methylphosphonate nucleic acids--new modified DNAs that increase the Escherichia coli RNase H cleavage rate of hybrid duplexes.

Several oligothymidylates containing various ratios of phosphodiester and isopolar 5'-hydroxyphosphonate, 5'-O-methylphosphonate and 3'-O-methylphosphonate internucleotide linkages were examined with respect to their hybridization properties with oligoriboadenylates and their ability to induce RNA cleavage by ribonuclease H (RNase H). The results demonstrated that the increasing number of 5'-hydroxyphosphonate or 5'-O-methylphosphonate units in antisense oligonucleotides (AOs) significantly stabilizes the heteroduplexes, whereas 3'-O-methylphosphonate AOs cause strong destabilization of the heteroduplexes. Only the heteroduplexes with 5'-O-methylphosphonate units in the antisense strand exhibited a significant increase in Escherichia coli RNase H cleavage activity by up to 3-fold (depending on the ratio of phosphodiester and phosphonate linkages) in comparison with the natural heteroduplex. A similar increase in RNase H cleavage activity was also observed for heteroduplexes composed of miRNA191 and complementary AOs containing 5'-O-methylphosphonate units. We propose for this type of AOs, working via the RNase H mechanism, the abbreviation MEPNA (MEthylPhosphonate Nucleic Acid).

Protonation effect of tyrosine in a segment of the SRF transcription factor: a combined optical spectroscopy, molecular dynamics, and density functional theory calculation study.

The high sensitivity to pH of a short segment (an octamer) of serum response factor (SRF), an important member of the MADS box family of transcription factors, was investigated by Raman scattering, infrared and circular dichroism spectroscopies. Molecular dynamics (MD) and density functional theory (DFT) calculations enabled interpretation of spectral changes in close detail. Although there was a negligible difference between spectra in acidic and neutral environments, the spectrum in basic pH was substantially different. The major changes were attributed to the deprotonation of tyrosine. The secondary structure of the SRF octamer fragment was estimated experimentally as well as predicted theoretically by MD. All techniques proved that it exists in a dynamical equilibrium among several conformations mostly close to ß turn, unordered conformations, and extended structure, in contrast to the stable secondary structure it possesses as a part of SRF. Generally, this approach represents a useful tool for the study of various short oligopeptides.

Raman spectroscopy of proteins and nucleoproteins.

A protein Raman spectrum comprises discrete bands representing vibrational modes of the peptide backbone and its side chains. The spectral positions, intensities, and polarizations of the Raman bands are sensitive to protein secondary, tertiary, and quaternary structures and to side-chain orientations and local environments. In favorable cases, the Raman spectrum serves as an empirical signature of protein three-dimensional structure, intramolecular dynamics, and intermolecular interactions. Quantitative analysis of Raman spectral series can be further boosted by advanced statistical approaches of factor analysis that allow fitting of specific theoretical models while reducing the amount of analyzed data. Here, the strengths of Raman spectroscopy are illustrated by considering recent applications from the authors' work that address (1) subunit folding and recognition in assembly of the icosahedral bacteriophages, (2) orientations of subunit main chains and side chains in native filamentous viruses, (3) roles of cysteine hydrogen bonding in the folding, assembly, and function of virus structural proteins, and (4) structural determinants of protein/DNA recognition in gene regulatory complexes. Conventional Raman and polarized Raman techniques are surveyed.

Structural changes of human RNase L upon homodimerization investigated by Raman spectroscopy.

RNase L, a key enzyme in the host defense system, is activated by the binding of 2'-5'-linked oligoadenylates (2-5A) to the N-terminal ankyrin repeat domain, which causes the inactive monomer to form a catalytically active homodimer. We focused on the structural changes of human RNase L as a result of interactions with four different activators: natural 2-5 pA(4) and three tetramers with 3'-end AMP units replaced with ribo-, arabino- and xylo-configured phosphonate analogs of AMP (pA(3)X). The extent of the RNase L dimerization and its cleavage activity upon binding of all these activators were similar. A drop-coating deposition Raman (DCDR) spectroscopy possessed uniform spectral changes upon binding of all of the tetramers, which verified the same binding mechanism. The estimated secondary structural composition of monomeric RNase L is 44% α-helix, 28% ß-sheet, 17% ß-turns and 11% of unordered structures, whereas dimerization causes a slight decrease in α-helix and increase in ß-sheet (ca. 2%) content. The dimerization affects at least three Tyr, five Phe and two Trp residues. The α-ß structural switch may fix domain positions in the hinge region (residues ca. 336-363) during homodimer formation.

A dual surface plasmon resonance assay for the determination of ribonuclease H activity.

There is a demand for efficient tools for the monitoring of RNase H activity. We report on a new assay which allows for simultaneous (1) real-time monitoring of RNase H activity and (2) detection of cleavage reaction products. The dual assay is implemented using a multichannel surface plasmon resonance (SPR) biosensor with two independently functionalized sensing areas in a single fluidic path. In the first sensing area the RNA cleavage by RNase H is monitored, while the products of the cleavage reaction are captured in the second sensing area with specific DNA probes. The assay was optimized with respect to AON concentration and temperature. A significant improvement was obtained with special chimeric probes, which contain RNA substrate for RNase H and a longer deoxyribonucleotide tail, which enhances the SPR signal. It has been shown that RNase H stabilizes the RNA:DNA hybrid duplex before the cleavage. The potential of the assay is demonstrated in the study in which the ability of natural and modified oligonucleotides to activate RNase H is examined.

Shielding effect of monovalent and divalent cations on solid-phase DNA hybridization: surface plasmon resonance biosensor study.

Solid-phase hybridization, i.e. the process of recognition between DNA probes immobilized on a solid surface and complementary targets in a solution is a central process in DNA microarray and biosensor technologies. In this work, we investigate the simultaneous effect of monovalent and divalent cations on the hybridization of fully complementary or partly mismatched DNA targets to DNA probes immobilized on the surface of a surface plasmon resonance sensor. Our results demonstrate that the hybridization process is substantially influenced by the cation shielding effect and that this effect differs substantially for solid-phase hybridization, due to the high surface density of negatively charged probes, and hybridization in a solution. In our study divalent magnesium is found to be much more efficient in duplex stabilization than monovalent sodium (15 mM Mg2+ in buffer led to significantly higher hybridization than even 1 M Na+). This trend is opposite to that established for oligonucleotides in a solution. It is also shown that solid-phase duplex destabilization substantially increases with the length of the involved oligonucleotides. Moreover, it is demonstrated that the use of a buffer with the appropriate cation composition can improve the discrimination of complementary and point mismatched DNA targets.

Structural and dynamic changes of the serum response element and the core domain of serum response factor induced by their association.

Transcriptional activity of serum response factor (SRF) is dependent on its binding to the CC(A/T)(6)GG box (CArG box) of serum response element (SRE). By Raman spectroscopy, we carried out a comparative analysis, in solution, of the complexes obtained from the association of core-SRF with 20-mer SREs bearing wild-type and mutated c-fos CArG boxes. In case of association with the wild type c-fos CArG box, the complex does not bring out the expected Raman signature of a stable bending of the targeted SRE but keeps a bend-linear conformer oligonucleotide interconversion. The linear conformer population is larger than that of free oligonucleotide. In the core-SRF moiety of the wild-type complex a large spectral change associated with the CO-groups from Asp and/or Glu residues shows that their ionization states and the strength of their interactions decrease as compared to those of mutated non-specific complexes. Structural constraints evidenced on the free core-SRF are released in the wild-type complex and environmental heterogeneities appear in the vicinity of Tyr residues, due to higher water molecule access. The H-bonding configuration of one Tyr OH-group, in average, changes with a net transfer from H-bond acceptor character to a combined donor and acceptor character. A charge repartition distributed on both core-SRF and targeted SRE stabilizes the specific complex, allowing the two partners to experience a variety of conformations.

Surface plasmon resonance study on HIV-1 integrase strand transfer activity.

Understanding the molecular mechanism of HIV-1 integrase (IN) activity is critical to find functional inhibitors for an effective AIDS therapy. A robust, fast, and sensitive method for studying IN activity is required. In this work, an assay for real-time label-free monitoring of the IN activity based on surface plasmon resonance was developed. This assay enabled direct monitoring of the integration of a viral doubled-stranded (ds) DNA into the host genome. The strand transfer reaction was detected by using two different DNA targets: supercoiled plasmid (pUC 19) and short palindrome oligonucleotide. The effect of the length of the DNA target on the possibility to monitor the actual process of the strand transfer reaction is discussed. The surface density of integrated ds-DNA was determined. IN binding to the oligonucleotide complexes and model DNA triplexes in the presence of various divalent ions as metal cofactors was investigated as well. The assay developed can serve as an important analytical tool to search for potential strand transfer reaction inhibitors as well as for the study of compounds interfering with the binding of ds long terminal repeats-IN complexes with the host DNA.

Time-resolved microspectrofluorometry and fluorescence imaging techniques: study of porphyrin-mediated cellular uptake of oligonucleotides.

Time-resolved confocal microspectrofluorometry and fluorescence microscopy imaging were applied to monitor the cellular uptake of fluorescent-labeled oligonucleotides (ONs) delivered by a porphyrin molecule. The fate of porphyrin-ON complexes inside living cells has also been monitored. Due to intrinsic fluorescence of the porphyrin and sensitivity of its characteristics to microenvironment, multicomponent analysis of time-resolved fluorescence provides unique information about stability of the porphyrin-ON complexes, ON interactions with their target sequences, and ON and porphyrin distributions after delivery inside the cells. Time-resolved confocal microspectrofluorometry indeed delivers additional information compared with fluorescence confocal microscopy imaging widely employed to study ON uptake.

SERS-activating effect of chlorides on borate-stabilized silver nanoparticles: formation of new reduced adsorption sites and induced nanoparticle fusion.

Changes in morphology, surface reactivity and surface-enhancement of Raman scattering induced by modification of borate-stabilized Ag nanoparticles by adsorbed chlorides have been explored using TEM, EDX analysis and SERS spectra of probing adsorbate 2,2'-bipyridine (bpy) excited at 514.5 nm and evaluated by factor analysis. At fractional coverages of the parent Ag nanoparticles by adsorbed chlorides <0.6, the Ag colloid/Cl(-)/bpy systems were found to be constituted by fractal aggregates of Ag nanoparticles fairly uniform in size (10 +/- 2 nm) and SERS spectra of Ag(+)-bpy surface species were detected. The latter result was interpreted in terms of the presence of oxidized Ag(+) and/or Ag(n)(+) adsorption sites, which have been encountered also in systems with the chemically untreated Ag nanoparticles. At chloride coverages >0.6, a fusion of fractal aggregates into the compact aggregates of touching and/or interpenetrating Ag nanoparticles has been observed and found to be accompanied by the formation of another surface species, Ag-bpy, as well as by the increase of the overall SERS enhancement of bpy by factor of 40. The same Ag-bpy surface species has been detected under the strongly reducing conditions of reduction of silver nitrate by sodium borohydride in the presence of bpy. The formation of Ag-bpy is thus interpreted in terms of the stabilization of reduced Ag(0) adsorption sites by adsorbed bpy. The formation of reduced adsorption sites on Ag nanoparticle surfaces at chloride coverages >0.6 is discussed in terms of local changes in the work function of Ag. Finally, the SERS spectral detection of Ag-bpy species is proposed as a tool for probing the presence of reduced Ag(0) adsorption sites in systems with chemically modified Ag nanoparticles.

C-->G base mutations in the CArG box of c-fos serum response element alter its bending flexibility. Consequences for core-SRF recognition.

By binding to the CArG box sequence, the serum response factor (SRF) activates several muscle-specific genes, as well as genes that respond to mitogens. The core domain of the SRF (core-SRF) binds as a dimer to the CArG box C-5C-4A-3T-2A-1T+1T+2A+3G+4G+5 of the c-fos serum response element (SREfos). However, previous studies using 20-mer DNAs have shown that the binding stoichiometry of core-SRF is significantly altered by mutations C-5-->G (SREGfos) and C-5C-4-->GG (SREGGfos) of the CArG box [A Huet, A Parlakian, M-C Arnaud, J-M Glandières, P Valat, S Fermandjian, D Paulin, B Alpert & C Zentz (2005) FEBS J272, 3105-3119]. To understand these effects, we carried out a comparative analysis of the three 20-mer DNAs SREfos, SREGfos and SREGGfos in aqueous solution. Their CD spectra were of the B-DNA type with small differences generated by variations in the mutual arrangement of the base pairs. Analysis by singular value decomposition of a set of Raman spectra recorded as a function of temperature, revealed a premelting transition associated with a conformational shift in the DNA double helices from a bent to a linear form. Time-resolved fluorescence anisotropy shows that the fluorescein reporter linked to the oligonucleotide 5'-ends experiences twisting motions of the double helices related to the interconversion between bent and linear conformers. The three SREs present various bent populations submitted, however, to particular internal dynamics, decisive for the mutual adjustment of binding partners and therefore specific complex formation.

Surface-enhanced resonance Raman scattering of porphyrins on gold nanoparticles attached to silanized glass plates.

Surface-enhanced resonance Raman scattering (SERRS) spectra of cationic 5,10,15,20-tetrakis(1-methyl-4-pyridyl) porphyrin (TMPyP) and anionic 5,10,15,20-tetrakis(4-sulfonatophenyl) porphyrin (TSPP) were measured from gold surfaces prepared by attaching citrate-reduced colloidal nanoparticles to glass slides silanized by 3-aminopropyltrimethoxysilane. SERRS spectra of both porphyrins obtained in a large concentration range (1 x 10(-4) to 1 x 10(-7)M) of primary solution do not show any sign of porphyrin metalation or perturbation of its native structure. Optimal adsorption time (15-20 min) and covering concentration limit (lower than 1 x 10(-5)M) of porphyrins have been estimated from the concentration and soaking time dependences of SERRS spectra.

Investigating oligonucleotide hybridization at subnanomolar level by surface plasmon resonance biosensor method.

We have optimized surface plasmon resonance (SPR) biosensor technology for a rapid, direct, and low-consumption label-free multianalyte screening of synthetic oligonucleotides (ONs) with modified internucleotide linkages potentially applicable in antisense therapy. Monitoring of the ONs hybridization is based on the formation of complex between the natural oligonucleotide probe immobilized on the sensor surface and the ON in solution in contact with the sensor surface. An immobilization chemistry utilizing the streptavidin-biotin interaction was employed to obtain desired ligand density and high hybridization efficiency. It was demonstrated that the sensor is capable of detecting complementary 23-mer ONs in concentrations as low as 0.1 nM with high specificity and reproducibility.

Structural features of a central mismatch in oligonucleotide hybrid duplexes visualized via Raman spectroscopy: model system for evaluation of potential "antisense" drugs.

Structural features of mismatched base pairs were studied on four nonamer hybrid duplexes formed between the 5'-d(GTGATATGC)-3' complement and its 5'-r(GCAUNUCAC)-3' (N = A, C, G, U) counterparts. This oligonucleotide set is considered a model molecular system for future systematic studies of various modifications of internucleotide linkages with respect to their impact on the structure of mismatched base pairs. Raman spectra, measured at 15 degrees C, revealed the prevailing A-like structure of the RNA strand and mixed A-like and B-like characteristics for the DNA strand. All three mismatches disturb only weakly the overall conformation of the hybrid duplex in contrast to analogous mismatched DNA duplexes. In particular, the dT x rG mismatch influences the global hybrid duplex geometry almost negligibly. The dT x rC and dT x rU mismatches induce somewhat more pronounced distortions of the backbone structure and of the thymine position, the latter being expressed by a change of the surrounding methylene group without effect on the carbonyl's vibrations. Structural effects of the mismatches correlate well with the duplex thermodynamic stabilities obtained by ultraviolet (UV) absorption, i.e., the dT x rG mismatch decreases the hybrid duplex stability very weakly while the effect of both pyrimidine-pyrimidine mismatches is considerable.

Probing of porphyrin surface chemistry in systems with laser-ablated Ag nanoparticle hydrosol: role of thiosulfate anions.

The influence of sodium thiosulfate (THS) concentration in Ag colloid/THS/H(2)TMPyP and Ag colloid/H2TMPyP/THS systems (H2TMPyP = 5,10,15,20-tetrakis(1-methyl-4-pyridyl)porphyrin) was investigated by a combination of surface-enhanced resonance Raman scattering (SERRS) spectroscopy, surface plasmon extinction (SPE) measurements, and transmission electron microscopy (TEM). THS was found to have a strong impact on Ag nanoparticle surface structure and aggregation state and on interaction with H2TMPyP probe molecules, as evidenced by variations of the SERRS spectrum. In the Ag colloid/THS/H2TMPyP system, when laser-ablated Ag colloid was THS pretreated prior to the porphyrin addition, a critical threshold THS concentration (4 x 10(-5) M) was discovered. At concentrations below the threshold, THS mainly reduces the number of Ag+ adsorption sites. This leads to increased Ag nanoparticle aggregation prior to the porphyrin addition and significant weakening of the overall SERRS signal. Dominant contributions in the SERRS spectrum correspond to free base H2TMPyP and Ag+ containing the AgTMPyP form. At concentrations above the threshold, THS mediates also the formation and stabilization of new adsorption sites, probably Ag(0) sites. This induces a turn in the aggregation state of the pretreated Ag-c/THS system, an increase of the overall SERRS signal, and the appearance of a new spectral form of Ag metalated porphyrin.