Multivariate curve resolution: a powerful tool for the analysis of conformational transitions in nucleic acids

Rapid and Highly Efficient Separation of i-Motif DNA Species by CE-UV and Multivariate Curve Resolution

The i-motif is a class of nonstandard DNA structure with potential biological implications. A novel capillary electrophoresis with an ultraviolet absorption spectrophotometric detection (CE-UV) method has been developed for the rapid analysis of the i-motif folding equilibrium as a function of pH and temperature. The electrophoretic analyses are performed in reverse polarity of the separation voltage with 32 cm long fused silica capillaries permanently coated with hydroxypropyl cellulose (HPC), after an appropriate conditioning procedure was used to achieve good repeatability. However, the electrophoretic separation between the folded and unfolded conformers of the studied cytosine-rich i-motif sequences (i.e., TT, Py39WT, and nmy01) is compromised, especially for Py39WT and nmy01, which result in completely overlapped peaks. Therefore, deconvolution with multivariate curve resolution-alternating least-squares (MCR-ALS) has been required for the efficient separation of the folded and unfolded species found at different concentration levels at pH 6.5 and between 12 and 40 °C, taking advantage of the small dissimilarities in the electrophoretic mobilities and UV spectra levels. MCR-ALS has also provided quantitative information that has been used to estimate melting temperatures (Tm), which are similar to those determined by UV and circular dichroism (CD) spectroscopies. The obtained results demonstrate that CE-UV assisted by MCR-ALS may become a very useful tool to get novel insight into the folding of i-motifs and other complex DNA structures.

Cancer Stem Cell Derived Extracellular Vesicles with Self-Functionalized 3D Nanosensor for Real-Time Cancer Diagnosis: Eliminating the Roadblocks in Liquid Biopsy

Liquid biopsy for determining the presence of cancer and the underlying tissue of origin is crucial to overcome the limitations of existing tissue biopsy and imaging-based techniques by capturing critical information from the dynamic tumor heterogeneity. A newly emerging liquid biopsy with extracellular vesicles (EVs) is gaining momentum, but its clinical relevance is in question due to the biological and technical challenges posed by existing technologies. The biological barriers of existing technologies include the inability to generate fundamental details of molecular structure, chemical composition as well as functional variations in EVs by gathering simultaneous information on multiple intra-EV molecules, unavailability of holistic qualitative analysis, in addition to the inability to identify tissue of origin. Technological barriers include reliance on EV isolation with a few labeled biomarkers, resulting in the inability to generate comprehensive information on the disease. A more favorable approach would be to generate holistic information on the disease without the use of labels. Such a marker-free diagnosis is impossible with the existing liquid biopsy due to the unavailability clinically validated cancer stem cells (CSC)-specific markers and dependence of existing technologies on EV isolation, undermining the clinical relevance of EV-based liquid biopsy. Here, CSC EVs were employed as an independent liquid biopsy modality. We hypothesize that tracking the signals of CSCs in peripheral blood with CSC EVs will provide a reliable solution for accurate cancer diagnosis, as CSC are the originators of tumor contributing to tumor heterogeneity. We report nanoengineered 3D sensors of extremely small nano-scaled probes self-functionalized for SERS, enabling integrative molecular and functional profiling of otherwise undetectable CSC EVs. A substantially enhanced SERS and ultralow limit of detection (10 EVs per 10 μL) were achieved. This was attributed to the efficient probe-EV interaction due to the 3D networks of nanoprobes, ensuring simultaneous detection of multiple EV signals. We experimentally demonstrate the crucial role of CSC EVs in cancer diagnosis. We then completed a pilot validation of this modality for cancer detection as well as for identification of the tissue of origin. An artificial neural network distinguished cancer from noncancer with 100% sensitivity and 100% specificity for three hard to detect cancers (breast, lung, and colorectal cancer). Binary classification to distinguish one tissue of origin against all other achieved 100% accuracy, while simultaneous identification of all three tissues of origin with multiclass classification achieved up to 79% accuracy. This noninvasive tool may complement existing cancer diagnostics, treatment monitoring as well as longitudinal disease monitoring by validation with a large cohort of clinical samples.

A Biopharmaceutical Perspective on Higher-Order Structure and Thermal Stability of mRNA Vaccines

Preservation of the integrity of macromolecular higher-order structure is a tenet central to achieving biologic drug and vaccine product stability toward manufacturing, distribution, storage, handling, and administration. Given that mRNA lipid nanoparticles (mRNA-LNPs) are held together by an intricate ensemble of weak forces, there are some intriguing parallels to biologic drugs, at least at first glance. However, mRNA vaccines are not without unique formulation and stabilization challenges derived from the instability of unmodified mRNA and its limited history as a drug or vaccine. Since certain learning gained from biologic drug development may be applicable for the improvement of mRNA vaccines, we present a perspective on parallels and contrasts between the emerging role of higher-order structure pertaining to mRNA-LNPs compared to pharmaceutical proteins. In a recent publication, the location of mRNA encapsulated within lipid nanoparticles was identified, revealing new insights into the LNP structure, nanoheterogeneity, and microenvironment of the encapsulated mRNA molecules [Brader et al. Biophys. J. 2021, 120, 2766]. We extend those findings by considering the effect of encapsulation on mRNA thermal unfolding with the observation that encapsulation in LNPs increases mRNA unfolding temperatures.

Conformational plasticity of DNA secondary structures: probing the conversion between i-motif and hairpin species by circular dichroism and ultraviolet resonance Raman spectroscopies

The promoter regions of important oncogenes such as BCL2 and KRAS contain GC-rich sequences that can form distinctive noncanonical DNA structures involved in the regulation of transcription: G-quadruplexes on the G-rich strand and i-motifs on the C-rich strand. Interestingly, BCL2 and KRAS promoter i-motifs are highly dynamic in nature and exist in a pH-dependent equilibrium with hairpin and even with hybrid i-motif/hairpin species. Herein, the effects of pH and presence of cell-mimicking molecular crowding conditions on conformational equilibria of the BCL2 and KRAS i-motif-forming sequences were investigated by ultraviolet resonance Raman (UVRR) and circular dichroism (CD) spectroscopies. Multivariate analysis of CD data was essential to model the presence and identity of the species involved. Analysis of UVRR spectra measured as a function of pH, performed also by the two-dimensional correlation spectroscopy (2D-COS) technique, showed the role of several functional groups in the DNA conformational transitions, and provided structural and dynamic information. Thus, the UVRR investigation of intramolecular interactions and of local and environmental dynamics in promoting the different species induced by the solution conditions provided valuable insights into i-motif conformational transitions. The combined use of the two spectroscopic tools is emphasized by the relevant possibility of working in the same DNA concentration range and by the heterospectral UVRR/CD 2D-COS analysis. The results of this study shed light on the factors that can influence at the molecular level the equilibrium between the different conformational species putatively involved in the oncogene expression.

Influence of pH and a porphyrin ligand on the stability of a G-quadruplex structure within a duplex segment near the promoter region of the SMARCA4 gene

In a previous work, the formation of G-quadruplex structures in a 44-nucleotide long sequence found near the promoter region of the SMARCA4 gene was reported. The central 25 nucleotides were able to fold into an antiparallel G-quadruplex structure, the stability of which was pH-dependent. In the present work, the effect of the presence of lateral nucleotides and the complementary cytosine-rich strand on the stability of this G-quadruplex has been characterized. Moreover, the role of the model ligand TMPyP4 has been studied. Spectroscopic and separation techniques, as well as multivariate data analysis methods, have been used with these purposes. The results have shown that stability of the G-quadruplex as a function of pH or temperature is greatly reduced in the presence of the lateral nucleotides. The influence of the complementary strand does not prevent the formation of the G-quadruplex. Moreover, attempts to modulate the equilibria by an external ligand led us to determine the influence of the TMPyP4 porphyrin on these complex equilibria. This study could eventually help to understand the regulation of SMARCA4 expression.

SVD-clustering, a general image-analyzing method explained and demonstrated on model and Raman micro-spectroscopic maps

An image analyzing method (SVD-clustering) is presented. Amplitude vectors of SVD factorization (V₁…V_i) were introduced into the imaging of the distribution of the corresponding U_i basis-spectra. Since each V_i vector contains each point of the map, plotting them along the X, Y, Z dimensions of the map reconstructs the spatial distribution of the corresponding U_i basis-spectrum. This gives valuable information about the first, second, etc. higher-order deviations present in the map. We extended SVD with a clustering method, using the significant V_i vectors from the V^T matrix as coordinates of image points in a n_e-dimensional space (n_e is the effective rank of the data matrix). This way every image point had a corresponding coordinate in the n_e-dimensional space and formed a point set. Clustering was applied to this point set. SVD-clustering is universal; it is applicable to any measurement where data are recorded as a function of an external parameter (time, space, temperature, concentration, species, etc.). Consequently, our method is not restricted to spectral imaging, it can find application in many different 2D and 3D image analyses. Using SVD-clustering, we have shown on models the theoretical possibilities and limitations of the method, especially in the context of creating, meaning/interpreting of cluster spectra. Then for real-world samples, two examples are presented, where we were able to reveal minute alterations in the samples (changing cation ratios in minerals, differently structured cellulose domains in plant root) with spatial resolution.

Study of conformational transitions of i-motif DNA using time-resolved fluorescence and multivariate analysis methods

Recently, the presence of i-motif structures at C-rich sequences in human cells and their regulatory functions have been demonstrated. Despite numerous steady-state studies on i-motif at neutral and slightly acidic pH, the number and nature of conformation of this biological structure are still controversial. In this work, the fluorescence lifetime of labelled molecular beacon i-motif-forming DNA sequences at different pH values is studied. The influence of the nature of bases at the lateral loops and the presence of a Watson–Crick-stabilized hairpin are studied by means of time-correlated single-photon counting technique. This allows characterizing the existence of several conformers for which the fluorophore has lifetimes ranging from picosecond to nanosecond. The information on the existence of different i-motif structures at different pH values has been obtained by the combination of classical global decay fitting of fluorescence traces, which provides lifetimes associated with the events defined by the decay of each sequence and multivariate analysis, such as principal component analysis or multivariate curve resolution based on alternating least squares. Multivariate analysis, which is seldom used for this kind of data, was crucial to explore similarities and differences of behaviour amongst the different DNA sequences and to model the presence and identity of the conformations involved in the pH range of interest. The results point that, for i-motif, the intrachain contact formation and its dissociation show lifetimes ten times faster than for the open form of DNA sequences. They also highlight that the presence of more than one i-motif species for certain DNA sequences according to the length of the sequence and the composition of the bases in the lateral loop.

Automated supervised learning pipeline for non-targeted GC-MS data analysis

Non-targeted analysis is nowadays applied in many different domains of analytical chemistry such as metabolomics, environmental and food analysis. Conventional processing strategies for GC-MS data include baseline correction, feature detection, and retention time alignment before multivariate modeling. These techniques can be prone to errors and therefore time-consuming manual corrections are generally necessary. We introduce here a novel fully automated approach to non-targeted GC-MS data processing. This new approach avoids feature extraction and retention time alignment. Supervised machine learning on decomposed tensors of segmented chromatographic raw data signal is used to rank regions in the chromatograms contributing to differentiation between sample classes. The performance of this novel data analysis approach is demonstrated on three published datasets.

Monitoring anthocyanin degradation in Hibiscus sabdariffa extracts with multi-curve resolution on spectral measurement during storage

This study aims to monitor composition changes in an anthocyanin-rich beverage during storage by the means of UV-VIS measurements associated with a multi-curve resolution procedure. Hibiscus sabdariffa extract was stored at 37 °C for 50 days and UV-VIS spectra were measured on the extract and the fractions of the extract every 5 days. MCR was carried out in two steps, first with the fraction and then the extract spectra. The results enabled the main polyphenols initially present to be identified, anthocyanins and chlorogenic acid, but also found the nature of the main degradation products: the polymers from anthocyanin condensation and scission products. In addition, comparison with HPLC analysis results showed that the MCR procedure recovered the correct shapes of the concentration profiles particularly of anthocyanin and polymer kinetics during storage. This work gives perspective for the use of a rapid and efficient technique to monitor pigment-rich beverage processing or storage.

Study of light-induced formation of photodimers in the i-motif nucleic acid structure by rapid-scan FTIR difference spectroscopy and hybrid hard- and soft-modelling

The i-motif is a DNA structure formed by cytosine-rich sequences, very relevant from a biochemical point of view and potentially useful in nanotechnology as pH-sensitive nanodevices or nanomotors. To provide a different view on the structural changes and dynamics of direct excitation processes involving i-motif structures, the use of rapid-scan FTIR spectroscopy is proposed. Hybrid hard- and soft-modelling based on the Multivariate Curve Resolution by Alternating Least Squares (MCR-ALS) algorithm has been used for the resolution of rapid-scan FTIR spectra and the interpretation of the photochemically induced time-dependent conformational changes of i-motif structures. The hybrid hard- and soft-modelling version of MCR-ALS (HS-MCR), which allows the introduction of kinetic models to describe process behavior, provides also rate constants associated with the transitions modeled. The results show that UV irradiation does not produce degradation of the studied sequences but induces the formation of photodimers. The presence of these affect much more the stability of i-motif structures formed by short sequences than that of those formed by longer sequences containing additional structural stabilizing elements, such as hairpins.

Determination of enantiomeric excess of some amino acids by second-order calibration of kinetic-fluorescence data

In this investigation a new non-separative kinetic-spectroflourimetric method is proposed for the determination of lysine (lys), leucine (leu) and phenylalanine (phe) enantiomers as their o-phthaldialdehyde (OPA) derivatives in the presence of an optically active chiral thiol compound, 1-mercapto-2-propanol (MP). At ambient temperature and in the borate buffer media of pH 9.6, MP, OPA, as highly selective fluorogenic reagents, and amino acid (AA) enantiomers reacts with each other to yield two fluorescent diasteriomers of D and L-AA with maximum difference in fluorescence intensity at about 450 nm. To achieve information from the small spectral changes, the data are analyzed by Multivariate Curve Resolution Alternating Least Squares (MCR-ALS) method. Linear calibration curves are achieved to distinct D and L-lys, leu and phe in different mole ratios by applying appropriate constraints in MCR-ALS procedures. This is the first application of MCR-ALS in determination of enantiomeric excess (ee) using OPA/MP adduct as chiral reagent, which benefits from direct time dependent-fluorescence spectral analysis and does not require prior separation of chiral analytes. Both the cross-validated correlation coefficient (Q²) and root mean squares error of prediction (RMSEP) indicated satisfactory prediction ability of this method.

Identification of protein secondary structures by laser induced autofluorescence: A study of urea and GnHCl induced protein denaturation

In the present study an attempt has been made to interrogate the bulk secondary structures of some selected proteins (BSA, HSA, lysozyme, trypsin and ribonuclease A) under urea and GnHCl denaturation using laser induced autofluorescence. The proteins were treated with different concentrations of urea (3M, 6M, 9M) and GnHCl (2M, 4M, 6M) and the corresponding steady state autofluorescence spectra were recorded at 281nm pulsed laser excitations. The recorded fluorescence spectra of proteins were then interpreted based on the existing PDB structures of the proteins and the Trp solvent accessibility (calculated using "Scratch protein predictor" at 30% threshold). Further, the influence of rigidity and conformation of the indole ring (caused by protein secondary structures) on the intrinsic fluorescence properties of proteins were also evaluated using fluorescence of ANS-HSA complexes, CD spectroscopy as well as with trypsin digestion experiments. The outcomes obtained clearly demonstrated GnHCl preferably disrupt helix as compared to the beta β-sheets whereas, urea found was more effective in disrupting β-sheets as compared to the helices. The other way round the proteins which have shown detectable change in the intrinsic fluorescence at lower concentrations of GnHCl were rich in helices whereas, the proteins which showed detectable change in the intrinsic fluorescence at lower concentrations of urea were rich in β-sheets. Since high salt concentrations like GnHCl and urea interfere in the secondary structure analysis by circular dichroism Spectrometry, the present method of analyzing secondary structures using laser induced autofluorescence will be highly advantageous over existing tools for the same.

The RNA Stem-Loop to G-Quadruplex Equilibrium Controls Mature MicroRNA Production inside the Cell

The biological role of the existence of overlapping structures in RNA is possible yet remains very unexplored. G-Rich tracts of RNA form G-quadruplexes, while GC-rich sequences prefer stem-loop structures. The equilibrium between alternate structures within RNA may occur and influence its functionality. We tested the equilibrium between G-quadruplex and stem-loop structure in RNA and its effect on biological processes using pre-miRNA as a model system. Dicer enzyme recognizes canonical stem-loop structures in pre-miRNA to produce mature miRNAs. Deviation from stem-loop leads to deregulated mature miRNA levels, providing readout of the existence of an alternate structure per se G-quadruplex-mediated structural interference in miRNA maturation. In vitro analysis using beacon and Dicer cleavage assays indicated that mature miRNA levels depend on relative amounts of K(+) and Mg(2+) ions, suggesting an ion-dependent structural shift. Further in cellulo studies with and without TmPyP4 (RNA G-quadruplex destabilizer) demonstrated that miRNA biogenesis is modulated by G-quadruplex to stem-loop equilibrium in a subset of pre-miRNAs. Our combined analysis thus provides evidence of the formation of noncanonical G-quadruplexes in competition with canonical stem-loop structure inside the cell and its effect on miRNA maturation in a comprehensive manner.

Application of merged spectroscopic data combined with chemometric analysis for resolution of hemoglobin intermediates during chemical unfolding

Using tetradecyltrimethylammonium bromide (TTAB) as a surfactant denaturant, and augmentation of different spectroscopic data, helped to detect the intermediates of hemoglobin (Hb) during unfolding process. UV-vis, fluorescence, and circular dichroism spectroscopy were used simultaneously to monitor different aspects of hemoglobin species from the tertiary or secondary structure points of view. Application of the multivariate curve resolution-alternating least square (MCR-ALS), using the initial estimates of spectral profiles and appropriate constraints on different parts of augmented spectroscopic data, showed good efficiency for characterization of intermediates during Hb unfolding. These results indicated the existence of five protein species, including three intermediate-like compounds in this process. The unfolding pathway in the presence of TTAB included conversion of oxyhemoglobin into deoxyhemoglobin, and then ferrylhemoglobin, ferrihemoglobin or aquamethemoglobin, which finally transformed into hemichrome. This is the first application of chemometric analysis on the merged spectroscopic data related to chemical denaturation of a protein. These types of analysis in multisubunit proteins not only increase the domain of information, but also can reduce the ambiguities of the obtained results.

The effect of loop residues in four-stranded dimeric structures stabilized by minor groove tetrads

Some DNA oligonucleotides can fold back and self-associate forming dimeric structures stabilized by intermolecular base pairs. The resulting antiparallel dimer is a tightly packed four-stranded structure formed by a core of minor groove tetrads connected by short loops of unpaired nucleotides. We have explored the sequential requirements for the loop residues and have found that this family of structures is only stable with one- and two-residue loops, with the stability of the former ones being only marginal. Two-residue loops with purines in the first position give rise to the most stable structures due to their enhanced stacking interaction with the adjacent minor groove tetrad. On the other hand, pyrimidines confer more stability than purines in the second position of the loop.

Multiway study of hybridization in nanoscale semiconductor labeled DNA based on fluorescence resonance energy transfer

The resolution of the ternary-binary complex competition of a target sequence and of its two complementary probes in sandwich DNA hybridization is reported. To achieve this goal, Fluorescence Resonance Energy Transfer (FRET) between oligonucleotide-functionalized quantum dot (QD) nanoprobes (QD donor-QD acceptor) upon hybridization with a label free target was monitored by two-dimensional photoluminescence excitation spectroscopy (2D-PLE). Detection of a target oligonucleotide strand, using sandwiched nanoassembly in a separation-free format, was performed with the appearance of a new feature in the photoluminescence excitation (PLE) plot. From the obtained data, energy transfer efficiency and Förster radius (R0) were calculated. In particular, our results demonstrated that energy transfer by using QD donor-QD acceptor FRET pairs is more efficient in comparison with QD donor-organic dye acceptor pairs. Soft and model based analysis of 2D-PLE data was implemented by means of PARAFAC and hard trilinear decomposition (HTD), allowing to fit a proper model for FRET-based sandwich DNA hybridization systems. This study is the first successful application of a multiway chemometric technique to consider FRET based DNA hybridization in sandwiched nanoassemblies. A multi-equilibria model was properly fitted to the data and confirmed there is a competition between ternary and binary complex formation. Equilibrium constants of DNA hybridization in sandwiched nanoassemblies were estimated for the first time. Equilibrium constants illustrated that the extent of hybridization in one side on the target strand depends on hybridization conditions on the other side of the strand. Effects of guanine (G) and cytosine (C) contents of strands on the extent and rate of hybridization were investigated. In addition to equilibrium constants of binary and ternary complexes, the pure profiles of all resolved structures were estimated. Ultimately, the described method calculated the analytical concentration of probes as a measure of surface modification yield with DNA using nonlinear fit analysis, without using any calibration sample.

Human telomeric G-quadruplex: thermodynamic and kinetic studies of telomeric quadruplex stability

Thermodynamic and kinetic studies complement high-resolution structures of G-quadruplexes. Such studies are essential for a thorough understanding of the mechanisms that govern quadruplex folding and conformational changes in quadruplexes. This perspective article reviews representative thermodynamic and kinetic studies of the folding of human telomeric quadruplex structures. Published thermodynamic data vary widely and are inconsistent; possible reasons for these inconsistencies are discussed. The key issue of whether such folding reactions are a simple two-state process is examined. A tentative energy balance for the folding of telomeric quadruplexes in Na(+) and K(+) solution, and for the conformational transition between these forms is presented.

Stability and kinetics of G-quadruplex structures

In this review, we give an overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function. The unifying theme in this review is energetics. The thermodynamic stability of quadruplexes has not been studied in the same detail as DNA and RNA duplexes, and there are important differences in the balance of forces between these classes of folded oligonucleotides. We provide an overview of the principles of stability and where available the experimental data that report on these principles. Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes. Techniques that are commonly applied to the determination of the structure, stability and folding are discussed in terms of information content and limitations. Quadruplex structures fold and unfold comparatively slowly, and DNA unwinding events associated with transcription and replication may be operating far from equilibrium. The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence.

Study of the interaction between the G-quadruplex-forming thrombin-binding aptamer and the porphyrin 5,10,15,20-tetrakis-(N-methyl-4-pyridyl)-21,23H-porphyrin tetratosylate

The G-quadruplex DNA structure has been suggested to be a potential target for anticancer therapies. Therefore, there is increasing interest in the development of drugs that could modulate the stability of G-quadruplex structures. In the current work, the interaction between the thrombin-binding aptamer (TBA, 5'-GGT TGG TGT GGT TGG-3'), which can form an intramolecular G-quadruplex structure, and the porphyrin 5,10,15,20-tetrakis-(N-methyl-4-pyridyl)-21,23H-porphyrin tetratosylate (TmPyP4) was studied. The application of a high-performance liquid chromatography-photodiode array (HPLC-PDA) detector-based method to study this kind of interaction was tested. Molecular absorption data recorded along the chromatographic runs were analyzed by means of multivariate data analysis methods. Moreover, biospecific interaction analysis (BIA) by surface plasmon resonance (SPR) and melting and mole ratio experiments monitored by UV-visible molecular absorption and circular dichroism spectroscopies, were applied to confirm and expand the chromatographic studies. The results showed the formation of an interaction complex with a stoichiometry 1:1 (TmPyP4/TBA) and logarithm of the equilibrium constant equal to 5.7+/-0.2. Melting and circular dichroism data reflected that the initial G-quadruplex structure of TBA is stabilized in the interaction complex, being slightly distorted by the presence of the ligand.

Multivariate curve resolution-alternating least squares (MCR-ALS) applied to spectroscopic data from monitoring chemical reactions processes

This paper overviews the application of multivariate curve resolution (optimized by alternating least squares) to spectroscopic data acquired by monitoring chemical reactions and other processes. The goals of the resolution methods and the principles for understanding their applications are described. Some of the problems arising from these evolving systems and the limitations of the multivariate curve resolution methods are also discussed. This article reviews most of the applications of multivariate curve resolution applied to reacting systems published between January 2000 and June 2007. Some basic papers dated before 2000 have also been included.

Biophysical characterization of double-stranded oligonucleotides using ETBR and isothermal fluorescence spectroscopy: implication for SNP genotyping

The UV-absorption, fluorescence and CD spectra of aps 23 bp oligoduplexes were performed for potential diagnostic purpose. These oligonucleotide sequences were mimicked from natural mutations (mitochondrial genome) of human population (unpublished). This work was designed on the basis of hybridization of non-self complementary oligoduplexes (aps) containing no mismatch, one-mismatch and two-mismatches. Since melting temperature is dependent on concentration of the oligoduplex, various concentrations were used in this study protocol. The thermal spectra profiles (UV absorbance and fluorescence) of these oligoduplexes (aps) are different for a particular concentration, and can be implicated for mutations. -dF/dT (or dA/dT) vs T, lnK (or RlnK) vs TM, DeltaG vs TM, DeltaS vs TM and DeltaH vs TM are also variable for those sequences. All these thermodynamic data were calculated from absorbance (at 260 nm) data. On the contrary to the 23 bp oligoduplexes (aps), the PCR products of 97 bp and 256 bp length were genotyped with ETBR (excitation 530 nm, emission 600 nm) fluorimetrically. But our attempts to genotype these PCR sequences with isothermal UV absorbance spectroscopy were unsuccessful. Isothermal UV absorbance spectra has a limitation of sequence length. However, the structural conformation (all B-type) of the oligoduplexes (aps) was determined using CD. The minor discrepancy in CD spectra of these oligoduplexes are not significant for mutational analysis. 97 bp nested PCR product was an amplicon having either GcT or AcC mutation of mitochondria of normal human population, whereas 256 bp PCR product was an amplicon of human BRCA2 gene (NCBI Accession No. AY151039) of chromosome 13 having either A or G mutation at position -26.

Spectroscopic study of the interaction of actinomycin D with oligonucleotides carrying the central base sequences -XGCY- and -XGGCCY- using multivariate methods

The interactions of actinomycin D (ACTD) with the oligonucleotides 5'-CAAAGCTTTG-3', 5'-CATGGCCATG-3' and 5'-TATGGCCATA-3' were investigated by means of acid-base titrations and mole-ratio and melting experiments monitored by molecular absorption and circular dichroism (CD) spectroscopies. For each experiment, CD and molecular absorption spectra were recorded at each point in the experiment, and later analyzed via appropriate multivariate data analysis methods. The study of the interactions between these oligonucleotides and ACTD at 25 degrees C showed the formation of an interaction complex with a stoichiometry of 1:1 (ACTD:duplex) and values for the log(formation constant) of 5.1+/-0.3, 6.4+/-0.2, and 5.6+/-0.2, respectively. An additional interaction complex at higher temperatures was also detected, which might be related to the single-stranded forms of the oligonucleotides.

Exploratory data analysis of DNA microarrays by multivariate curve resolution

In this work, the application of a multivariate curve resolution procedure based on alternating least squares optimization (MCR-ALS) for the analysis of data from DNA microarrays is proposed. For this purpose, simulated and publicly available experimental data sets have been analyzed. Application of MCR-ALS, a method that operates without the use of any training set, has enabled the resolution of the relevant information about different cancer lines classification using a set of few components; each of these defined by a sample and a pure gene expression profile. From resolved sample profiles, a classification of samples according to their origin is proposed. From the resolved pure gene expression profiles, a set of over- or underexpressed genes that could be related to the development of cancer diseases has been selected. Advantages of the MCR-ALS procedure in relation to other previously proposed procedures such as principal component analysis are discussed.

Resolution of a structural competition involving dimeric G-quadruplex and its C-rich complementary strand

The resolution of the dimeric intermolecular G-quadruplex/duplex competition of the telomeric DNA sequence 5′-TAG GGT TAG GGT-3′ and of its complementary 5′ ACC CTA ACC CTA-3′ is reported. To achieve this goal, melting experiments of both sequences and of the mixtures of these sequences were monitored by molecular absorption, molecular fluorescence and circular dichroism spectroscopies. Molecular fluorescence measurements were carried out using molecular beacons technology, in which the 5′-TAG GGT TAG GGT-3′ sequence was labelled with a fluorophore and a quencher at the ends of the strand. Mathematical analysis of experimental spectroscopic data was performed by means of multivariate curve resolution, allowing the calculation of concentration profiles and pure spectra of all resolved structures (dimeric antiparallel and parallel G-quadruplexes, Watson–Crick duplex and single strands) present in solution. Our results show that parallel G-quadruplex is more stable than antiparallel G-quadruplex. When the complementary C-rich strand is present, a mixture of both G-quadruplex structures and Watson–Crick duplex is observed, the duplex being the major species. In addition to melting temperatures, equilibrium constants for the parallel/antiparallel G-quadruplex equilibrium and for the G-quadruplex/duplex equilibrium were determined from the concentration profiles.

Application of multivariate resolution methods to the study of biochemical and biophysical processes

Multivariate resolution methods make up a set of mathematical tools that may be applied to the analysis and interpretation of spectroscopic data recorded when monitoring a physical or chemical process with multichannel detectors. The goal of resolution methods is the recovery of chemical and/or physical information from the experimental data. Such data include, for example, the number of intermediates present in a reaction, the rate or equilibrium constants, and the spectra for each one of those intermediates. Multivariate resolution methods have been shown to be useful for the study of biophysical and biochemical processes such as folding/unfolding of proteins or nucleic acids. The present article reviews the most frequently used resolution methods, the limitations on their use, and their latest applications in protein and nucleic acid research.

Multivariate Curve Resolution Applied to the Analysis and Resolution of Two-Dimensional [1H,15N] NMR Reaction Spectra

Multivariate curve resolution is proposed for the study of complex chemical reactions monitored by two-dimensional (2D) NMR spectroscopy. In particular, in this work, multivariate curve resolution is applied to the study of the reaction between (15)N-labeled cisplatin and the amino acid-nucleotide hybrid (Phac-Met-linker-p(5')dG). At several stages of the reaction, 2D [(1)H,(15)N] HSQC NMR spectra were acquired and stored in data matrices. In a first step, multivariate curve resolution was applied to analyze individually each one of these 2D spectra, allowing the resolution of the corresponding (1)H and (15)N one-dimensional correlation spectra. In a second step, the whole set of 2D spectra recorded along the reaction were simultaneously analyzed by multivariate curve resolution, allowing the resolution of the kinetic concentration profiles and of the pure 2D NMR spectra of each of the species detected along the reaction. Results finally obtained confirmed previously postulated reaction mechanisms involving the existence of two monofunctional adducts and of two bifunctional adducts, with the structure of one of them not completely resolved.

Multivariate curve resolution methods in imaging spectroscopy: influence of extraction methods and instrumental perturbations

Imaging spectroscopy is becoming a key field of analytical chemistry. In the face of more and more complex samples, we actually need accurate microscopic insight. Nowadays, the methods used to produce concentration maps of the pure compounds from spectral data sets are based on the classical univariate approach although multivariate approaches are sometimes investigated. But in any case, the analytical quality of the chemical images thus provided cannot be discussed since no reference methods are at our disposal. Thus the proposed research focuses on the application of multivariate methods such as Orthogonal Projection Approach (OPA), SIMPLE-to-use Self-modeling Mixture Analysis (SIMPLISMA), Multivariate Curve Resolution - Alterning Least Squares (MCR-ALS), and Positive Matrix Factorization (PMF) for imaging spectroscopy. A systematic and quantitative characterization of the accuracy of spectra and images extraction is investigated on mid-infrared spectral data sets. Of special interest is the influence of instrumental perturbations such as noise and spectral shift on the extraction ability to access the algorithm's robustness.

Synthesis, stability, and protonation studies of a self-complementary dodecamer containing the modified nucleoside 2'-deoxyzebularine

The nucleoside 2'-deoxyzebularine (K) was incorporated into the self-complementary dodecamer 5'-CGTACGKGTACG-3' by solid-phase 2-cyanoethylphosphoramidite chemistry using dimethoxytrityl (DMT) as the 5'-hydroxyl protecting group. Standard synthesis cycles using trichloroacetic acid and short ammonia treatment (50 degrees C for 30 min) were found to be the optimal conditions to obtain the desired dodecamer with minimum acid and basic degradation of the acid- and base-sensitive 2-pyrimidinone residue. The protonation equilibria of the K nucleoside and of the dodecamer at 37 degrees C were studied by means of spectroscopically monitored titrations. For the K nucleoside, a pK(a) value of 3.13 +/- 0.09 was obtained. For the dodecamer, four acid-base species were found in the pH range 2-12, with pK(a) values of 9.60 +/- 0.07, 4.46 +/- 0.16, and 2.87 +/- 0.19. Melting experiments were carried out to confirm the proposed acid-base concentration profiles. Finally, kinetic experiments were also carried out at several pH values to evaluate the stability of the K nucleoside and of the dodecamer. An increased stability was shown by the K nucleoside when incorporated into the dodecamer. Multivariate methods based on both hard- and soft-modeling were applied for the analysis of spectroscopic data, allowing the estimation of concentration profiles and pure spectra.

Resolution of parallel and antiparallel oligonucleotide triple helices formation and melting processes by multivariate curve resolution

A procedure is described for the complete resolution of concentration profiles of oligonucleotide triplexes as a function of pH and temperature. The pH and temperature ranges at which triplexes are present and the relative concentrations of all the species involved in acid-base and conformational equilibria are successfully estimated from Multivariate Curve Resolution analysis of UV absorbance spectra recorded along acid-base titrations and melting experiments of single stranded, hairpin and their mixtures. The dependence of formation constants upon pH was successfully estimated. The hairpin h26 (5'-GAAGGAGGAGA-TTTT-TCTCCTCCTTC-3'), and the single stranded oligonucleotides s11CT (5'-CTTCCTCCTCT-3'), s11AG (5'-AGAGGAGGAAG-3') and s11TG (5'-TGTGGTGGTTG-3') were synthesized and their protonation and conformational equilibria were studied in detail. The procedure was shown to be especially useful for the study of triplexes with a low hypochromism upon formation.