Premelting Changes in DNA Conformation

Beyond amyloid proteins: Thioflavin T in nucleic acid recognition

Thioflavin T (ThT) is a commercially available fluorescent dye that is commonly used in biomedical research for over five decades. It was first reported as an extrinsic fluorescent probe for the detection of amyloid fibrils and related processes and it has also been used extensively for assessing protein binding in fluorescence-based assays. Although the nucleic acid binding of ThT was reported half of a century ago in the 1970s, it was not widely explored until the start of this decade. In recent years, Thioflavin T has become a major tool in the recognition of many types of non-canonical nucleic acid conformations including duplexes, triplexes, and G-quadruplexes. The propensity of ThT binding is more towards base aberrations, bulges, and mismatches highlighting its importance in serving as a diagnostic tool in a variety of ailments/disease conditions. In this review, we cover major advancements in nucleic acid detection/binding by ThT to a variety of nucleic acid structures.

Fluctuations in the DNA double helix: A critical review

A critical overview of the extensive literature on fluctuations in the DNA double helix is presented. Both theory and experiment are comprehensively reviewed and analyzed. Fluctuations, which open up the DNA double helix making bases accessible for hydrogen exchange and chemical modification, are the main focus of the review. Theoretical descriptions of the DNA fluctuations are discussed with special emphasis on most popular among them: the nonlinear-dynamic Peyrard-Bishop-Dauxois (PBD) model and the empirical two-state (or helix-coil) model. The experimental data on the issue are comprehensibly overviewed in the historical retrospective with main emphasis on the hydrogen exchange data and formaldehyde kinetics. The theoretical descriptions are critically evaluated from the viewpoint of their applicability to describe DNA in water environment and from the viewpoint of agreement of their predictions with the reliable experimental data. The presented analysis makes it possible to conclude that, while the two-state model is most adequate from theoretical viewpoint and its predictions, based on an empirical parametrization, agree with experimental data very well, the PBD model is inapplicable to DNA in water from theoretical viewpoint on one hand and it makes predictions totally incompatible with reliable experimental data on the other. In particular, it is argued that any oscillation movements of nucleotides, assumed by the PBD model, are severely damped in water, that no "bubbles", which the PBD model predicts, exist in reality in linear DNA well below the melting range and the lifetime of an open state in DNA is actually 5 orders of magnitude longer than the value predicted by the PBD model.

Early stage of nucleic acid electrochemistry. Detection of DNA damage in X-ray-irradiated rats

First papers on electroactivity of DNA and RNA were published more then 50 years ago. For about 8 years oscillographic polarography at controlled a.c. (OP, proposed by J. Heyrovský already in 1941) was the method of choice for DNA analysis. Since approximately 1954 Robert Kalvoda developed OP for wide application in various fields. It is shown that already before 1960 it was possible to detect damage to DNA in X-ray-irradiated rats by means of OP. DNA samples from irradiated animals produced significantly larger OP anodic guanine signal indicating changes in the DNA structure. At present, radiation-induced strand breaks and damage to bases in DNA can be electrochemically detected at high sensitivity.

New approaches in the development of DNA sensors: hybridization and electrochemical detection of DNA and RNA at two different surfaces

Up to now, the development of the electrochemical DNA hybridization sensors relied on solid electrodes, on which both the hybridization and detection steps have been performed. Here we propose a new method in which the DNA hybridization is performed at commercially available magnetic beads and electrochemical detection on detection electrodes (DE). Due to minimum nonspecific DNA adsorption at the magnetic beads, very high specificity of the DNA hybridization is achieved. Optimum DE can be chosen only with respect to the given electrode process. It is shown that high sensitivity and specificity in the detection of relatively long target DNAs can be obtained (a) by using cathodic stripping voltammetry at mercury or solid mercury amalgam DEs for the determination of purine bases, released from DNA by acid treatment, and (b) by enzyme-linked immunoassay of target DNA modified by osmium tetroxide,2,2'-bipyridine (Os,bipy) at carbon DEs. Direct determination of Os,bipy at mercury and carbon electrodes is also possible.

Intermediate filaments reconstituted from vimentin, desmin, and glial fibrillary acidic protein selectively bind repetitive and mobile DNA sequences from a mixture of mouse genomic DNA fragments

Employing the whole-genome PCR technique, intermediate filaments (IFs) reconstituted from vimentin, desmin, and glial fibrillary acidic protein were shown to select repetitive and mobile DNA sequence elements from a mixture of mouse genomic DNA fragments. The bound fragments included major and minor satellite DNA, telomere DNA, minisatellites, microsatellites, short and long interspersed nucleotide elements (SINEs and LINEs), A-type particle elements, members of the mammalian retrotransposon-like (MaLR) family, and a series of repeats not assignable to major repetitive DNA families. The latter sequences were either similar to flanking regions of genes; possessed recombinogenic elements such as polypurine/polypyrimidine stretches, GT-rich arrays, or GGNNGG signals; or were characterized by the distribution of oligopurine and pyrimidine motifs whose sequential and vertical alignment resulted in patterns indicative of high recombination potentials of the respective sequences. The different IF species exhibited distinct quantitative differences in DNA selectivities. Complexes consisting of vimentin IFs and DNA fragments containing LINE, (GT)(n) microsatellite, and major satellite DNA sequences were saturable and dynamic and were formed with high efficiency only when the DNAs were partially denatured. The major-groove binder methyl green exerted a stronger inhibitory effect on the binding reaction than did the minor-groove binder distamycin A; the effects of the two compounds were additive. In addition, DNA footprinting studies revealed significant configurational changes in the DNA fragments on interaction with vimentin IFs. In the case of major satellite DNA, vimentin IFs provided protection of the T-rich strand from cleavage by DNase I, whereas the A-rich strand was totally degraded. Taken together, these observations suggest that IF protein(s) bind to double-stranded DNAs at existing single-stranded sites and, taking advantage of their helix-destabilizing potential, further unwind them via a cooperative effort of their N-terminal DNA-binding regions. A comparison of the present results with literature data, as well as a search in the NCBI database, showed that IF proteins are related to nuclear matrix attachment region (MAR)-binding proteins, and the DNA sequences they interact with are very similar or even identical to those involved in a plethora of DNA recombination and related repair events. On the basis of these comparisons, IF proteins are proposed to contribute in a global fashion, not only to genetic diversity, but also to genomic integrity, in addition to their role in gene expression.

Voltammetric response and determination of DNA with a silver electrode

A current from DNA was obtained using a silver electrode with low overpotentials for the first time. Experimental results revealed that the voltammetric response of DNA was attributed to the redox reactions of purine bases. It was also shown that such a method provided a convenient and practical way to determine DNA. A linear dependence of the peak currents on ssDNA concentrations was observed in the range 0.5-2.5 microg/mL. The relative standard deviation was 3.5% for six successive determinations at 0.5 microg/mL. The detection limit was 50 ng/mL. Influence of the structure and the length of the nucleic acids on their electrochemical behavior was discussed. In view of the merits of the silver electrode, this technique might provide new possibilities for further electrochemical research and determination of nucleic acids.

NMR study on the binding of d(GGAAATTTCC)2 with a positively charged pentacosapeptide

To obtain a better understanding of the electrostatic nature of protein-nucleic acid interactions, we have investigated the interaction of a double-stranded decamer d(GGAAATTTCC)2 with a synthetic arginine and lysine-rich pentacosapeptide (Pep25), using NMR and optical spectroscopy. The chemical shift data of the decamer under various experimental conditions show that the binding of Pep25 changes the conformation of the decamer in a different way, as compared to the conformational changes induced by a variation in temperature or ionic strength. The chemical shift results are interpreted in terms of ring current effects that emerge into a model for the conformational change, in which the double-stranded helix of the decamer undergoes a decrease of twist and rise to accommodate Pep25. The binding results indicate that the positively charged arginine and lysine side chains of Pep25 not only have a stabilising electrostatic interaction with the negatively charged backbone phosphates of d(GGAAATTTCC)2, but also that a stabilisation of the base pairs of d(GGAAATTTCC)2 by Pep25 takes place.

Effect of temperature on DNA secondary structure in the absence and presence of 0.5 M tetramethylammonium chloride

Changes in the average secondary structures of three different linear DNAs over the premelting region from 5 to 60 degrees C were investigated by measuring their CD spectra and also their torsion elastic constants (<alpha>) by time-resolved fluorescence polarization anisotropy. For one of these DNAs, the Haell fragment of pBR322, the apparent diffusion coefficients [Dapp(k)] at small and large scattering vectors (k) were also measured by dynamic light scattering. With increasing temperature, all three DNAs exhibited typical premelting changes in their CD spectra, and these were accompanied by 1.4- to 1.7-fold decreases in <alpha>. Also for the 1876 base pair fragment, Dapp(k) at large scattering vectors, which is sensitive to the dynamic bending rigidity, decreased by 17%, even though there was no change at small scattering vectors, where Dapp(k) = D0 is the translational diffusion coefficient of the center-of-mass. These observations demonstrate conclusively that the premelting CD changes of these DNAs are associated with a significant change in average secondary structure and mechanical properties, though not in persistence length. In the presence of 0.5 M tetramethylammonium chloride (TMA-Cl) the premelting change in CD is largely suppressed, and the corresponding changes in <alpha> and Dapp(k) at large scattering vectors are substantially diminished. These observations suggest that TMA-Cl, which binds preferentially to A.T-rich regions and stabilizes those regions (relative to G.C-rich regions) against melting, effectively stabilizes the prevailing low-temperature secondary structure sufficiently that the DNA is effectively trapped in that state over the temperature range observed.

Abolition of intrinsically bent DNA structure components in AT clusters by netropsin interaction; titration viscometric investigations

It is argued that the enhancement of the apparent DNA contour length by the specifically binding non-intercalating drug netropsin (Nt) (Reinert et al., NAR 9, 2335, 1981) at very low Nt/DNA-phosphate ratios essentially is the result of an abolition of periodically arranged intrinsic helix bends in A.T rich tracts of base pairs. In the preceding paper the existence of pronounced DNA tertiary structure components has been postulated for (two species of) natural eukaryotic DNA. The resulting model suggests local apparent solenoid-related DNA tertiary structure components at high sodium ion concentration cs, partly/totally molten out at 45/60 C. With decreasing cs the tertiary structure components have been found to be gradually reduced, at least below cs = 0.010 M, as titration viscometrically revealed by a gradual rise of the apparent DNA contour length (Reinert et al., JBSD 9, 537, 1991). Hence, we performed titration viscometric analyses about Nt interaction with calf thymus DNA (ctDNA) at cs = 0.075 M, 0.010 M and 0.004 M Na+. The concomitant DNA conformational changes are quantitatively described in terms of the relative changes of both DNA persistence length and hydrodynamically operative apparent DNA contour length for the three first resolved interaction modes below a Nt/DNA-P ratio of 0.03. These experiments, together with previous respective analyses at cs = 0.20 M Na+ and different temperatures (l.c.), suggest that those DNA sites binding Nt most strongly predominantly are responsible for the formation of solenoid-related DNA tertiary structure components. Most probably these are A tract-containing sequences. As the essential factor for their apparent elongation effect at low Na+ concentrations, a gradual alteration of the number of base pairs per helix turn seems to occur below cs = 0.010 M Na+ and, concomitantly, a change in phasing between intrinsic helix bends and helix screw.

Local opening of the DNA double helix in eukaryotic cells detected by osmium probe and adduct-specific immunofluorescence

The structure of DNA in mouse fibroblast 3T3 cells has been investigated with the single-strand-selective probe, the complex of osmium tetroxide and 2,2′-bipyridine (Os,bipy). DNA-Os,bipy adducts in the cells were detected by immunofluorescence using a highly specific, affinity-purified polyclonal antibody. Treatment of living cells with the chemical probe led to a distinct but nonuniform nuclear staining. We attribute the positive nuclear staining to the existence of single-stranded and distorted DNA regions in the living cell. Confocal laser scanning microscopy revealed dark areas corresponding to nucleoli and regions of condensed chromatin. These conclusions were supported by the results of experiments in which the chemical probe was applied to fixed cells treated with 45% acetic acid or with acidic buffers (pH 1.8-2.5). An inverse staining pattern was obtained, characterized by intense immunofluorescence of the condensed chromatin regions. Thus, the structural transitions and/or chemical alterations (e.g. depurination) induced by acid treatment increase the accessibility of normally unreactive DNA bases. We conclude that open DNA structures recognized by the chemical probe in the cells prior to their fixation are contained mainly in decondensed and transcriptionally active chromatin, but are virtually absent from nucleoli and condensed chromatin.

Local supercoil-stabilized DNA structures

The DNA double helix exhibits local sequence-dependent polymorphism at the level of the single base pair and dinucleotide step. Curvature of the DNA molecule occurs in DNA regions with a specific type of nucleotide sequence periodicities. Negative supercoiling induces in vitro local nucleotide sequence-dependent DNA structures such as cruciforms, left-handed DNA, multistranded structures, etc. Techniques based on chemical probes have been proposed that make it possible to study DNA local structures in cells. Recent results suggest that the local DNA structures observed in vitro exist in the cell, but their occurrence and structural details are dependent on the DNA superhelical density in the cell and can be related to some cellular processes.

Environment-induced changes in DNA conformation as probed by ethidium bromide fluorescence

The interaction of the ethidium cation with calf thymus DNA is investigated in solutions of different ionic strength and temperature by observation of the enhancement of fluorescence of ethidium upon intercalation in the duplex structure. The quantum yield of the fluorescence of the intercalated dye is found to increase either upon lowering the Na+ concentration or upon increasing the temperature. The existence of a correlation between the geometry of the intercalation complex and the features of the secondary structure of DNA is suggested. Binding isotherms under corresponding environmental conditions are also quantitated by fluorescence enhancement and interpreted in terms of the neighbor exclusion model. Large contributions from change in hydration to the thermodynamics of binding are demonstrated by the temperature dependences of the equilibrium constants. The neighbor exclusion range is found to be practically independent of the salt concentration but its value increases from an average of 2.4 around room temperature to 4-5 at 80 degrees C, as inferred from the binding curves in 0.15 and 0.5 M [Na+] or from the DNA hypochromism vs temperature profiles of complexes at 10(-3) M [Na+]. All the data point to a possible sequence-conformation specificity in the intercalation of ethidium which in heterogeneous DNA is mediated by environmental changes.

Physical studies of DNA premelting equilibria in duplexes with and without homo dA.dT tracts: correlations with DNA bending

We have employed a variety of physical methods to study the equilibrium melting and temperature-dependent conformational dynamics of dA.dT tracts in fractionated synthetic DNA polymers and in well-defined fragments of kinetoplast DNA (kDNA). Using circular dichroism (CD), we have detected a temperature-dependent, "premelting" event in poly(dA).poly(dT) which exhibits a midpoint near 37 degrees C. Significantly, we also detect this CD "premelting" behavior in a fragment of kDNA. By contrast, we do not observe this "premelting" behavior in the temperature-dependent CD spectra of poly[d(AT)].poly[d(AT)], poly(dG).poly(dC), poly[d(GC)].poly[d(GC)], or calf thymus DNA. Thus, poly(dA).poly(dT) and kDNA exhibit a common CD-detected "premelting" event which is absent in the other duplex systems studied in this work. Furthermore, we find that the anomalous electrophoretic retardation of the kDNA fragments we have investigated disappears at temperatures above approximately 37 degrees C. We also observe that the rotational dynamics of poly(dA).poly(dT) and kDNA as assessed by singlet depletion anisotropy decay (SDAD) and electric birefringence decay (EBD) also display a discontinuity near 37 degrees C, which is not observed for the other duplex systems studied. Thus, in the aggregate, our static and dynamic measurements suggest that the homo dA.dT sequence element [common to both poly(dA).poly(dT) and kDNA] is capable of a temperature-dependent equilibrium between at least two helical states in a temperature range well below that required to induce global melting of the host duplex. We suggest that this "preglobal" melting event may correspond to the thermally induced "disruption" of "bent" DNA.

Electron microscopy of supercoiled pEJ4 DNA containing homopurine.homopyrimidine sequences

Supercoiled pEJ4 DNA (a derivative of pUC19 containing an insert with 60-bp-long homopurine.homopyrimidine tract from the sea urchin P. miliaris histone gene spacer) was investigated by electron microscopy using three different spreading techniques i.e., formamide and aqueous variants of the Kleinschmidt technique and protein-free benzyldimethyl-alkyl ammonium chloride (BAC) technique at different pHs. If the specimens for electron microscopy were prepared at pH 5.6 and pH 4.0 (i.e., under conditions where the homopurine.homopyrimidine tract assumes an unusual conformation) a single thick "stem" or a "denaturation bubble" in a large number of DNA molecules were observed. No such changes were found in samples prepared at neutral pH and in linearized pEJ4 DNA prepared at pH 5.6. In specimens of a control supercoiled pUC19 DNA prepared at pH 5.6 and 4.0 practically no local changes were detected. The "denaturation bubbles" were observed by BAC techniques (probably due to secondary local DNA denaturation during the specimen preparation) while the more gentle formamide technique revealed only "stems". The "stems" were almost always positioned at the sites where the curvature of supercoiled DNA molecules occurred. The results are in agreement with presence of a protonated triplex H-form in homopurine.homopyrimidine tract bringing the first evidence of curvature or kinking of the DNA molecule connected with the occurrence of the H-form in supercoiled DNA.

Chemically reversible electroreduction of guanine in a polynucleotide chain

It was shown that synthetic polynucleotides containing guanine display in cyclic voltammetry (CV) an anodic peak close to -0.3 V (against a saturated calomel electrode). A condition for the appearance of this peak is the previous polarization of the mercury electrode to sufficiently negative potentials (around -1.8 V). The results of CV measurements with electrode polarization by repeated cycles indicate that in negative potentials there is a reduction of guanine residues and in the anodic process reoxidation of the reduction product to guanine. This chemically reversible process takes place even when a polynucleotide contains adenine and/or cytosine residues in addition to guanine, where reduction leads to the formation of products blocking the electrode surface.

Circular dichroism study of stacking properties of oligodeoxyadenylates and polydeoxyadenylate. A three-state conformational model

The temperature dependence of the circular dichroism (CD) spectra of a series of deoxyadenylates (dA)n, n = 2, 3, 6, 9, 12, infinity, in aqueous solution was studied. The data were interpreted on the basis of a new conformational model for the stacked state suggested by our previous proton NMR studies on (dA)2 and (dA)3 [C. S. M. Olsthoorn, L. J. Bostelaar, J. H. van Boom & C. Altona (1980) Eur. J. biochem. 112, 95-110]. In this model the stacked regions of the single-stranded oligomers consist of residues taking up a geometry resembling that of the B-DNA genus of structures (all sugars S or C2'-endo) except those residues at the 3' end that do not 'feel' a following stacking interaction. The deoxyribose rings in the latter residues retain (or regain when melting out removes a stacking interaction somewhere along the chain) the conformational freedom (S in equilibrium N, N = C3'-endo) that these rings possess in the monomers 2'-deoxyadenosine 5'-methylphosphate or in 2'-deoxyadenosine 3',5'-bis(methylphosphate), as the case may be. It is shown that this model allows (a) construction of the CD spectra of (dA)n, n = 3, 6, 9, 12, from those of the dimer and the polymer; (b) the separation of the weak CD displayed by the regular S-S stacking mode and the far stronger CD exhibited by the 3'-end S-N stacking (the latter CD resembles that of the A-DNA genus of structures); (c) delineation of the thermodynamics of stacking. The melting temperature remains constant and independent of chain length (about 50 degrees C) whereas delta H degrees and delta S degrees show a slight increase in absolute values on increasing n from 2 to infinity owing to small cooperativity effects. Near 0 degrees C the dimer occurs for about 90% in the stacked form, the oligomers attain even higher conformational purities. It is suggested that premelting phenomena observed in the CD spectra of double-helical DNAs may also involve local transitions from the normal B-like ----S-S-s---- stacking mode to an A-like ----S-S-N---- stacking geometry.

Effect of tetramethylammonium ion on the helix-to-coil transition of poly(deoxyadenylylthymidine): a nuclear magnetic resonance and calorimetric investigation

Differential scanning calorimetry, temperature-dependent NMR, and UV spectroscopy are used to investigate the helix-to-coil transition of poly(deoxyadenylylthymidine) [poly(dA-dT)] in 1 M NaCl and 1 M Me4NCl (tetramethylammonium chloride). All three methods reveal that the polymer has a melting temperature, tm, that is approximately 6 degree C higher in 1 M Me4NCl than in 1 M NaCl. The NMR data show that this increased stability does not result from fundamental changes in base stacking or base pairing in going from 1 M NaCl to 1 M Me4NCl. Consistent with this observation, the calorimetric measurements yield essentially equal enthalpies for the helix-to-coil transition under the two salt conditions (6.8 kcal per base pair in 1 M NaCl and 7.0 kcal per base pair in M Me4NCl). Analysis of the shapes of the calorimetric curves shows that the transition is more cooperative in Me4NCl than in NaCl. Comparison of the calorimetric and van't Hoff enthalpies allows specification of the size of the cooperative unit: 27 base pairs in 1 M NaCl and 32 base pairs in 1 M Me4NCl. The NMR data reveal that the major Me4NCl-induced structural alterations (relative to NaCl) are a change in one glycosidic torison angle and a partial resolution of the two phosphates. The calorimetric experiments indicate that in the absence of fortuitous compensation these conformational changes are not accompanied by a significant enthalpy effect. On the basis of these data, we suggest that in 1 M NaCl poly(dA-dT) assumes predominantly a B-DNA-like conformation where the symmetry repeat occurs every base pair. By contrast, in 1 M Me4NCl the predominant conformation exhibits a dinucleotide repeat consistent with a right-handed alternating B-DNA structure.

Effect of tetramethylammonium ions on conformational changes of DNA in the premelting temperature range

The reversible conformational change of DNAs and polydeoxyribonucleotides occurring before melting was followed by circular dichroism. deltatheta/deltaT, the rate of change of ellipticity theta with temperature, was used mainly as a measure of this premelting phenomenon. If sodium ions were replaced by tetramethylammonium ions deltatheta/deltaT decreased for poly (dA) poly (dT) and poly (dA.dT) poly (dT.dA), but increased for poly (dG.dC) poly (dC.dG). DNAs of different base composition showed no more premelting (deltatheta/deltaT approximately 0) even at low molarities of TMACl provided the Na/TMA ratio was very small. For all cases studied the theta values at 0 degrees C and at a given ionic strength were smaller in NaCl than in TMACl. When studying the series of ammonium ions from NH4+ to (C2H5)4N+, the deltatheta/deltaT values first decreased, going through zero with TMA+ ions, and then increased again. A tentative and qualitative explanation of our results can be given: (a) Hydration of the polymers increases in presence of TMA ions and their average stability decreases; locally, however, (AT) pairs are preferentially stabilized by TMA ions owing to a specific interaction at the level of O2 of thymine. (b) In order to explain the different behaviour of (AT) polymers and DNA, it is assumed that only the B structure is able to accommodate TMA ions in the small groove of the double stranded helix.