Influence of defects on the electrophoretic, thermodynamic and dielectric properties of a 21 base pair DNA in solution

Melting of DNA oligomers: dynamical models and comparison with experimental results

We compare experimental melting curves of short heterogeneous DNA oligomers with theoretical curves derived from statistical mechanics. Partition functions are computed with the one-dimensional Peyrard-Bishop (PB) Hamiltonian, already used in the study of the melting of long DNA chains. Working with short chains we take into account, in the computations, not only the breaking of the interstrand hydrogen bonds, but also the complete dissociation of the double helix into separate single strands. Since this dissociation equilibrium is of general relevance, independent of the particular microscopic model, we give some details of its treatment. We discuss how the non bonded three-dimensional interactions, not explicitly considered in the one-dimensional PB model, are taken into account through the treatment of the dissociation equilibrium. We also evaluate the relevance of the dissociation as a function of the chain length.

Theoretical evaluation of dielectric absorption of microwave energy at the scale of nucleic acids

A theoretical model is proposed for the evaluation of dielectric properties of the cell nucleus between 0.3 and 3 GHz, as a function of its nucleic acids (NA) concentration (CNA). It is based on literature data on dielectric properties of DNA solutions and nucleoplasm. In skeletal muscle cells, the specific absorption rate (SAR) ratio between nucleoplasm and cytoplasm is found to be larger than one for CNA above 30 mg/ml. A nearly linear relationship is found between CNA and this nucleocytoplasmic SAR ratio. Considering the nanoscale of the layer of condensed counterions and bound water molecules at the NA-solution interface, the power absorption per unit volume is evaluated at this precise location. It is found to be between one and two orders of magnitude above that in muscle tissue as a whole. Under realistic microwave (MW) exposure conditions, however, these SAR inhomogeneities do not generate any significant thermal gradient at the scale considered here. Nevertheless, the question arises of a possible biological relevance of nonnegligible and preferential heat production at the location of the cell nucleus and of the NA molecules.

Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays

RNA binding to high-density oligonucleotide arrays has shown tantalizing differences with solution experiments. We analyze here its sequence specificity, fitting binding affinities to sequence composition in large datasets. Our results suggest that the fluorescent labels interfere with binding, causing a catch-22. To be detected, the RNA must both glow and bind: without labels it cannot be seen even if bound, while with too many it will not bind. A simple model for the binding of labeled oligonucleotides sheds light on the interplay between binding energies and labeling probability.

YY1-DNA interaction results in a significant change of electronic context as measured by capacitance

The detailed mechanism behind the processes of DNA-dependent RNA transcription initiation is largely unknown. When transcription initiation factors bind DNA, a significant change in the electrostatic state of the complex can result. Using electrical capacitance measurements of solutions of the YY1 zinc finger transcription initiation factor and the adeno-associated viral P5 promoter DNA, we observed a specific dielectric change when a protein-DNA complex was formed. We propose that complexation results in electrostatic changes that may trigger the markedly different electrical behavior, and offer a possible explanation for our results.

DNA hybridization to mismatched templates: a chip study

High-density oligonucleotide arrays are among the most rapidly expanding technologies in biology today. In the GeneChip system, the reconstruction of the sample mRNA concentrations depends upon the differential signal generated by hybridizing the RNA to two nearly identical templates: a perfect match probe (PM) containing the exact biological sequence; and a single mismatch (MM) differing from the PM by a single base substitution. It has been observed that a large fraction of MMs repetitively bind targets better than the PMs, against the obvious expectation of sequence specificity. We examine this problem via statistical analysis of a large set of microarray experiments. We classify the probes according to their signal to noise (S/N) ratio, defined as the eccentricity of a (PM,MM) pair's "trajectory" across many experiments. Of those probes having large S/N (>3) only a fraction behave consistently with the commonly assumed hybridization model. Our results imply that the physics of DNA hybridization in microarrays is more complex than expected, and suggest estimators for the target RNA concentration.

Effect of defects on thermal denaturation of DNA oligomers

Effect of defects on the melting profile of short heterogeneous DNA chains is calculated using the Peyrard-Bishop Hamiltonian. On-site potential on a defect site is represented by a potential that has only a short-range repulsion and a flat part without well of the Morse potential. Stacking energy between two neigbouring pairs involving a defect site is also modified. The results are found to be in good agreement with the experiments.

Fluorescence energy transfer analysis of DNA structures containing several bulges and their interaction with CAP

DNA molecules with three bulges separated by double-stranded helical sections of B-DNA were constructed to be used as substrates for DNA-protein binding assays. Fluorescence resonance energy transfer (FRET) between dye molecules attached to the 5'-ends of the DNA molecules is used to monitor the protein binding. The A5 bulge, which consists of five unpaired adenine nucleotides, alters the direction of the helical axis by approximately 80 to 90 at every bulge site. Computer molecular modeling facilitated a pre-selection of suitable helix lengths that bring the labeled ends of the three-bulge DNA molecules (60 to 70 base-pairs long) into close proximity. The FRET experiments verified that the labeled ends of the helices of these long molecules were indeed close. A series of FRET experiments was carried out with two A5 and two A7 bulge molecules. The relative positions of the bulges were varied along the central helical DNA sequence (between the bulges) in order to determine the relative angular juxtapositions of the outlying helical arms flanking the central helical region. The global structural features of the DNA molecules are manifested in the FRET data. The FRET experiments, especially those of the two-bulge series, could be interpreted remarkably well with molecular models based on the NMR structure of the A5 bulge. These models assume that the DNA molecules do not undergo large torsional conformational fluctuations at the bulge sites. The magnitude of the FRET efficiency attests to a relatively rigid structure for many of the long 5'-end-labeled molecules. The changes in the FRET efficiency of three-bulge structures containing the specific binding sequence of the catabolite activator protein (CAP) demonstrated significant deformation of the DNA upon binding of CAP. No direct interaction of CAP with the dyes was observed.

Alpha-particle-induced changes in the stability and size of DNA

The effect of alpha-particle radiation on the thermal stability and size of calf thymus DNA molecules in deoxygenated aqueous solutions was investigated by thermal transition spectrophotometry, pulsed-field gel electrophoresis, and standard agarose gel electrophoresis. The thermal transition of DNA from helix to coil was studied through analysis of the UV A(260) absorbance. The results obtained for alpha particles of mean LET of 128 keV microm(-1) reveal a dual dose response: a tendency for thermal stability of the DNA helix at "low" doses, followed by an increasing instability at higher doses. The same phenomenon was observed for the mean molecular weight of DNA molecules exposed to alpha particles. The results reported here for alpha particles in the low-dose region of 0-16 Gy are consistent with our previous hypothesis of inter- and intramolecular interactions of a covalent character in gamma-irradiated DNA molecules in the dose region of 0-4 Gy.

Dielectric studies of chain melting and denaturation in native DNA

Dielectric methods, based on time domain reflectometry (TDR), have been employed to characterise DNA chain melting and denaturation. A dielectric dispersion has been identified, centred in the low megahertz region, which has been attributed to the fluctuation of counterions along short segments of the DNA chain. Chain melting studies have shown that the magnitude of this dispersion is dependent not only on the relative proportions of single to double stranded DNA but also on the intermolecular interactions between the DNA chains.

DNA structure and flexibility in the sequence-specific binding of papillomavirus E2 proteins

The papillomavirus E2 proteins are transcriptional regulators that bind to a consensus DNA sequence ACCG NNNN CGGT. Multiple copies of this binding site are found in the viral genomes. The affinities of the naturally occurring binding sites for the E2 proteins are predominantly dependent upon the sequence of the NNNN spacer. The hierarchies of binding site affinities among the sites present in the viral genomes result in differential occupancy during the viral life-cycle. In turn, this differential binding regulates transcription from viral promoters, including those for the oncogenes E6 and E7. Structural and biochemical studies have shown that E2 proteins bend the DNA to which they specifically bind. Atomic resolution structures of complexes of the bovine papillomavirus strain 1 (BPV-1) E2 protein and DNA show that the protein does not contact the spacer DNA. A direct comparison of the binding of the DNA-binding domains of the E2 proteins from BPV-1 and human papillomavirus strain 16 (HPV-16) to a series of binding sites as a function of the sequence of their central spacer and/or the presence of a nick or gap in one strand of the spacer DNA is presented in this paper. The BPV-1 E2 DNA-binding domain is only moderately sensitive to the nature of the central spacer; less than several fold differences in affinity were observed when the DNA sequence of the spacer was varied and/or a nick or gap was introduced. In contrast, the HPV-16 E2 DNA-binding domain binds to sites containing A:T-rich central spacers with significantly increased affinity. The introduction of a nick or gap into the spacer of these high affinity sequences is very detrimental to HPV-16 E2 binding while comparable nicks or gaps have only small effects in the low affinity sequences. These results suggest that the HPV-16 E2 protein recognizes the structure of the DNA spacer and that the mechanism of DNA-sequence specific binding of the homologous HPV-16 E2 and BPV-1 E2 proteins is significantly different.

Dielectric studies of intermolecular interactions in native DNA

The concentration dependence of the high frequency dielectric dispersion exhibited by solutions of DNA and the sensitivity of this to the ionic strength of the solution are described. Dielectric data obtained are consistent with a model involving the fluctuation of counterions along short segments of the DNA chain. The concentration and ion strength dependencies are discussed in terms of intermolecular interactions which are considered responsible for the existence of structure in DNA solutions.

Dielectric studies of ion fluctuation and chain bending in native DNA

The high-frequency dielectric dispersion exhibited by solutions of native DNA is characterised as a function of electrolyte concentration, counterion type, temperature and pH. The data are interpreted in terms of counterion fluctuation along short segments (subunits) of the DNA chain. From calculation of the subunit length from dielectric relaxation time and increment, information is derived regarding the static and dynamic bending of the DNA chain. Activation enthalpies for the ion fluctuation process are obtained from temperature-dependent dielectric data.

Effect of thymine dimer introduction in a 21 base pair oligonucleotide

It is well known that the pyrimidine dimers are the main damage produced by UV radiation on the DNA structure. However, while studies on the photoproduct structure have been carried out extensively, uncertainties still exist on the implication that a single damaging event has on the overall conformation. In particular, the extension of the damage influence on the polynucleotide chain is a matter of debate. This problem is especially important to understanding some steps of the repair mechanisms. In this study we performed a chemical-physical characterization of 21 base pair oligonucleotides containing a single thymine dimer in one strand. Thermodynamic parameters were determined by means of thermal denaturation experiments, and static fluorescence measurements were performed to unequivocally define the primary structure-conformation relationship in this specific case. We used hydroxyl radicals, produced by means of gamma-irradiation of the sample solution, to detect fine structure changes. Our data show that the introduction of a single thymine dimer might cause only a slight distortion of the helix geometry, as judged by the evaluation of the enthalpic and the entropic terms and by the small changes observed in the binding of ethidium bromide to DNA. The modifications in the sugar phosphate backbone subsequent to the damaging event are especially evident, near the thymine dimer, toward the 5'-end direction in the strand containing the dimer.