PubMed Health⌕ Search

Biomedical subjects

Krystyna Zakrzewska

Publications and source records attributed to Krystyna Zakrzewska.

9 recordsLinked to original sources
PubMed2006

DNA-directed assembly of polyanilines: modified cytosine nucleotides transfer sequence programmability to a conjoined polymer.

A series of polyaniline (PANI) oligomers was constructed from monomer units covalently linked to duplex DNA through N-(2-aminoethyl) groups bonded through cytosines. DNA oligomers containing the aniline monomers were treated with horseradish peroxidase (HRP) and H2O2 under conditions known to cause polymerization of aniline. No change in the absorption spectrum of the DNA was observed for samples containing fewer than four contiguous aniline groups. However, for oligomers containing four, five, or six aniline units, treatment with HRP and H2O2 led to the appearance of absorption features characteristic of the conducting "proton doped" emeraldine oxidation state of PANI. Molecular modeling shows that the DNA is distorted in the region of the PANI, but flanking regions of the DNA maintain their B-form structure. These findings provide a method to exploit the self-recognition, self-assembly, and sequence programmability of DNA for the formation of conducting polymers.

Aniline Compounds↗
PubMed2006

Different behavior of erythrovirus B19 and torquetenovirus in response to a single step of albumin purification.

BACKGROUND: The safety of human serum albumin (HSA) is of special interest with respect to virus transmission because of the wide use of this blood product as a therapeutic agent and also, added to other products, as an excipient or a stabilizer. Conflicting data are reported concerning HSA contamination by small, naked viruses such as the erythrovirus B19 (B19V) and the anellovirus torquetenovirus (TTV). This study has been performed to assess the effect of the HSA purification procedures on the viral contamination. STUDY DESIGN AND METHODS: Known concentrations of B19V and TTV virus were spiked in raw Fraction V, the starting material from fractionated human plasma for HSA purification, which was subsequently submitted to the depth filtration procedure. After spiking, B19V and TTV genome copies were determined by real-time quantitative polymerase chain reaction assays in the mixture at the end of Fraction V dissolution, to determine the virus concentration achieved, in the HSA solution after the filtration step, in the filtered postwashing fluid, and in the supernatant of resuspended Celite. RESULTS: B19V was completely adsorbed by the Celite used as a filter aid in the depth filtration process and was thus undetectable in the resulting HSA-containing fraction. In contrast, in 2 out of 3 experiments, TTV was detected in all samples. CONCLUSION: The different behavior of the two viruses might be a reflection of their different surface charge.

Adsorption↗
PubMed2005

Exciton states of dynamic DNA double helices: alternating dCdG sequences.

The present communication deals with the excited states of the alternating DNA oligomer (dCdG)5.(dCdG)5 which correspond to the UV absorption band around 260 nm. Their properties are studied in the frame of the exciton theory, combining molecular dynamics simulations and quantum chemistry data. It is shown that the dipolar coupling undergoes important variations with the site and the helix geometry. In contrast, the energy of the monomer transitions within the double helix is not sensitive to the local environment. It is thus considered to be distributed over Gaussian curves whose maximum and width are derived from the experimental absorption spectra of nucleosides in aqueous solution. The influence of the spectral width on the excited state delocalization and the absorption spectra is much stronger than that of the oligomer plasticity. About half of the excited states are delocalized over at least two bases. Many of them result from the mixing of different monomer states and extend on both strands. The trends found in the simulated spectra, when going from non-interacting monomers to the duplex, are in agreement with experimental observations. Conformational changes enhance the diversity of the states which can be populated upon excitation at a given energy. The states with larger spatial extent are located close to the maximum of the absorption spectrum.

DNA↗
PubMed2005

UV spectra and excitation delocalization in DNA: influence of the spectral width.

The singlet excited states of the model DNA duplex (dA)10.(dT)10 are studied. Calculations are performed in the exciton theory framework. Molecular dynamics calculations provide the duplex geometry. The dipolar coupling is determined using atomic transition charges. The monomer transition energies are simulated by Gaussian functions resembling the absorption bands of nucleosides in aqueous solutions. Most of the excited states are found to be delocalized over at least two bases and result from the mixing of different monomer states. Their properties are only weakly affected by conformational changes of the double helix. On average, the highest oscillator strength is carried by the upper eigenstates. The duplex absorption spectra are shifted a few nanometers to higher energies with respect to the spectra of noninteracting monomers. The states with larger spatial extent are located close to the maximum of the absorption spectrum.

DNA↗
PubMed2004

DNA and its counterions: a molecular dynamics study.

The behaviour of mobile counterions, Na+ and K+, was analysed around a B-DNA double helix with the sequence CCATGCGCTGAC in aqueous solution during two 50 ns long molecular dynamics trajectories. The movement of both monovalent ions remains diffusive in the presence of DNA. Ions sample the complete space available during the simulation time, although individual ions sample only about one-third of the simulation box. Ions preferentially sample electronegative sites around DNA, but direct binding to DNA bases remains a rather rare event, with highest site occupancy values of <13%. The location of direct binding sites depends greatly on the nature of the counterion. While Na+ binding in both grooves is strongly sequence-dependent with the preferred binding site in the minor groove, K+ mainly visits the major groove and binds close to the centre of the oligomer. The electrostatic potential of an average DNA structure therefore cannot account for the ability of a site to bind a given cation; other factors must also play a role. An extensive analysis of the influence of counterions on DNA conformation showed no evidence of minor groove narrowing upon ion binding. A significant difference between the conformations of the double helix in the different simulations can be attributed to extensive alpha/gamma transitions in the phosphate backbone during the simulation with Na+. These transitions, with lifetimes over tens of nanoseconds, however, appear to be correlated with ion binding to phosphates. The ion-specific conformational properties of DNA, hitherto largely overlooked, may play an important role in DNA recognition and binding.

Binding Sites↗
PubMed2004

Sequence and pH effects of LNA-containing triple helix-forming oligonucleotides: physical chemistry, biochemistry, and modeling studies.

Triple helix-forming oligonucleotides (TFOs) have been demonstrated to be capable of interfering with gene expression and modifying genomic DNA in a sequence-specific manner. Partial incorporation of 2'-O,4'-C-methylene linked locked nucleic acid (LNA) residues in TFOs has been shown to enhance significantly triple helix formation, whereas the full-length LNA TFO failed to form a stable triplex. This work is aimed at understanding the triple helix-forming properties of LNA-containing TFOs and at optimally designing their sequences. Both DNA thermal melting, gel retardation, and restriction enzyme experiments as well as modeling studies by molecular mechanics were carried out to investigate the base composition/sequence and pH-dependence effects of LNA-containing TFOs, as well as their structural features underlying triple helix formation. Alternating LNA substitution every 2-3 nucleotides in TFOs is mandatory, whereas the use of thymine LNA residues should be favored under neutral pH conditions. A rule for designing optimal LNA-containing TFOs is proposed. In addition, alternative LNA and 2'-O-methyl residues in TFOs do not significantly improve triple helix formation.

Base Sequence↗
PubMed2003

Theoretical study of the interaction between a high-valent manganese porphyrin oxyl-(hydroxo)-Mn(IV)-TMPyP and double-stranded DNA.

Cationic porphyrin derivatives such as meso-tetrakis(4-N-methylpyridinium)porphyrin, TMPyP, have been shown to interact with double-stranded DNA. The manganese derivative, Mn(III)-TMPyP, activated by an oxygen donor like potassium monopersulfate, provides an efficient DNA-cleaving system. Previous experimental work1 has shown that DNA cleavage by the Mn(III)-TMPyP/KHSO(5) system was due to an oxidative attack, within the minor groove of B-DNA, at the C5' or C1' carbons of deoxyribose units. The aim of this study was to use molecular modeling to elucidate the specificity of the interactions between the transient active species oxyl-Mn(IV)-TMPyP and the DNA target. Geometric parameters, charges, and force field constants consistent with the AMBER 98 force field were calculated by DFT methods. Molecular modeling (mechanics and dynamic simulations) were performed for oxyl-(hydroxo)-Mn(IV)-TMPyP bound in the minor groove of the dodecamer d(5'-TCGTCAAACCGC)-d(5'-GCGGTTTGACGA). Geometry, interactions, and binding energy of the metalloporphyrin located at the A.T triplet region of the dodecamer were analyzed. These studies show no significant structural change of the DNA structure upon ligand binding. Mobility of the metalloporphyrin in the minor groove was restrained by the formation of a hydrogen bond between the hydroxo ligand trans to the metal-oxyl and a DNA phosphate, restricting the access of the oxyl group to the (pro-S) H atom at C5'.

Base Sequence↗
PubMed1996

Persistent parvovirus B19 infections with different clinical outcomes in renal transplant recipients: diagnostic relevance of polymerase chain reaction (PCR) and of quantification of B19 DNA in sera.

OBJECTIVE: To study parvovirus B19 infection in immunocompromised subjects such as renal transplantation recipients. METHODS: Two cases of B19 infection in renal transplant recipients have been included in the study. The outcome of the infection has been studied by both serologic and virologic methods. A monitoring of the DNAemia was done by a nested PCR in endpoint titration assays. RESULTS: In one patient with severe anemia an acute B19 infection was diagnosed by PCR 26 days after the transplant; a high level of DNAemia persisted until an intravenous immunoglobulin treatment. Then a sharp decrease of the DNAemia was shown, without full clearance of B19 virus. In a lymphocyte suspension from the organ donor, B19 DNA was detected. In the other patient, who recovered spontaneously from anemia, a persistent B19 infection was demonstrated at day 106 after transplantation and was still demonstrable after 470 days. CONCLUSIONS: A high level of B19 DNAemia was associated with symptomatic infection, with severe anemia, whereas low-level DNAemia was long-lasting in asymptomatic subjects with impaired immunologic responses. The endpoint titration assay by nested PCR was very useful for the monitoring of B19 infection, particularly following the therapeutic intravenous immunoglobulin administration.

Journal Article↗