Showing papers by "Michaela Vorlíčková published in 2001"
TL;DR: It is found that the conformational spectrum of the (GCC)(n) strand is wider than has been shown so far and the homodimer is a bimolecular tetraplex formed by two parallel-oriented hairpins held together by hemi-protonated intermolecular C.C(+) pairs.
Abstract: UV absorption and CD spectroscopy, along with polyacrylamide gel electrophoresis, were used to study conformational properties of DNA fragments containing the trinucleotide repeat (GCC)n (n = 4, 8 or 16), whose expansion is correlated with the fragile X chromosome syndrome. We have found that the conformational spectrum of the (GCC)n strand is wider than has been shown so far. (GCC)n strands adopt the hairpin described in the literature under a wide range of salt concentrations, but only at alkaline (>7.5) pH values. However, at neutral and slightly acid pH (GCC)4 and (GCC)8 strands homodimerize. Our data suggest that the homodimer is a bimolecular tetraplex formed by two parallel-oriented hairpins held together by hemi-protonated intermolecular C·C + pairs. The (GCC)16 strand forms the same tetraplex intramolecularly. We further show that below pH 5 (GCC)n strands generate intercalated cytosine tetraplexes, whose molecularity depends on DNA strand length. They are tetramolecular with (GCC)4, bimolecular with (GCC)8 and monomolecular with (GCC)16. i-Tetraplex formation is a complex and slow process. The neutral tetraplex, on the other hand, arises with fast kinetics under physiological conditions. Thus it is a conformational alternative of the (GCC)n strand duplex with a complementary (GGC)n strand.
72 citations
TL;DR: In this article, the authors used CD spectroscopy, NMR and unrestrained molecular dynamics simulations to study conformational properties of a DNA duplex formed by the self-complementary octamer d(GGGGCCCC) and found that half of the bases stack in an A-like fashion, whereas the other half stack in a B-like way.
57 citations
Journal Article•
TL;DR: A remarkable propensity of the guanine runs to stack in an A-like fashion even within the B-DNA framework is demonstrated, which explains why the oligo(dG) tracts switch into structure A so easily and may influence replication.
56 citations
TL;DR: The results reveal that guanine-guanine stacking is a structural invariant conserved in various nucleic acid conformers and is likely to cohere with evolution of the genetic molecules and be important for fundamental functions, e.g. initiation of transcription.
Abstract: Using a series of suitably chosen oligonucleotides, we demonstrate that the DNA duplex of d(CCCCGGGG) provides an almost identical CD spectrum as the parallel-stranded tetraplex of d(GGGG). The CD spectra are very sensitive to base stacking in DNA so that the above observation indicates that guanine-guanine stacking is essentially the same within the duplex of d(CCCCGGGG) and the tetraplex of d(GGGG). A very similar CD spectrum is also provided by the A-form of d(CCCCGGGG) induced by trifluoroethanol. These results reveal that guanine-guanine stacking is a structural invariant conserved in various nucleic acid conformers. The structural invariance is likely to cohere with evolution of the genetic molecules and be important for fundamental functions, e.g. initiation of transcription.
31 citations
TL;DR: The conformational repertoire of (CGA)(4) includes parallel, anti-parallel, right-handed, and left-handed homoduplexes, compared with (CAG)(4), which invariably adopts only a single conformation, namely the very stable hairpin.
24 citations
TL;DR: It is shown that stability of the above four conformers strongly depends on the GAC repeat number.
Abstract: The human gene for cartilage oligomeric matrix protein contains five tandem repeats of the GAC trinucleotide. Its expansion by one repeat causes multiple epiphyseal dysplasia, while expansion by two repeats or, remarkably, deletion of one repeat causes pseudoachondroplasia. Here we used CD spectroscopy, PAGE and UV absorption spectroscopy to compare conformational properties of the DNA strands containing four, five, six and seven repeats of the GAC trinucleotide. The (GAC)n strands were found to form four distinct ordered conformations, depending on the solution conditions. The first was a foldback, stable at slightly alkaline pH values and low and medium ionic strengths. Increasing salt concentration induced a transition of the foldback into an antiparallel right-handed homoduplex. Both the conformers contained the Watson-Crick G.C pairs while the intervening adenines contributed little to their B-like conformation. Thirdly, the strands associated into a parallel homoduplex stabilized by the hemiprotonated C+.C pairs and by the GpA steps that both favor the parallel DNA strand orientation. The parallel homoduplex was stable even at neutral pH. The fourth conformation was the left-handed Z-DNA, which formed easier with (GAC)n than with (GC)n of comparable length, indicating that the adenines of (GAC)n promoted the left-handed duplex. The paper shows that stability of the above four conformers strongly depends on the GAC repeat number.
22 citations
TL;DR: To the best of the authors' knowledge, this is the first known ordered conformer of DNA that is stabilized by dimethylsulfoxide, which might be a DNA analog of the protein alpha helix, which is an interesting idea for thinking about the evolution of DNA.
Abstract: Circular dichroism spectroscopy and other methods are used to show that the addition of dimethylsulfoxide causes reversible folding of the (GA)(10) strand of DNA into an ordered single-stranded conformer. The ordered conformer melts in a cooperative way and it does not contain protonated adenine. The (TA)(10), (A)(20), and (G)(20) are all unstable in this conformer. To the best of our knowledge, this is the first known ordered conformer of DNA that is stabilized by dimethylsulfoxide. This conformer might be a DNA analog of the protein alpha helix, which is an interesting idea for thinking about the evolution of DNA.
13 citations