B to Z transitions of the short DNA hairpins formed from the oligomer sequences: d[(CG)3×4(CG)3] (X = A, T, G, C)

Amaratunga, Mohan; Pančoška, Petr; Paner, Teodoro M.; Benight, Albert S.

doi:10.1093/nar/18.3.577

Cited by 18 publications

(17 citation statements)

References 31 publications

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“…Additionally it was found that homomismatches of C-C pairing are energetically more favourable than other hetero mismatches explaining this unusual stability [33]. The observed CD spectrum can be brought into accordance with a hairpin B-DNA structure [32] and it can be also assumed that the T-A pairing, which has been validated by the results of Fig. 2 and Fig.…”

Section: Resultssupporting

confidence: 70%

Unfolding mechanism and the free energy landscape of a single stranded DNA i-motif

Smiatek,

Chen,

Liu

et al. 2011

Preprint

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We present Molecular Dynamics simulations of a single stranded unprotonated DNA i-motif in explicit solvent. Our results indicate that the native structure in non-acidic solution at 300 K is unstable and completely vanishes on a time scale up to 10 ns. Two unfolding mechanisms with decreasing connectivity between the initially interacting nucleobases can be identified where one pathway is characterized as entropically more favorable. The entropic preference can be mainly explained by strong water ordering effects due to hydrogen bonds for several occurring structures along the pathways. Finally we are able to indicate via free energy calculations the most stable configurations belonging to distinct hairpin structures in good agreement to experimental results.

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Section: Resultssupporting

confidence: 70%

Unfolding mechanism and the free energy landscape of a single stranded DNA i-motif

Smiatek,

Chen,

Liu

et al. 2011

Preprint

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“…This interpretation is further supported by the CD of short oligonucleotides in the presence of ZR. Unmodified hairpins with a stem built by merely three d(CG) dinucleotide steps can be completely flipped from B to Z at room temperature in 4 M NaClO 4 (46). In contrast, the ZR peptide used in these studies shows a less pronounced effect.…”

Section: Discussionmentioning

confidence: 90%

Spectroscopic Characterization of a DNA-Binding Domain, Zα, from the Editing Enzyme, dsRNA Adenosine Deaminase: Evidence for Left-Handed Z-DNA in the Zα−DNA Complex

et al. 1998

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Double-stranded RNA adenosine deaminase (ADAR1) is an ubiquitous enzyme in metazoa that edits pre-mRNA changing adenosine to inosine in regions of double-stranded RNA. Zalpha, an N-terminal domain of human ADAR1 encompassing 76 amino acid residues, shows apparent specificity for the left-handed Z-DNA conformation adopted by alternating (dGdC) polymers modified by bromination or methylation, as well as for (dGdC)13 inserts present in supercoiled plasmids. Here, a combination of circular dichroism, fluorescence, and gel-retardation studies is utilized to characterize recombinant Zalpha peptide and to examine its interaction with DNA. Results from laser-Raman spectroscopy experiments provide direct evidence for the existence of Z-DNA in peptide-DNA complexes.

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“…53 Factor analysis treats the CD spectra as a set of vectors and then, without imposing external constraints, solves for an orthogonal set of subspectra or basis vectors that can be linearly combined to construct the original set of spectra. For each molecule, the input data were the D" values measured every 0.2 nm from 205.2 to 320 nm comprising the CD spectrum.…”

Section: Analysis Of CD Spectramentioning

confidence: 99%

Studies of DNA dumbbells VIII. Melting analysis of DNA dumbbells with dinucleotide repeat stem sequences

et al. 2005

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Melting curves and circular dichroism spectra were measured for a number of DNA dumbbell and linear molecules containing dinucleotide repeat sequences of different lengths. To study effects of different sequences on the melting and spectroscopic properties, six DNA dumbbells whose stems contain the central sequences (AA)(10), (AC)(10), (AG)(10), (AT)(10), (GC)(10), and (GG)(10) were prepared. These represent the minimal set of 10 possible dinucleotide repeats. To study effects of dinucleotide repeat length, dumbbells with the central sequences (AG)(n), n = 5 and 20, were prepared. Control molecules, dumbbells with a random central sequence, (RN)(n), n = 5, 10, and 20, were also prepared. The central sequence of each dumbbell was flanked on both sides by the same 12 base pairs and T(4) end-loops. Melting curves were measured by optical absorbance and differential scanning calorimetry in solvents containing 25, 55, 85, and 115 mM Na(+). CD spectra were collected from 20 to 45 degrees C and [Na(+)] from 25 to 115 mM. The spectral database did not reveal any apparent temperature dependence in the pretransition region. Analysis of the melting thermodynamics evaluated as a function of Na(+) provided a means for quantitatively estimating the counterion release with melting for the different sequences. Results show a very definite sequence dependence, indicating the salt-dependent properties of duplex DNA are also sequence dependent. Linear DNA molecules containing the (AG)(n) and (RN)(n), sequences, n = 5, 10, 20, and 30, were also prepared and studied. The linear DNA molecules had the exact sequences of the dumbbell stems. That is, the central repeat sequence in each linear duplex was flanked on both sides by the same 12-bp sequence. Melting and CD studies were also performed on the linear DNA molecules. Comparison of results obtained for the same sequences in dumbbell and linear molecular environments reveals several interesting features of the interplay between sequence-dependent structural variability, sequence length, and the unconstrained (linear) or constrained (dumbbell) molecular environments.

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B to Z transitions of the short DNA hairpins formed from the oligomer sequences: d[(CG)₃×₄(CG)₃] (X = A, T, G, C)

Cited by 18 publications

References 31 publications

Unfolding mechanism and the free energy landscape of a single stranded DNA i-motif

Unfolding mechanism and the free energy landscape of a single stranded DNA i-motif

Spectroscopic Characterization of a DNA-Binding Domain, Zα, from the Editing Enzyme, dsRNA Adenosine Deaminase: Evidence for Left-Handed Z-DNA in the Zα−DNA Complex

Studies of DNA dumbbells VIII. Melting analysis of DNA dumbbells with dinucleotide repeat stem sequences

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