Thermodynamic and spectral properties of DNA miniduplexes with the terminal G·A mispairs and 3′ or 5′ dangling bases

Lokhov, S. G.; Pyshnyi, D. V.

doi:10.1016/s0014-5793(97)01502-0

Cited by 42 publications

(21 citation statements)

References 28 publications

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“…Absorbance at 260, 270, and 300 nm was measured. Absorbance at 300 nm was used as a baseline and was subtracted from the two other denaturation curves [ 50 ]. The melting temperature (Tm) of RNAs was calculated as the maxima of the first derivative of absorbance on temperature.…”

Section: Methodsmentioning

confidence: 99%

Nucleotide Modifications Decrease Innate Immune Response Induced by Synthetic Analogs of snRNAs and snoRNAs

Степанов

Zhuravlev

Shender

et al. 2018

Genes

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Short nuclear regulatory RNAs play a key role in the main stages of maturation of the precursors of the major RNA species. Small nuclear RNAs (snRNAs) form the core of the spliceosome and are responsible for the splicing of pre-mRNA molecules. Small nucleolar RNAs (snoRNAs) direct post-transcriptional modification of pre-rRNAs. A promising strategy for the development of non-coding RNA (ncRNAs) mimicking molecules is the introduction of modified nucleotides, which are normally present in natural ncRNAs, into the structure of synthetic RNAs. We have created a set of snoRNAs and snRNA analogs and studied the effect of base modifications, specifically, pseudouridine (Ψ) and 5-methylcytidine (m5C), on the immune-stimulating and cytotoxic properties of these RNAs. Here, we performed a whole-transcriptome study of the influence of synthetic snoRNA analogs with various modifications on gene expression in human cells. Moreover, we confirmed the role of PKR in the recognition of snoRNA and snRNA analogs using the short hairpin RNA (shRNA) technique. We believe that the data obtained will contribute to the understanding of the role of nucleotide modification in ncRNA functions, and can be useful for creating the agents for gene regulation based on the structure of natural snoRNAs and snRNAs.

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Section: Methodsmentioning

confidence: 99%

Nucleotide Modifications Decrease Innate Immune Response Induced by Synthetic Analogs of snRNAs and snoRNAs

Степанов

Zhuravlev

Shender

et al. 2018

Genes

View full text Add to dashboard Cite

show abstract

“…The magnitude of the value of the free energy of this nick is likely to be a lower limit since it has been determined relative to a gap complex that has a 3'A-A sequence adjacent to the duplex component under study. It is known that single strand 3' overhangs of this type can stabilise an adjoining duplex (26)(27)(28). In particular, it has been shown that a 3'A-A overhang adjacent to a C base on an adjoining duplex, similar to that employed in this study exhibits a stabilisation contribution of -0.5 kcal/mol (29).…”

Section: Discussionmentioning

confidence: 67%

Effect of Base Stacking on the Relative Thermodynamic Stability of Oligonucleotide Complexes: A Spectroscopic Study

Murphy¹,

Doyle²,

Eritja

et al. 2004

Journal of Biomolecular Structure and Dynamics

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Three-strand oligonucleotide complexes are employed to assess the effect of base stacking and base pair mismatch on the relative thermodynamic stabilities of oligonucleotide duplexes. The melting behavior of three-strand oligonucleotide complexes incorporating nicks and gaps as well as internal single base mismatches is monitored using temperature-dependent optical absorption spectroscopy. A sequential three-state equilibrium model is used to analyze the measured melting profiles and evaluate thermodynamic parameters associated with dissociation of the complexes. The free-energy of stabilization of a nick complex compared to a gap complex due to base stacking is determined to be -1.9 kcal/mol. The influence of a mispaired base in these systems is shown to destabilize a nick complex by 3.1 kcal/mol and a gap complex by 2.8 kcal/mol, respectively.

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“…The optical data were collected every 0.2°C. Thermodynamic parameters of the duplex formation (changes of enthalpy Δ H °, entropy Δ S ° and Gibbs free energy at 37°C, Δ G ° 37 ) were obtained by direct non-linear fitting and concentration methods ( 31 ). Fitting of the melting curves were performed using a two-state model corrected for intramolecular hairpin formation as described ( 32 ).…”

Section: Methodsmentioning

confidence: 99%

Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation

Gruber

Toner

Miears

et al. 2018

Nucleic Acids Research

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DNA damage can affect various regulatory elements of the genome, with the consequences for DNA structure, dynamics, and interaction with proteins remaining largely unexplored. We used solution NMR spectroscopy, restrained and free molecular dynamics to obtain the structures and investigate dominant motions for a set of DNA duplexes containing CpG sites permuted with combinations of 5-methylcytosine (mC), the primary epigenetic base, and 8-oxoguanine (oxoG), an abundant DNA lesion. Guanine oxidation significantly changed the motion in both hemimethylated and fully methylated DNA, increased base pair breathing, induced BI→BII transition in the backbone 3′ to the oxoG and reduced the variability of shift and tilt helical parameters. UV melting experiments corroborated the NMR and molecular dynamics results, showing significant destabilization of all methylated contexts by oxoG. Notably, some dynamic and thermodynamic effects were not additive in the fully methylated oxidized CpG, indicating that the introduced modifications interact with each other. Finally, we show that the presence of oxoG biases the recognition of methylated CpG dinucleotides by ROS1, a plant enzyme involved in epigenetic DNA demethylation, in favor of the oxidized DNA strand. Thus, the conformational and dynamic effects of spurious DNA oxidation in the regulatory CpG dinucleotide can have far-reaching biological consequences.

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Thermodynamic and spectral properties of DNA miniduplexes with the terminal G·A mispairs and 3′ or 5′ dangling bases

Cited by 42 publications

References 28 publications

Nucleotide Modifications Decrease Innate Immune Response Induced by Synthetic Analogs of snRNAs and snoRNAs

Nucleotide Modifications Decrease Innate Immune Response Induced by Synthetic Analogs of snRNAs and snoRNAs

Effect of Base Stacking on the Relative Thermodynamic Stability of Oligonucleotide Complexes: A Spectroscopic Study

Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation

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