Calorimetric, spectroscopic and computational investigation of DNA triplexes containing a 3′–3′ internucleoside junction

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Publication Date
DOI 10.1039/A906347A
Impact Factor 3.676
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Abstract

Triple helix (triplex) formation between a 24-mer oligonucleotide double helix (duplex) and two kinds of 24-mer single strands containing a 3′–3′ phosphodiester bond was investigated by calorimetric, spectroscopic and computational techniques in order to analyze the effect of chemical modification of the third strand on the stability of DNA triplex. The duplex target is composed of two adjacent oligopurine–oligopyrimidine domains where the oligopurine sequences alternate on the two duplex strands. The third strands differ between each other from the substitution of cytosine with a thymine at the junction point. The two triplexes exhibit different CD spectra, suggesting that they have non-equivalent conformational states. Differential scanning calorimetric data show that the triplex with a cytosine–thymine junction (CT-triplex) is thermodynamically less stable than that with a cytosine–cytosine junction (CC-triplex). Molecular mechanics calculations revealed that the two triplexes have different geometries at the junction point. The thermodynamic data are successfully discussed in relation to the molecular models of the two triplexes.

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Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics
CiteScore: 5.5
Self-citation Rate: 10.3%
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Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.

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