Cooperative recognition of T:T mismatch by echinomycin causes structural distortions in DNA duplex

Pei-Ching Wu; Shu-Ling Tzeng; Chung-ke Chang; Ya-Fen Kao; Michael J Waring; Ming-Hon Hou

doi:10.1093/nar/gky345

Modelling the thermal evolution of enzyme-created bubbles in DNA

Journal of The Royal Society Interface ◽

10.1098/rsif.2004.0024 ◽

2005 ◽

Vol 2 (2) ◽

pp. 89-95 ◽

Cited By ~ 5

Author(s):

D Hennig ◽

J.F.R Archilla ◽

J.M Romero

Keyword(s):

Thermal Evolution ◽

Excision Repair ◽

Heat Bath ◽

Dna Duplex ◽

Nonlinear Network ◽

Structural Distortions ◽

Oscillating Bubbles ◽

The Stability ◽

The Impact ◽

Thermal Perturbations

The formation of bubbles in nucleic acids (NAs) is fundamental in many biological processes such as DNA replication, recombination, telomere formation and nucleotide excision repair, as well as RNA transcription and splicing. These processes are carried out by assembled complexes with enzymes that separate selected regions of NAs. Within the frame of a nonlinear dynamics approach, we model the structure of the DNA duplex by a nonlinear network of coupled oscillators. We show that, in fact, from certain local structural distortions, there originate oscillating localized patterns, that is, radial and torsional breathers, which are associated with localized H-bond deformations, reminiscent of the replication bubble. We further study the temperature dependence of these oscillating bubbles. To this aim, the underlying nonlinear oscillator network of the DNA duplex is brought into contact with a heat bath using the Nosé–Hoover method. Special attention is paid to the stability of the oscillating bubbles under the imposed thermal perturbations. It is demonstrated that the radial and torsional breathers sustain the impact of thermal perturbations even at temperatures as high as room temperature. Generally, for non-zero temperature, the H-bond breathers move coherently along the double chain, whereas at T =0 standing radial and torsional breathers result.

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CO2 Activation on Heterostructures of Bi2O3-Nanocluster Modified TiO2: Promoting the Critical First Step in CO2 Conversion

10.26434/chemrxiv.5917351.v1 ◽

2018 ◽

Cited By ~ 1

Author(s):

Michael Nolan

Keyword(s):

Metal Oxide ◽

Density Functional ◽

Initial Step ◽

Difficult Problem ◽

Carbonate Formation ◽

Structural Distortions ◽

Strong Adsorption ◽

Two Factors ◽

Key Steps ◽

Recent Experimental Work

The conversion of CO2 to fuels is of significant importance in enabling the production of sustainable fuels, contributing to alleviating greenhouse gas emissions. While there are a number of key steps required to convert CO2, the initial step of adsorption and activation by the catalyst is critical. Well-known metal oxides such as oxidised TiO2 or CeO2 are unable to promote this step. In addressing this difficult problem, recent experimental work shows the potential for bismuth-containing materials to activate and convert CO2, but the origin of this activity is not yet clear. Additionally, nanostructures can show enhanced activity towards CO2. In this paper we present density functional theory (DFT) simulations of CO2 activation on heterostructured materials composed of extended rutile and anatase TiO2 surfaces modified with nanoclusters with Bi2O3 stoichiometry. These heterostructures show low coordinated Bi sites in the nanoclusters and a valence band edge that is dominated by Bi-O states. These two factors mean that supported Bi2O3 nanoclusters are able to adsorb and activate CO2. Computed adsorption energies lie in the range of -0.54 eV to -1.01 eV. In these strong adsorption modes, CO2 is activated, in which the molecule bends giving O-C-O angles of 126 - 130o and elongation of C-O distances up to 1.28 Å, with no carbonate formation. The electronic properties show a strong CO2-Bi-oxygen interaction that drives the interaction of CO2 to induce the structural distortions. Bi2O3-TiO2 heterostructures can be reduced to form Bi2+ and Ti3+ species. The interaction of CO2 with this electron-rich, reduced system can produce CO directly, reoxidising the heterostructure or form an activated carboxyl species (CO2-) through electron transfer from the heterostructure to CO2. These results highlight that a semiconducting metal oxide modified with suitable metal oxide nanoclusters can activate CO2, thus overcoming the difficulties associated with the difficult first step in CO2 conversion.

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To Bend or Not to Bend, the Dilemma of Multiple Bonds

10.26434/chemrxiv.8066747.v1 ◽

2019 ◽

Author(s):

Michele Pizzocchero ◽

Matteo Bonfanti ◽

Rocco Martinazzo

Keyword(s):

First Principles ◽

2D Materials ◽

Main Group ◽

First Principles Calculations ◽

Group 14 ◽

Multiple Bonds ◽

Main Group Elements ◽

Structural Distortions

The manuscript addresses the issue of the structural distortions occurring at multiple bonds between high main group elements, focusing on group 14. These distortions are known as trans-bending in silenes, disilenes and higher group analogues, and buckling in 2D materials likes silicene and germanene. A simple but correlated \sigma + \pi model is developed and validated with first-principles calculations, and used to explain the different behaviour of second- and higher- row elements.

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