Dark times: iminothioindoxyl--nucleoside fluorescence quenchers with defined location and minimal perturbation in DNA.

Fluorescence quenchers for application in DNA - like the BHQ family - tend to be large molecules which need to be attached, often post-synthetically, long linkers. In this study, we present two new iminothioindoxyl--nucleosidic quenchers which are very compact, feature a native backbone and can be introduced into DNA regular solid-phase synthesis. Especially with d as juxtaposed nucleobase, they have a defined location and orientation in a DNA duplex with minimal perturbation of the structure and hence interaction capabilities.

Controlled destabilization of caged circularized DNA oligonucleotides predicted by replica exchange molecular dynamics simulations.

Spatiotemporal control is a critical issue in the design of strategies for the photoregulation of oligonucleotide activity. Efficient uncaging, , activation by removal of photolabile protecting groups (PPGs), often necessitates multiple PPGs. An alternative approach is based on circularization strategies, exemplified by intrasequential circularization, also denoted photo-tethering, as introduced in [Seyfried , , 2017, , 359].

First-Principles Quantum and Quantum-Classical Simulations of Exciton Diffusion in Semiconducting Polymer Chains at Finite Temperature.

We report on first-principles quantum-dynamical and quantum-classical simulations of photoinduced exciton dynamics in oligothiophene chain segments, representative of intrachain exciton migration in the poly(3-hexylthiophene) (P3HT) polymer. Following up on our recent study (Binder R.; Burghardt, I.

The symmetrical quasi-classical approach to electronically nonadiabatic dynamics applied to ultrafast exciton migration processes in semiconducting polymers.

In the last several years, a symmetrical quasi-classical (SQC) windowing model applied to the classical Meyer-Miller (MM) vibronic Hamiltonian has been shown to be a simple, efficient, general, and quite-accurate method for treating electronically nonadiabatic processes at the totally classical level. Here, the SQC/MM methodology is applied to ultrafast exciton dynamics in a Frenkel/site-exciton model of oligothiophene (OT) as a model of organic semiconductor polymers. In order to keep the electronic representation as compact and efficient as possible, the adiabatic version of the MM Hamiltonian was employed, with dynamical calculations carried out in the recently developed "kinematic momentum" representation, from which site/monomer-specific (diabatic) excitation probabilities were extracted using a new procedure developed in this work.

Multidimensional Langevin Modeling of Nonoverdamped Dynamics.

Based on a given time series, data-driven Langevin modeling aims to construct a low-dimensional dynamical model of the underlying system. When dealing with physical data as provided by, e.g.