Single-Molecule Spectroscopic Study of Dynamic Nanoscale DNA Bending Behavior of HIV-1 Nucleocapsid Protein

We have studied the conformational dynamics associated with the nanoscale DNA bending induced by human immunodeficiency virus type 1 (HIV-1) nucleocapsid (NC) protein using single-molecule Förster resonance energy transfer (SM-FRET). To gain molecular-level insights into how the HIV-1 NC locally distorts the structures of duplexed DNA segments, the dynamics, reversibility, and sequence specificity of the DNA bending behavior of NC have been systematically studied. We have performed SM-FRET measurements on a series of duplexed DNA segments with varying sequences, lengths, and local structures in the presence of the wide-type HIV-1 NC and NC mutants lacking either the basic N-terminal domain or the zinc fingers. On the basis of the SM-FRET results, we have proposed a possible mechanism for the NC-induced DNA bending in which both NC’s zinc fingers and N-terminal domain are found to play crucial roles. The SM-FRET results reported here add new mechanistic insights into the biological behaviors and functions of HIV-1 NC as a retroviral DNA-architectural protein which may play critical roles in the compaction, nuclear import, and integration of the proviral DNA during the retroviral life cycle

Mimicking Conjugated Polymer Thin-Film Photophysics with a Well-Defined Triblock Copolymer in Solution

Conjugated polymers (CPs) are promising materials for use in electronic applications, such as low-cost, easily processed organic photovoltaic (OPV) devices. Improving OPV efficiencies is hindered by a lack of a fundamental understanding of the photophysics in CP-based thin films that is complicated by their heterogeneous nanoscale morphologies. Here, we report on a poly­(3-hexylthiophene)-<i>block</i>-poly­(<i>tert</i>-butyl acrylate)-<i>block</i>-poly­(3-hexylthiophene) rod–coil–rod triblock copolymer. In good solvents, this polymer resembles solutions of P3HT; however, upon the addition of a poor solvent, the two P3HT chains within the triblock copolymer collapse, affording a material with electronic spectra identical to those of a thin film of P3HT. Using this new system as a model for thin films of P3HT, we can attribute the low fluorescence quantum yield of films to the presence of a charge-transfer state, providing fundamental insights into the condensed phase photophysics that will help to guide the development of the next generation of materials for OPVs

Conformational Effect on Energy Transfer in Single Polythiophene Chains

Herein we describe the use of regioregular (<i>rr-</i>) and regiorandom (<i>rra-</i>) P3HT as models to study energy transfer in ordered and disordered single conjugated polymer chains. Single molecule fluorescence spectra and excitation/emission polarization measurements were compared with a Förster resonance energy transfer (FRET) model simulation. An increase in the mean single chain polarization anisotropy from excitation to emission was observed for both <i>rr-</i> and <i>rra-</i>P3HT. The peak emission wavelengths of <i>rr-</i>P3HT were at substantially lower energies than those of <i>rra-</i>P3HT. A simulation based on FRET in single polymer chain conformations successfully reproduced the experimental observations. These studies showed that ordered conformations facilitated efficient energy transfer to a small number of low-energy sites compared to disordered conformations. As a result, the histograms of spectral peak wavelengths for ordered conformations were centered at much lower energies than those obtained for disordered conformations. Collectively, these experimental and simulated results provide the basis for quantitatively describing energy transfer in an important class of conjugated polymers commonly used in a variety of organic electronics applications

Regioregularity and Single Polythiophene Chain Conformation

The regioregularity of a conjugated polymer can greatly affect bulk film morphologies and properties. However, it remains unclear how regioregularity affects the conformation of isolated individual chains where interchain interactions are absent. Here, the effect of the regioregularity on the conformations adopted by regioregular (<i>rr-</i>) and regiorandom (<i>rra-</i>) poly(3-hexylthiophene) (P3HT) chains was studied using single molecule fluorescence excitation polarization spectroscopy. While every <i>rr-</i>P3HT chain within an ensemble was found to fold into a highly ordered conformation, single <i>rra-</i>P3HT chains adopted a wide variety of conformations, ranging from highly ordered to isotropic. This distribution is likely due to variations in the positions of nonhead-to-tail linkages of the side-chains along the backbone of the different polymer chains. Molecular dynamics simulation on atomistic models of <i>rr-</i> and <i>rra-</i>P3HT chains supports the effect of regioregularity on the collapsed conformations. These results demonstrate that side-chains govern the morphology of P3HT, even at the single chain level