Structure of Rhodamine 6G−DNA Complexes from Molecular Dynamics Simulations

A New Architecture for DNA-Templated Synthesis in Which Abasic Sites Protect Reactants from Degradation

The synthesis of artificial sequence-defined polymers that match and extend the functionality of proteins is an important goal in materials science. One way of achieving this is to program a sequence of chemical reactions between precursor building blocks by means of attached oligonucleotide adapters. However, hydrolysis of the reactive building blocks has so far limited the length and yield of product that can be obtained using DNA-templated reactions. Here, we report an architecture for DNA-templated synthesis in which reactants are tethered at internal abasic sites on opposite strands of a DNA duplex. We show that an abasic site within a DNA duplex can protect a nearby thioester from degradation, significantly increasing the yield of a DNA-templated reaction. This protective effect has the potential to overcome the challenges associated with programmable, sequence-controlled synthesis of long non-natural polymers by extending the lifetime of the reactive building blocks.

Advances in quantitative FRET-based methods for studying nucleic acids

Förster resonance energy transfer (FRET) is a powerful tool for monitoring molecular distances and interactions at the nanoscale level. The strong dependence of transfer efficiency on probe separation makes FRET perfectly suited for "on/off" experiments. To use FRET to obtain quantitative distances and three-dimensional structures, however, is more challenging. This review summarises recent studies and technological advances that have improved FRET as a quantitative molecular ruler in nucleic acid systems, both at the ensemble and at the single-molecule levels.

A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: structure and dynamics

Molecular dynamics (MD) simulations and ab initio quantum chemical calculations were employed to investigate the structure, dynamics and interactions of the QSY 21 nonfluorescent quencher and the fluorescence dye Rhodamine 6G bound to a B-DNA decamer. For QSY 21, two binding motifs were observed. In the first motif, the central xanthene ring is stacked on one base of the adjacent cytosine-guanine DNA base pair, whereas one of the 2,3-dihydro-1-indolyl aromatic side rings is stacked on the other base. In the second motif, the QSY 21 stacking interaction with the DNA base pair is mediated only by one of the side rings. Several transitions between the motifs are observed during a MD simulation. The ab initio calculations show that none of these motifs is energetically preferred. Two binding motifs were found also for Rhodamine 6G, with the xanthene ring stacked predominantly either on the cytosine or on the guanine. These results suggest that the side rings of QSY 21 play a crucial role in its stacking on the DNA and indicate novel binding mode absent in the case of Rhodamine 6G, which lacks aromatic side rings.

Conformation and dynamics of a rhodamine probe attached at two sites on a protein: implications for molecular structure determination in situ

Replica exchange molecular dynamics (REMD) calculations were used to determine the conformation and dynamics of bifunctional rhodamine probes attached to pairs of cysteines in three model systems: (a) a polyalanine helix, (b) the isolated C helix (residues 53-66) of troponin C, and (c) the C helix of the N-terminal region (residues 1-90) of troponin C (sNTnC). In each case, and for both diastereoisomers of each probe-protein complex, the hydrophobic face of the probe is close to the protein surface, and its carboxylate group is highly solvated. The visible-range fluorescence dipole of the probe is approximately parallel to the line joining the two cysteine residues, as assumed in previous in situ fluorescence polarization studies. The independent rotational motion of the probe with respect to the protein on the nanosecond time scale is highly restricted, in agreement with data from fluorescence polarization and NMR relaxation studies. The detailed interaction of the probe with the protein surface depends on steric factors, electrostatic and hydrophobic interactions, hydrogen bonds, and hydration effects. The interaction is markedly different between diastereoisomers, and multiple preferred conformations exist for a single diasteroisomer. These results show that the combination of the hydrophobic xanthylium moiety of bifunctional rhodamine with the carboxylate substitution in its pendant phenyl ring causes the probe to be immobilized on the protein surface, while the two-site cysteine attachment defines the orientation of its fluorescence dipole. These features allow the orientation of protein components to be accurately determined in situ by polarized fluorescence measurements from bifunctional rhodamine probes.