In RNA, A-form helices are commonly terminated by tetraloops or 3' dangling ends. Aside from helices themselves, these helix-breaking motifs appear to be among the most frequent and repetitive structural elements of large folded RNAs. We show here that within a frequent type of tetraloop, cGNRAg (G is guanine, N is any base, R is purine, A is adenine), a tension exists between the backbone tors...

The free energy of an RNA fold is a combination of favorable base pairing and stacking interactions competing with entropic costs of forming loops. Here we show how loop entropy, surprisingly, can promote tertiary order. A general formula for the free energy of forming multibranch and other RNA loops is derived with a polymer-physics based theory. We also derive a formula for the free energy of...

The stacking of phenanthroline(phen) ligand within base pair sequences is one of the important factors for the stabilization of metalphen complex within DNA. The stacking ability of this ligand has been assessed to deduce the base pair selectivity as well as to identify the favored region of intercalation. Different level of theories have been used to predict the favorable regions for stacking ...

Parallel-displaced π-stacking in the benzene dimer and larger polycyclic aromatic hydrocarbons is driven by competition between dispersion exchange-repulsion interactions. The present work examines whether same true porous frameworks that exhibit stacking interactions, including [18]annulene dimer, porphyrin several models of covalent organic framework known as COF-1. Interaction energies their...

High level ab initio methods have been used to study stacking interactions in ten unique base pair steps both in A-RNA and in B-DNA duplexes. The protocol for selection of geometries based on molecular dynamics (MD) simulations is proposed, and its suitability is demonstrated by comparison with stacking in steps at fiber diffraction geometries. It is shown that fiber diffraction geometries are ...

We report measurements of the spatial distribution of stacking faults in colloidal crystals formed by means of an oscillatory shear field at a particle volume fraction of 52% in a system where the pair potential interactions are mildly repulsive. Stacking faults are directly visualized via confocal laser scanning microscopy. Consistent with previous scattering studies, shear orders the initiall...

Highly stable cyclic dimers have been assembled through a combination of non-covalent interactions, including multiple hydrogen bonding, parallel stacking and hydrophobic shielding.

The binding of a tetrapeptide lysyltryptophylglycyllysine to nucleosome core particles has been investigated using UV absorption and fluorescence spectroscopy. Modifications of the absorption spectra and fluorescence quenching of the tryptophyl residue are consistent with stacking between the indole ring and nucleic acid bases. Therefore DNA interactions with histones do not prevent stacking of...