A quantitative measure of chirality inside nucleic acid databank

Abstract

We show the capability of a chirality index (Pietropaolo et al., Proteins 2008;70:667-677) to investigate nucleic acid structures because of its high sensitivity to helical conformations. By analyzing selected structures of DNA and RNA, we have found that sequences rich in cytosine and guanine have a tendency to left-handed chirality, in contrast to regions rich in adenine or thymine which show strong negative, right-handed, chirality values. We also analyze RNA structures, where specific loops and hairpin motifs are characterized by a well-defined chirality value. We find that in nucleosome the chirality is exalted, whereas in ribosome it is reduced. Our results illustrate the sensitivity of this descriptor for nucleic acid conformations.

Effect of Different Z‐Inducers on the Stabilization of Z Portion in BZ‐DNA Sequence: Correlation Between Experimental and Simulation Data

“…The free energy profile of the B‐Z junction and its brominated variant at position 8 of G2’ and G4’ (Fig. ) was reconstructed along a chiral descriptor represented by the z G coordinate . The z G coordinate indicates how far a given conformation sampled during the simulation is from the X‐ray structure of the B‐Z junction( pdb code 2ACJ ).…”

“…This kind of calculation runs over a nucleic acid fragment of 30 atoms allowing a good differentiation among the nucleic acid handedness . The indexes i, j, k, l run on all the 4!…”

“…are not included since they introduce an excessive computational cost that is too demanding for a molecular dynamics simulation. Moreover, the sum is restricted to a fragment of 15 atoms, verifying that this does not result in a loss of accuracy in the free energy description . This allows the calculations of chirality to be speeded up during the MD simulation process.…”

Molecular Mechanism of Polyacrylate Helix Sense Switching across Its Free Energy Landscape

“…Combining atomistic simulations with free energy methods , allows a direct quantitative estimate of energetics and structure. Recently, a chirality index , designed for biopolymers and later introduced into the more general path-collective variable of the metadynamics algorithm was proposed in order to quantify and discriminate helix handedness along the macromolecular chain. Its peculiarity is that it displays high sensitivity toward the helix sense without the typical artifacts due to the degeneracy introduced by using periodic angular descriptors …”