Classification of nucleic acids structures by means of the chemometric analysis of circular dichroism spectra

Abstract

DNA can adopt structures in solution apart from the well-known Watson-Crick double helix, ranging from disordered single strands to high-order structures such as triplexes or quadruplexes. Moreover, different topologies can be adopted depending on the polarity of the DNA strands. The elucidation of the structure and topology adopted by a DNA sequence is usually carried out by means of spectroscopic techniques, such as circular dichroism. In this work, the ability of several chemometric methods to efficiently classify DNA structures from circular dichroism data is tested. With this objective in mind, a dataset including 50 experimental spectra corresponding to different DNA structures (random coil, duplex, hairpin, reversed and normal triplex, parallel and antiparallel G-quadruplex, and i-motif) has been analyzed by means of unsupervised hierarchical clustering analysis, principal component analysis and partial least squares discriminant analysis. The results have shown than those methods allow efficiently the classification of DNA structures from circular dichroism spectra. Moreover, these classification methods also provided the most characteristic wavelengths used in the classification procedures.

Urine metabolomics analysis for adrenal incidentaloma activity detection and biomarker discovery

“…HCA is calculating the distance matrices of data objects, and organizing objects which possess greatest similarity in clusters. The applicability of this method has been recognized in many studies on biomolecules [22][23][24][25]. The dendrogram depicting separation between the samples from patient and control group is shown in Fig.…”

G‐Quadruplex Secondary Structure Obtained from Circular Dichroism Spectroscopy

“…[2] A recent chemometric analysis of nucleic acid CD spectra was used to classify nucleic acid structures using a library of sequences and structures that expanded the range of topologies to include multistranded triplex and quadruplex forms. [4] As of yet no quantitative analysis has been attempted for nucleic acids that is analogous to the approach used to quantify CD spectra of proteins to obtain more detailed structural information. The goal of this study is to develop such an analytical approach to provide quantitative secondary structural information about quadruplexes from their measured CD spectra.…”

G-quadruplex secondary structure from circular dichroism spectroscopy

“…[2] A recent chemometric analysis of nucleic acid CD spectra was used to classify nucleic acid structures using a library of sequences and structures that expanded the range of topologies to include multistranded triplex and quadruplex forms. [8] As of yet no quantitative analysis has been attempted for nucleic acids that is analogous to the approach used to quantify CD spectra of proteins to obtain more detailed structural information. The goal of this study is to develop such an analytical approach to provide quantitative secondary structural information about quadruplexes from their measured CD spectra.…”