An Analytical and Computational Infrared Spectroscopic Review of Vibrational Modes in Nucleic Acids

Review Article

Austin J Anal Pharm Chem. 2016; 3(1): 1058.

An Analytical and Computational Infrared Spectroscopic Review of Vibrational Modes in Nucleic Acids

A Heidari*

Faculty of Chemistry, California South University, 14731 Comet St. Irvine, CA 92604, USA

*Corresponding author: A Heidari, Faculty of Chemistry, California South University (CSU), 14731 Comet St. Irvine, CA 92604, USA

Received: February 16, 2016; Accepted: March 07, 2015; Published: March 09, 2016

Abstract

In this review, we are reviewing single nucleotide bases using Attenuated Total Reflectance (ATR–FTIR) spectra before moving onto more complex oligionucleotides and ultimately DNA/RNA. This work will lay a foundation to understanding the spectroscopy of DNA/RNA in response to hydration and has important implications for understanding how cells respond to environmental stresses such as dehydration. Also, we are using quantum chemical methods to model DNA/RNA conformation to predict the frequencies and intensity differences in ATR–FTIR spectra. The computational review will initially focus on modelling small– to medium–sized oligonucleotides with the view of correlating predicted results with experimental spectra of these oligonucleotides. The effect of explicit and implicit solvent will be reviewed concurrently.

Keywords: Nucleic Acids; Vibrational Modes; Infrared Spectroscopy; Quantum Chemical Methods; DNA/RNA Conformation; ATR–FTIR Spectra; Modelling; Analytical Chemistry; Computational Chemistry

Background

Deoxyribonucleic acid (DNA) is the fundamental molecule of life encoding the genetic code for the development and functioning of every living organism and a large variety of viruses. RNA, proteins, and DNA are the main macromolecules, which are necessary for every form of life. The genetic system is encoded in the form of a sequence of nucleotides (guanine, adenine, thymine, and cytosine), which are denoted by the letters G, A, T, and C. Most DNA molecules consist of double–stranded helices (Figure 1) [1], composed of two long polymers made of simple units named nucleotides, molecules with backbones constructed of alternating sugars (deoxyribose) and phosphate groups (relative of phosphoric acid), with the nucleobases (G, A, T, C) joined to the sugars. DNA is a suitable store for biological information, because the DNA backbone resists cleavage and the double–stranded structure allows the molecule to have a built–in duplicate of the encoded data.