Changes in the Infrared Microspectroscopic Characteristics of DNA Caused by Cationic Elements, Different Base Richness and Single-Stranded Form

Abstract

Background

The infrared (IR) analysis of dried samples of DNA and DNA-polypeptide complexes is still scarce. Here we have studied the FT-IR profiles of these components to further the understanding of the FT-IR signatures of chromatin and cell nuclei.

Methodology/Principal Findings

Calf thymus and salmon testis DNA, and complexes of histone H1, protamine, poly-L-lysine and poly-L-arginine (histone-mimic macromolecules) with DNA were analyzed in an IR microspectroscope equipped with an attenuated total reflection diamond objective and Grams software. Conditions including polypeptides bound to the DNA, DNA base composition, and single-stranded form were found to differently affect the vibrational characteristics of the chemical groups (especially, PO ₂ ⁻) in the nucleic acid. The antisymmetric stretching (ν _as) of the DNA PO ₂ ⁻ was greater than the symmetric stretching (ν _s) of these groups and increased in the polypeptide-DNA complexes. A shift of the ν _as of the DNA PO ₂ ⁻ to a lower frequency and an increased intensity of this vibration were induced especially by lysine-rich histones. Lysine richness additionally contributed to an increase in the vibrational stretching of the amide I group. Even in simple molecules such as inorganic phosphates, the vibrational characteristics of the phosphate anions were differently affected by different cations. As a result of the optimization of the DNA conformation by binding to arginine-rich polypeptides, enhancements of the vibrational characteristics in the FT-IR fingerprint could be detected. Although different profiles were obtained for the DNA with different base compositions, this situation was no longer verified in the polypeptide-DNA complexes and most likely in isolated chromatin or cell nuclei. However, the ν _as PO ₂ ⁻/ν _s PO ₂ ⁻ ratio could discriminate DNA with different base compositions and DNA in a single-stranded form.

Conclusions/Significance

FT-IR spectral profiles are a valuable tool for establishing the vibrational characteristics of individualized chromatin components, such as DNA and DNA-polypeptide complexes in dried samples.