Conformational Transitions of Double-Stranded DNA in Thin Films

Kristina Serec,Nikola Šegedin,Maria Krajačić,Sanja Dolanski Babić

doi:10.3390/app11052360

Abstract

Conformational transitions of double-stranded DNA in different environments have long been studied as vital parts of both in vitro and in vivo processes. In this study, utilizing Fourier transform infrared spectroscopy (FTIR), we provide detailed analysis of dynamics of A- to B-form transitions in DNA thin films of different hydrated states based on a statistical analysis of a substantial number of spectra and band shape analysis (peak fitting) in both the phosphate (1150–1000 cm−1) and sugar–phosphate (900–750 cm−1) region. Hydration of DNA thin films is systematically controlled by the time spent in the desiccator chamber (from 3 min to 40 min) allowing conformation and hydration signatures, in addition to variations due to ambient conditions, to be resolved in the spectra. Conformation transition from A-form to more ordered B-form is observed if sufficient time in the desiccator chamber is allowed and is confirmed by changes on the bands at ≈890, 860, 837, and 805 cm−1. Phosphate vibrations at ≈1230 cm−1 and 1089 cm−1, and backbone vibrations at ≈1030 cm−1 and 765 cm−1 were found to be sensitive to changes in hydration rather than conformation. Additionally, we found that spectral variations caused by ambient conditions can be significantly reduced without inducing conformational changes, which serves as a good basis for quality assurance.

Highlights

The double-stranded helix of deoxyribonucleic acid can exist in a great variety of different geometries, depending on the base stacking interactions, hydrogen bonding, and long-range intra- and inter-backbone forces renormalized by water-mediated interactions with the entities situated in the DNA hydration shells [1,2]. important and biologically relevant are A-form and B-form helices because they can be found in prokaryotic and eukaryotic cells
In order to obtain thin films, 30 μL of the respective DNA stock solutions were deposited on optical grade silicon transmission windows and placed inside a desiccator chamber under an active vacuum from 3 min to 40 min after which thin films were recorded (a) immediately after their removal from the desiccator chamber and (b) 5 min after their removal from the desiccator chamber, allowing the samples to come to ambient conditions, i.e., to stabilize
We utilized Fourier transform infrared spectroscopy (FTIR) spectroscopy to monitor the structural organization of double-stranded helix of deoxyribonucleic acid (dsDNA) in thin films obtained in carefully controlled and monitored hydration conditions

Summary

Introduction

Important and biologically relevant are A-form and B-form helices because they can be found in prokaryotic and eukaryotic cells. All the subtleties in the structure between the two forms determine the accessibility of other molecules to DNA binding sites and reveal distinct surfaces of DNA susceptible to different environments. Both forms may be detected simultaneously because segments of DNA can adopt different forms; in this case, %Aand %B-form can be estimated [2,5]. Conformational transitions are often fundamental in the studies of drug- and anti-cancer drug-DNA interaction, resistance to DNA damage induced by radiation, heat, and desiccation, and are extremely important tools in the detection of cancer markers and other abnormalities

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