# Conformational Transitions of Double-Stranded DNA in Thin Films
## 1 Introduction  
The double-stranded helix of deoxyribonucleic acid (dsDNA) can exist in a great variety of different geometries (conformations), 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]. Particularly important and biologically relevant are A-form and B-form helices because they can be found in prokaryotic and eukaryotic cells. In both A- and B-form, the helix is right-handed and the sizes of the major and minor grooves are distinctly defined; A-form dsDNA is broader, shorter, and has a wider minor groove than B-form dsDNA [1, 3]. In A-form, the sugar-based block adopts the C\({}_{3}\)- endo/anti conformation, and in the B-form, the C\({}_{2}\) endo/anti conformation. A-form is usually associated with the decreased number of water molecules per phosphate (lower hydration), whereas, in a fully hydrated state, dsDNA adopts B-form [4]. 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, %A- and %B-form can be estimated [2, 5]. Certain conditions may trigger structural A \(\rightarrow\) B and B \(\rightarrow\) A transitions in living cells and organisms and in vitro. These conformational transitions may be a vital step in some processes such as transcription and binding of specific proteins or drugs or can provide protection from desiccation in simple organismssuch as bacteria [2]. Consequently, 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. Over the years, structural techniques such as X-ray crystallography and nuclear magnetic resonance spectroscopy (NMR) provided valuable information on conformational heterogeneity in the structures of dsDNA [6]. While X-ray improved understanding of different crystal structures of DNA, high-resolution NMR experiments provided detailed information on the dsDNA conformation in solution. Both techniques established phosphate-ester conformation as the most variable part of nucleic acid structure [7]. Thus, a great part of understanding the structure and dynamics of DNA, in addition to protein-DNA recognition and drug-DNA interactions, lies in untangling important roles of phosphate-sugar moieties in DNA. Even though powerful, X-ray crystallography requires the macromolecule to be ordered in a crystal lattice; thus, the conformation of DNA in the crystal structure may not be identical to the one observed in solution or DNA confined in reduced spatial dimensions, such as thin films [6]. Additionally, NMR studies are usually restricted to short DNA sequences as there is increased difficulty in interpretation of the spectra of biomolecules with large molecular weights [7; 8]. Thus, different experimental methods such as infrared spectroscopy (IR), UV spectrophotometry, dielectric spectroscopy, etc. have been utilized in order to elucidate DNA structural features in diverse environments. Infrared spectroscopy methods such as Fourier transform infrared spectroscopy (FTIR) and Raman spectroscopy have long been utilized as non-destructive and sensitive techniques for probing DNA structure and function in different concentrations, ionic strengths, and without limitations to DNA length. In particular, \"textbook\" A- and B-form geometries were associated with different spectral characteristics; markers of A- and B-form dsDNA were established that are now common in the literature [2].