# Conformational Transitions of Double-Stranded DNA in Thin Films
## 1 Introduction
Even though there is consensus as to what constitutes spectral profiles of the two forms, inconsistencies can be found because spectra can be obtained from different types of DNA samples, i.e., short oligonucleotides, polynucleotides, genomic or synthetic DNA, DNA isolated from various cells, and tissues. Moreover, spectra can be obtained from various physical states of DNA such as solutions, gels, thin films, and crystals; all of this contributes to the final spectral profile of the studied DNA sample with each state providing different advantages. In DNA thin films, hydration conditions of the samples can be distinctly controlled by various simple techniques such as air-drying or drying under a stream of inert gasses such as nitrogen, or more advanced techniques that imply the use of home-built humidity chambers or cells where DNA thin films are prepared over the course of several hours (usually after 24 h) [9]. Thus, a great variety of hydration conditions from fully hydrated to fully dehydrated state can be obtained and dehydration and rehydration experiments can be performed. Additionally, impeding absorptions from the bulk water can be avoided, and with the right substrate, the spectral range can be greatly increased. Another important advantage of DNA thin film is the ability to use these samples in (imaging) techniques such as FTIR microspectroscopy [10; 11] and atomic force microscopy (AFM) [12]. These fast-growing techniques require the deposition of DNA on a substrate (thus forming DNA thin films) and have great capabilities of resolving different structural properties of DNA. Recently, there is a rise in research utilizing different spectroscopic techniques in the field of biomedicine with intention of expanding and improving diagnostic methods making them faster, less expensive, and less invasive [13]. Even though fluorescence spectroscopy has long been used in clinical settings, due to the development of techniques such as immunofluorescence and fluorescence-activated cell sorting (FACS), IR spectroscopy techniques are not yet common in clinical applications. (FT)IR-based diagnostics is a promising field due to the technique being inexpensive, non-destructive, fast, and easy to operate [14]. However, in order to establish FTIR spectroscopy techniques in clinical applications several setbacks, such as precise acquisition and unambiguous interpretation of the spectra, statistically acceptable number, and sample size, must be overcome. FTIR spectroscopy has proven useful in detecting conformational transitions in DNA thin films and related biological samples with the intent of detecting cancer markers [2; 15; 16; 17] and other abnormalities caused by various types of DNA damage in cells and tissues [3; 18], before and after drug administration [19], and tracking anti-cancer drug efficiency [20; 21]. These studies are dependent on the ability to identify and preserve DNA in certain conformation and rely on the correct interpretation of conformation-related markers [2]. Thus, in order to improve the ability of IR spectroscopy techniques to be more accurately used in cancer diagnostics, damage detection, and drug efficiency, there is a need to further improve the interpretation of the spectra of DNA in different hydration and conformation states and to distinguish between the two. In this study, utilizing FTIR spectroscopy, we provide detailed analysis of dynamics of A- to B-form transitions in DNA thin films obtained from sodium salt lyophilized DNA in NaCl solution under different hydration conditions based on a statistical analysis of a substantial number of spectra and extensive band shape analysis (peak fitting) in both the phosphate (1150-1000 cm\({}^{-1}\)) and sugar-phosphate region (900-750 cm\({}^{-1}\)). Systematically controlled hydration of DNA thin films provides information on dynamics and reorganization of hydration shells; the conformational transition from A-form to more ordered B-form is observed when sufficient time for conformation transition to take place is allowed.