# Conformational Transitions of Double-Stranded DNA in Thin Films
## 4 Discussion
If enough time is allowed, after approximately 10 min, structural organization of DNA is complete and 10-40 min thin films reflect similar, B-like conformation. Again, note that after 3-5 min, there are no more changes in the pressure in the desiccator chamber (left inset of Figure 1); thin films merely stay up to 30 additional minutes in the same atmosphere, which does not have as strong an influence on the spectra as the first few minutes of the process. Consequently, 10-40 min films show similar spectral features in the conformation-related 900-750 cm\({}^{-1}\) region. Different stages of B-form formation in 3-min and 10-min films, as indicated by the FTIR spectra and calculated using integrated absorptions of 860 cm\({}^{-1}\), 805 cm\({}^{-1}\), and 836 cm\({}^{-1}\) bands, are presented in Figure 8 and compared to DNA manganese salt thin films obtained in our previous work [31]. Due to increased screening of Mn\({}^{2+}\) ions, in DNA manganese salt prepared by similar protocol (10 min desiccation time and same DNA type and concentration) complete formation of B-form is evident; 860 cm\({}^{-1}\) and 805 cm\({}^{-1}\) markers are missing in the spectra and ratio of integrated absorptions yield 94% B-form. However, in DNA sodium salt presented in this study, only 805 cm\({}^{-1}\) marker completely vanishes, while 860 cm\({}^{-1}\) marker experiences intensity and integrated intensity decrease, as evident in Figure 8. Thus, even though 10-min film reflects mostly B-like conformation, some traces of A-form are identified in the spectra. The coexistence of A- and B-forms in DNA in which sections of phosphate groups are in different conformations was also reported by different NMR [32] and FTIR studies [2]. Finally, we address the issue of resolving hydration-, conformation-, and ambient-related signatures in the spectra. In a fully hydrated state, DNA is surrounded by several hydration shells. The primary hydration shell of DNA is different from the bulk water and at 80% relative humidity it is considered complete with about 20 water molecules per nucleotide [1]. In this hydrated state, DNA assumes B-form and changes in hydration may trigger conformational transitions that occur stepwise and cooperatively [1]. One of the first studies that studied the structural organization of water molecules upon rehydration by [PERSON] et al. concluded that water is first absorbed by the PO\({}_{2}\)\({}^{-}\) groups, then by C-O and C-C groups of the phosphodiester linkage, and finally by the DNA bases [33]. [PERSON] and [PERSON] found their study complementing and observed spectral changes of DNA phase transitions in terms of two concurrent effects--conformational change and hydration of the phosphate groups [9]. Their study suggested that when the radical conformational transition takes place (fully hydrated DNA sample in B-form opposed to dry DNA pellet in A-form) substantial shifts in the frequency of asymmetric stretching PO\({}_{2}\)\({}^{-}\) vibration from 1225 cm\({}^{-1}\) to 1238 cm\({}^{-1}\) and symmetric stretching PO\({}_{2}\)\({}^{-}\) vibration from 1088 cm  
Figure 8: FTIR spectra of DNA thin films and comparison of different levels of B-form. DNA sodium salt with the coexistence of both 3-min (purple) and 10-min (green) films. DNA manganese salt (blue), in which the full formation of B-form is evident, is shown for comparison (data taken from [31]). to 1093 cm\({}^{-1}\) occur. On the other hand, hydration effects are recognized by infrared absorption intensity changes of the two phosphate vibrations due to an increase in the local dielectric of the surroundings of the phosphate groups [9]. A nice correlation with our data can be found for their two hydrated pallets, i.e., 1090 cm\({}^{-1}\) and 1235 cm\({}^{-1}\) and 1088 cm\({}^{-1}\) and 1229 cm\({}^{-1}\), respectively, compared to our thin films 1088 cm\({}^{-1}\) and 1230-1234 cm\({}^{-1}\).