Abstract
DNA oligomers are studied at 0% and 92% relative humidity, corresponding to N < 2 and N > 20 water molecules per base pair. Two-dimensional (2D) infrared spectroscopy of DNA backbone modes between 920 and 1120 cm−1 maps fluctuating interactions at the DNA surface. At both hydration levels, a frequency fluctuation correlation function with a 300 fs decay and a slow decay beyond 10 ps is derived from the 2D lineshapes. The fast component reflects motions of DNA helix, counterions, and water shell. Its higher amplitude at high hydration level reveals a significant contribution of water to the fluctuating forces. The slow component reflects disorder-induced inhomogeneous broadening.
Highlights
Since the discovery of the double helix structure of deoxyribonucleic acid (DNA),1 the arrangement of water molecules around DNA and the role of water in defining and stabilizing the double helix have been major topics of DNA research.2,3 The level of hydration as characterized by, e.g., the relative humidity (r.h.) of the environment has a decisive influence on the helix conformation, in particular, on the geometry of the deoxyribose-phosphodiester backbone (Fig. 1)
The relative absorbance of the vibrational bands, of the modes with a high contribution from the motion of the ester linkage between the phosphate and the sugar group (L1; L2), changes significantly with hydration level. This reflects the changes of the vibrational transition dipoles due to a modification of the backbone geometry and the interfacial environment that typically accompany the transition from a hydrated to dehydrated helix structure
Dynamics at the DNA surface in the region of the backbone have been studied in artificial DNA helices at hydration levels of 0% and 92% relative humidity
Summary
Since the discovery of the double helix structure of deoxyribonucleic acid (DNA), the arrangement of water molecules around DNA and the role of water in defining and stabilizing the double helix have been major topics of DNA research. The level of hydration as characterized by, e.g., the relative humidity (r.h.) of the environment has a decisive influence on the helix conformation, in particular, on the geometry of the deoxyribose-phosphodiester backbone (Fig. 1). The level of hydration as characterized by, e.g., the relative humidity (r.h.) of the environment has a decisive influence on the helix conformation, in particular, on the geometry of the deoxyribose-phosphodiester backbone (Fig. 1). (more than 20 waters/base pair), while many DNA structures assume the A-form (Fig. 1(b)) at low hydration level.. The fastest motions of both the helix and the water environment occur on femto- to picosecond time scales, corresponding to frequencies on the order of 10 to approximately 1000 cmÀ1. While detailed knowledge exists on the fluctuating structure of neat water from both femtosecond vibrational spectroscopy, in particular two-dimensional (2D) infrared methods and molecular dynamics simulations, much less is known on the time scales of and mechanisms behind structural fluctuations of hydrated DNA and its
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