Site- and sequence-selective ultrafast hydration of DNA

Abstract

Water molecules in the DNA grooves are critical for maintaining structural integrity, conformational changes, and molecular recognition. Here we report studies of site-and sequence-specific hydration dynamics, using 2-aminopurine (Ap) as the intrinsic fluorescence probe and with femtosecond resolution. The dodecamer d[CGCA(Ap)ATTTGCG]2 was investigated, and we also examined the effect of a specific minor groove-binding drug, pentamidine, on hydration dynamics. Two time scales were observed: Ϸ1 ps (bulklike) and 10 -12 ps (weakly bound type), consistent with layer hydration observed in proteins and DNA. However, for denatured DNA, the cosolvent condition of 40% formamide hydration is very different: it becomes that of bulk (in the presence of formamide). Well known electron transfer between Ap and nearby bases in stacked assemblies becomes inefficient in the single-stranded state. The rigidity of Ap in the single strands is significantly higher than that in bulk water and that attached to deoxyribose, suggesting a unique role for the dynamics of the phosphate-sugarbase in helix formation. The disparity in minor and major groove hydration is evident because of the site selection of Ap and in the time scale observed here (in the presence and absence of the drug), which is different by a factor of 2 from that observed in the minor groove-drug recognition.T he influence of hydration on the conformation and interactions of DNA has been the subject of many investigations using x-ray crystallography, NMR, molecular dynamics, and thermodynamic techniques (for recent reviews see refs. 1-4). The important role of water in the three-dimensional structures adopted by DNA is summarized in one of these reviews (1). At the interface between DNA and proteins (5, 6), water molecules in the first hydration shell of DNA ''mark'' the positions where protein residues hydrogen-bond to DNA. Even for specificity of cleavage in DNA, water activity affects site-specific recognition of DNA by EcoRI (6) as it does in protein function (7).In the minor groove of a B-form DNA duplex, hydration and its role in drug binding are striking. In a recent publication (8) from this laboratory, we described how the drug (Hoechst 33258) bound in the minor groove of DNA can be used to probe the dynamics of the water layer. For a DNA dodecamer duplex d(CGCAAATTTGCG) 2 , two well separated hydration times were found: 1.4 and 19 ps, compared with 0.2 and 1.2 ps for the same drug in bulk water. For comparison, we also studied genomic calf thymus DNA for which the hydration exhibits time scales similar to those of the dodecamer DNA.In this study, we use a DNA base analog, 2-aminopurine (Ap), in the same dodecamer B-DNA duplex d(CGCAApATTTGCG) 2 as an intrinsic fluorescence probe. Ap has been shown by NMR spectroscopy and thermodynamic measurements to form a stable base pair with thymine in a DNA oligomer, stabilized by two hydrogen bonds in a Watson-Crick geometry (9, 10) (see Fig. 1). Thus it is reasonable to consider that the modification by Ap does not alte...

Anomalous power law decay in solvation dynamics of DNA: a mode coupling theory analysis of ion contribution

“…In the case of DNA solvation dynamics, two different approaches have been adopted. [22][23][24][25][26][27][28][29] In one approach, a base of the DNA duplex is replaced biochemically by a dye molecule, such as coumarin or aminopurine. [29] In another approach a fluorescent probe is intercalated to one of the grooves of the DNA.…”

“…[22][23][24][25][26][27][28][29] In one approach, a base of the DNA duplex is replaced biochemically by a dye molecule, such as coumarin or aminopurine. [29] In another approach a fluorescent probe is intercalated to one of the grooves of the DNA. [22][23][24][25][26][27][28] While these two approaches do not give identical results, some common features have been detected.…”

“…It seems to appear in the longer time. [29,30] The power law seems to exist over four to five decades of time, typically arises after a substantial initial decay but appears when the amplitude of correlation is still significant. The origin of this power law decay component has remained ill-understood, although it has been attributed tentatively to the relaxation of ions in and around DNA.…”

“…[22][23][24][25] As already mentioned the experiments of Zewail, Pal and co-workers did not find evidence of any slow decay where they used amino purine as a substitute base to probe the solvation dynamics around DNA. [29] Computer simulations [30] conformations is expected to introduce a slow quasi-exponential decay unless it is coupled to solvent (water molecules) and ions to involve a range of timescales. Second, it is not clear that the experiments of Berg, Sen and co-workers employ a DNA that is seriously damaged, particularly when the probe is located in the groove.…”

“…[22][23][24][25][26][27] It seems fare to assume that DNA is not damaged in the studies performed by Zewail and co-workers. [29] Thus the issue of the power law remains largely unresolved.…”