Ultrafast decay and hydration dynamics of DNA bases and mimics

Pal, Samir Kumar; Peón, Jörge; Zewail, Ahmed H.

doi:10.1016/s0009-2614(02)01149-1

Cited by 61 publications

(61 citation statements)

References 24 publications

(36 reference statements)

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“…It should be noted that the SE will most likely show a dynamic Stokes shift which is reported to take place within 4 ps [20], comparable with the 1.3 ps time we find. Interestingly, when state 2 evolves into 3 the ESA increases around $500 nm while it goes down at $400 nm.…”

Section: Data Analysis and Discussionsupporting

confidence: 89%

Electronic states in 2-aminopurine revealed by ultrafast transient absorption and target analysis

Larsen

Stokkum

Groot

et al. 2003

Chemical Physics Letters

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Subpicosecond polarized transient-absorption measurements on the fluorescent adenine analogue 2-aminopurine have been performed in the wavelength region from 320 to 690 nm. Global target analysis of the data reveals structural heterogeneity of the chromophore in the excited state. Two distinct states with remarkably different spectroscopic properties were resolved. One state does show stimulated emission, whereas the other state does not and exposes a very long excited-state lifetime.

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Section: Data Analysis and Discussionsupporting

confidence: 89%

Electronic states in 2-aminopurine revealed by ultrafast transient absorption and target analysis

Larsen

Stokkum

Groot

et al. 2003

Chemical Physics Letters

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“…Thus, solvation redshift (Ϸ7,000 cm Ϫ1 ) is dominant over the intramolecular Stokes shift. This dominance of solvation was confirmed by studies of two probes (tryptophan and 2-aminopurine) at low and high vibrational energy (4,32,33). These observations are further supported by the fact that the shapes of time-resolved emission spectra at early times are not significantly different from those obtained at later times and that the ANS transients in different solvents (water, methanol, and ethanol) give the characteristic solvation times obtained with other probes.…”

Section: Fig 2 (Upper)mentioning

confidence: 55%

Ultrafast surface hydration dynamics and expression of protein functionality: α-Chymotrypsin

Pal

Peón

Zewail

2002

Proc. Natl. Acad. Sci. U.S.A.

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117

138

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We report studies of hydration dynamics at the surface of the enzyme protein bovine pancreatic ␣-chymotrypsin. The probe is the well known 1-anilinonaphthalene-8-sulfonate, which binds selectively in the native state of the protein, not the molten globule, as shown by x-ray crystallography. With femtosecond time resolution, we examined the hydration dynamics at two pHs, when the protein is physiologically in the inactive state (pH 3.6) or the active state (pH 6.7); the global structure and the binding site remain the same. The hydration correlation function, C(t), whose decay is governed by the rotational and translational motions of water molecules at the site, shows the behavior observed in this laboratory for other proteins, Subtilisin Carlsberg and Monellin, using the intrinsic amino acid tryptophan as a probe for surface hydration. However, the time scales and amplitudes vary drastically at the two pHs. For the inactive protein state, C(t) decays with an ultrafast component, close to bulk-type behavior, but 50% of the C(t) decays at a much slower rate, ‫؍‬ 43 ps. In contrast, for the active state, the ultrafast component becomes dominant (90%) and the slow component changes to a faster decay, ‫؍‬ 28 ps. These results indicate that in the active state water molecules in the hydration layer around the site have a high degree of mobility, whereas in the inactive state the water is more rigidly structured. For the substrate-enzyme complex, the function and dynamics at the probe site are correlated, and the relevance to the enzymatic action is clear.A lmost all biological macromolecules (proteins, enzymes, and DNA) are inactive in the absence of water. The hydration shell formed by water molecules in close vicinity of a protein͞ enzyme is particularly important for the stability of the structure and the function or recognition at a specific site. This role of hydration in enzyme catalysis is well known and has recently been reviewed in a number of publications (see, e.g., refs. 1-3). In one of these studies it was shown that the dehydration of a protein, which makes it more rigid and increases its denaturation temperature, is correlated with the loss of its physiological function (1). An understanding of the dynamics of water molecules at the surface of the protein, with spatial molecular and temporal femtosecond resolution of a single site, is important for elucidating a molecular picture and was the goal of a series of publications from this laboratory (4-6).Using the intrinsic single-tryptophan amino acid as a probe (4, 5), we found that the hydration dynamics at the surface of two different proteins, Subtilisin Carlsberg (SC) (4) and Monellin (5), occur on two well separated time scales: 800 fs and 38 ps for SC and 1.3 ps and 16 ps for Monellin. The slow and fast components are of similar magnitude. From these results, we discussed two types of water hydration trajectories: one fast, bulk type and another much slower, surface-bound type. When these experiments were made on a probe away from the surface by Ϸ1...

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“…The effect of solvation on the Ap emission (solvatochromism) has been studied (12). Ap shows red shift in its emission maximum with the increase in solvent polarity.…”

Section: Resultsmentioning

confidence: 99%

Site- and sequence-selective ultrafast hydration of DNA

Pal

Zhao

Xia

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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107

137

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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...

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Ultrafast decay and hydration dynamics of DNA bases and mimics

Cited by 61 publications

References 24 publications

Electronic states in 2-aminopurine revealed by ultrafast transient absorption and target analysis

Electronic states in 2-aminopurine revealed by ultrafast transient absorption and target analysis

Ultrafast surface hydration dynamics and expression of protein functionality: α-Chymotrypsin

Site- and sequence-selective ultrafast hydration of DNA

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