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Mrevlishvili, G. M.; Carvalho, Ana Paula S.M.C.; Silva, M. A. V. Ribeiro da; Mdzinarashvili, Tamaz; Razmadze, G. Z.; Tarielashvili, T. Z.

doi:10.1023/a:1012491716200

Cited by 20 publications

(20 citation statements)

References 25 publications

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“…The most weakly bound water molecules are of critical importance to biological function (41) and are unlikely to be seen in crystal structures or by NMR (41). They are part of total hydration, which influences structural and biological activities (42,43). The residence times of weakly bound water are only an order of magnitude different from that of bulk, and they are the ones that have to be probed with femtosecond resolution.…”

Section: Discussionmentioning

confidence: 99%

Water at DNA surfaces: Ultrafast dynamics in minor groove recognition

Pal

Zhao

Zewail

2003

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

229

290

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Water molecules at the surface of DNA are critical to its equilibrium structure, DNA-protein function, and DNA-ligand recognition. Here we report direct probing of the dynamics of hydration, with femtosecond resolution, at the surface of a DNA dodecamer duplex whose native structure remains unperturbed on recognition in minor groove binding with the bisbenzimide drug (Hoechst 33258). By following the temporal evolution of fluorescence, we observed two well separated hydration times, 1.4 and 19 ps, whereas in bulk water the same drug is hydrated with time constants of 0.2 and 1.2 ps. For comparison, we also studied calf thymus DNA for which the hydration exhibits similar time scales to that of dodecamer DNA. However, the time-resolved polarization anisotropy is very different for the two types of DNA and clearly elucidates the rigidity in drug binding and difference in DNA rotational motions. These results demonstrate that hydration at the surface of the groove is a dynamical process with two general types of trajectories; the slowest of them (Ϸ20 ps) are those describing dynamically ordered water. Because of their ultrafast time scale, the ''ordered'' water molecules are the most weakly bound and are accordingly involved in the entropic (hydration͞dehydration) process of recognition. H ydration of DNA plays important role in its structure, conformation, and function. Of significance to the function is the selective recognition by DNA of small molecules (ref. 1 and references therein). X-ray crystallography, NMR, dielectric relaxation, and molecular dynamics simulation studies have shown that a significant amount of water molecules are bound to DNA (for reviews, see refs. 2-6). For example, measurements of dielectric relaxation caused by water molecules bound to DNA in mixed water-ethanol solutions have found that 18-19 water molecules per nucleotide are present in B-DNA, but only 13-14 water molecules are bound in A-DNA (5). The study also suggested that a structural transition of poly(dG-dC)⅐poly(dGdC) DNA from its B to Z form takes place on the removal of the bound water molecules, preferentially from the phosphate groups.The molecular picture of hydration in the minor groove of B-DNA is unique. An x-ray crystallographic investigation (7) followed by solution NMR study (8) on a model dodecamer B-DNA duplex (for the sequence of A͞T tracts, CGCGAAT-TCGCG) showed that the minor groove is hydrated in an extensive and regular manner, with a zigzag ''spine'' of firstand second-shell hydration along the f loor of the groove. In contrast, hydration within the major groove is principally confined to a monolayer of water molecules. The conformational energy calculation suggested that the presence of the spine of hydration is the prime reason for the further narrowing of minor groove (9).The influence of drug binding on DNA hydration is striking. Acoustic and densimetric studies have shown that a fraction (not total) of the water molecules is released on recognition (10, 11). Hence, the balance between enthalpic and entr...

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Section: Discussionmentioning

confidence: 99%

Water at DNA surfaces: Ultrafast dynamics in minor groove recognition

Pal

Zhao

Zewail

2003

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

229

290

View full text Add to dashboard Cite

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“…DNA hydration has been extensively studied by several gravimetric, spectroscopic, osmotic stress, calorimetric, and scattering methods. [14][15][16][17][18][19][20][21][22][23][24] However, to our knowledge, simultaneous free energy and enthalpy data have not been reported previously.…”

Section: Discussionmentioning

confidence: 99%

The Hydration of a DNA−Amphiphile Complex

et al. 2004

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We present measurements of isothermal DNA-hexadecyltrimethylammonium (DNACTA) complex and pure DNA hydration at 25°C using a sorption microcalorimeter. This calorimeter provides simultaneous measurement of (i) water activity (sorption isotherms) and (ii) the partial molar enthalpy of water as a function of water uptake. For pure DNA, hydration is exothermic over the studied concentration range and we find an approximately linear relation between the partial molar enthalpy and the partial molar free energy. A kink in the isotherm appears at 20.0 ( 0.3 water molecules per base pair for a water activity of 0.80, consistent with A-B transition of the DNA. There is no detectable heat effect associated with this transition. At low water contents, the hydration of the DNACTA (1:1) complex is exothermic as for the pure DNA, but after incorporation of the first 7.0 ( 0.1 water molecules, the enthalpy changes sign. At 22 water molecules per base pair, the enthalpy levels off to 2.7 ( 0.2 kJ/mol. In a separate experiment, the swelling limit for the DNACTA complex was found to be 27 ( 1 waters per base pair. The DNACTA complex is arranged in a hexagonal structure. We propose a model for the DNACTA complex based on the packing of the components in an electroneutral way consisting of six DNA helices, presumably in an A configuration, placed around a central CTA + cylinder. The hydration of the complex is seen as a balance between the attractive electrostatic interaction causing the formation of the complex and a repulsive component arising from a hexagonal deformation of CTA + cylinders. An important contribution to the partial molar enthalpy of water comes, in this interpretation, from the release of conformational constraints of the CTA ion alkyl chains.

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“…However, breakage of the hydrogen bonds between the bases in each strand of dsDNA will only begin to occur significantly at temperatures above ca. 340 K, the melting point [16].…”

Section: Article In Pressmentioning

confidence: 99%