INTERFACIAL AND CONFINED WATER Part 7 pptx

182 Interfacial and confined water

Its conformation is compatible with any base pair sequence, and it is

separated from the B-form by only a modest energy barrier [616]. Due

to all these features, reversible local B ↔ A transitions represent one of

the modes for governing protein–DNA interactions [617]. The B ↔ A

transitions can be also induced in vitro by changing the DNA environ￾ment [488, 618–620]. In condensed preparations, that is, in crystalline

and amorphous fibers as well as in films, DNA adopts the B-form under

high relative humidity, but it can be reversibly driven to the A-form by

placing the samples under relative humidity below 80% [488, 618, 620].

DNA molecules exhibit reversible B ↔ A transition in aqueous solu￾tions upon addition of some organic solvents [613, 619]. In all cases,

the transition occurs at about the same water activity, suggesting that

the B ↔ A conformational switch is driven by the hydration state of the

double helix [492].

Hydration of nucleic acids has a number of distinctions due to their

polyionic character and uneven nonspherical shapes [487]. In physiolog￾ical conditions, the double-helical DNA directly interacts with solvent

ions in several water layers from its surface; therefore, the functional

DNA hydration shell is very thick. Under limited hydration, there is a

strict relationship between the state of DNA and hydration number Γ

measured as the number of water molecules per nucleotide (or phos￾phate). When Γ is reduced below 30, the common B-form of DNA is

already perturbed, but it is maintained until Γ ≈ 20 [487, 488]. Below this

hydration, DNA undergoes different conformational transitions, among

which the transition from B- to A-form [489] with a midpoint at about

Γ = 15 is the most studied (see Section 6).

Formation of a spanning network of hydration water at the DNA surface

upon hydration was studied by computer simulations [200, 621] using the

water drop methods [622, 623]. Simulations were carried out for a rigid

dodecamer fragment of double-helical DNA. The structures of the canon￾ical B-DNA and A-DNA [624] were fixed in space. The system involved

24 bases and 22 phosphate groups in two DNA strands surrounded by a

mobile hydration shell of 22 Na+ ions and 24Γ water molecules. Evo￾lution of the cluster size distribution nS on the surface of B-DNA upon

increasing hydration is shown in Fig. 104. At low hydrations (Γ = 12,

13, and 14), nS shows deviations upward from the power law (19) at

the intermediate cluster sizes S. At high hydrations (Γ = 17, 18, 19, and

Water in low-hydrated biosystems 183

10 100

S

nS

1

10213

10211

1029

1027

1025

1023

1021

nS ~ S22.05

Figure 104: The size distributions nS of water clusters at various hydrations

Γ from 12 (top) to 20 (bottom). The distributions are shifted consecutively, each

by one order of magnitude starting from the top. The hydration levels Γ = 15

and 16, closest to the percolation threshold, are shown by closed symbols.

Reprinted, with permission, from [200].

20), a drop of nS is clearly seen before the hump at large S. The size

distribution nS follows the universal law (19) in the widest range of S

when Γ = 15 and 16 (closed symbols in Fig. 104). Note that this con￾clusion does not depend on the assumed dimensionality of the system

being studied, that is water adsorbed on the DNA surface. Due to the

groove shape of the DNA double helix, the 2D character of its hydration

water is not obvious. The mean cluster size shows a skewed maximum

at Γ = 14 and suggests that the percolation threshold is located above

this hydration level [200]. Probability distribution of the size Smax of the

largest water cluster allows calculation of the spanning probability R,

which achieves 50% at Γ = 14.3. So, analysis of the various cluster prop￾erties evidences the percolation transition of hydration water at the sur￾face of B-DNA when Γ ≈ 15.5 and midpoint of the percolation transition

at Γ ≈ 14.

184 Interfacial and confined water

The primary water shell around B-DNA is usually estimated as about

20 water molecules per nucleotide [490]. Therefore, the percolation

threshold of hydration water on the surface of rigid B-DNA corresponds

to about 80% of one full hydration layer. Approximately 65% and 50% of

a monolayer coverage is necessary to form a spanning hydration network

on smooth hydrophilic surfaces [394] and the surface of the lysozyme

molecule [401, 508], respectively. It is reasonable to attribute a relatively

high percolation threshold for B-DNA to the presence of Na+ ions in a

hydration shell. The key role of free metal ions in low-hydration poly￾morphism of DNA is well established by experimental studies [625]. By

changing the amount and the type of ions, one can shift the midpoints

of polymorphic transitions and even their pathways [626]. Almost noth￾ing is known about the detailed mechanisms involved in such effects.

A step toward elucidation of these problems is study of water clustering

and percolation with and without free ions. As small hydration shells

around charged DNA fragments are inherently unstable [622], DNA

molecules should be neutralized artificially. Neutralization of DNA has

been used in simulations since long ago [627], and usually this is done

by reducing phosphate charges. For electrostatically neutral B-DNA

obtained by reducing charges of phosphate oxygens, water does not show

a percolation transition in the course of gradual hydration. The probabil￾ity distribution P (Smax) of the size of the largest cluster behaves as if the

system consists of small water droplets that merge into one large water

patch with increased hydration [621]. This scenario is also suggested

by the absence of the sigmoid behavior for spanning probability R, the

absence of maximum of Smean, a monotonous change of ΔSmax etc. For￾mation of a large continuous water patch was found to be typical for water

near hydrophobic surfaces or in mixtures with hydrophobic solutes [204],

which is surprising because, even with phosphates neutralized, the DNA

surface remains highly polar.

It turned out, however, that the behavior of hydration water near neutral

DNA depends on how its surface was neutralized. Properties of hydration

water were found to be similar in the cases when the neutralizing charge

was uniformly distributed over the whole system including DNA and

water and between all DNA atoms only. In both cases, water undergoes

a normal percolation transition with increasing Γ. With ions removed,

the percolation threshold of hydration water is shifted by ΔΓ ≈ 4 toward