Intrusion of Counterions into the Spine of Hydration in the Minor Groove of B-DNA:  Fractional Occupancy of Electronegative Pockets

Abstract

A sequence of ordered solvent peaks in the electron density map of the minor groove region of ApT-rich tracts of the double helix is a characteristic of B-form DNA well established from crystallography. This feature, termed the “spine of hydration”, has been discussed as a stabilizing feature of B-DNA, the structure of which is known to be sensitive to environmental effects. Nanosecond-range molecular dynamics simulations on the DNA duplex of sequence d(CGCGAATTCGCG) have been carried out, including explicit consideration of ∼4000 water molecules and 22 Na+ counterions, and based on the new AMBER 4.1 force field with the particle mesh Ewald summation used in the treatment of long-range interactions. The calculations support a dynamical model of B-DNA closer to the B form than any previously reported. Analysis of the dynamical structure of the solvent revealed that, in over half of the trajectory, a Na+ ion is found in the minor groove localized at the ApT step. This position, termed herein the “ApT pocket”, was noted previously (Lavery, R.; Pullman, B. J. Biomol. Struct. Dyn. 1985, 5, 1021) to be of uniquely low negative electrostatic potential relative to other positions of the groove, a result supported by the location of a Na+ ion in the crystal structure of the dApU miniduplex [Seeman, N.; et al. J. Mol. Biol. 1976, 104, 109) and by additional calculations described herein based on continuum electrostatics. The Na+ ion in the ApT pocket interacts favorably with the thymine O2 atom on opposite strands of the duplex and is well articulated with the water molecules which constitute the remainder of the minor groove spine. This result indicates that counterions may intrude on the minor groove spine of hydration on B-form DNA and subsequently influence the environmental structure and thermodynamics in a sequence-dependent manner. The observed narrowing of the minor groove in the AATT region of the d(CGCGAATTCGCG) structure may be due to direct binding effects and also to indirect modulation of the electrostatic repulsions that occur when a counterion resides in the minor groove “AT pocket”. The idea of localized complexation of otherwise mobile counterions in electronegative pockets in the grooves of DNA helices introduces a heretofore mostly unappreciated source of sequence-dependent effects on local conformational, helicoidal, and morphological structure and may have important implications in understanding the functional energetics and specificity of the interactions of DNA and RNA with regulatory proteins, pharmaceutical agents, and other ligands.

Free Energy Analysis of Protein–DNA Binding: The EcoRI Endonuclease–DNA Complex

“…For the purposes of this study, we proceed according to the following rationale. From the results of Manning theory [38], we expect that condensed monovalent counterions per se neutralize only ∼76% of the DNA charge, a result independently supported by recent large-scale MD simulations [67,68]. Thus, a model with enough fully charged sodium counterions condensed on the DNA to provide local electroneutrality would be unrealistic.…”

“…This necessitates an ad hoc model for counterion release that, no matter how plausible, remains a simplified assumption. The development of dynamical models for counterion behavior around DNA from MD simulations including explicit consideration of all solvent has been reported recently [67,68]. Scaled up to protein DNA complexes, MD holds the promise of providing an ab initio model for counterion release.…”

Crystal structures of nucleic acids and their drug complexes

“…These features are sensitive to the protocols used in the crystallographic refinement, 12 which further underlines the inadvisability of deriving general conclusions about the detailed features of sequence-dependent DNA structure from one of even a few crystal structures. The AT region of the minor groove in d(CGCGAATTCGCG) was found to contain an ordered array of water molecules, the 'spine of hydration', whose existence has more recently been confirmed by NMR spectroscopic 13 and simulation 14 studies. There is an increasing realisation of the importance of structured water molecules, not only in stabilising particular aspects of DNA (and RNA) structure, but in acting as probes for nucleic acid recognition.…”

Temperature dependence of fast fluctuations in single- and double-stranded DNA molecules: a neutron scattering investigation

“…Electronic spin resonance measurements [3] have revealed the existence of base motions on the nanosecond timescale in RNA and DNA single-and double-stranded systems. In addition, fast conformational motions in the picosecond and nanosecond time-window, already revealed by molecular dynamics (MD) [4,5] and time-resolved fluorescence depolarization [6] measurements, seem to be crucial in many functionally important processes such as chemical reactions involving local interactions with the reacting site and sequences recognition by enzymes [7]. A major role in determining the DNA conformational dynamics is played by hydration water [8], which is important for stabilisation and function as well [9][10][11].…”