Water and ion binding around r(UpA)₁₂and d(TpA)₁₂Oligomers - comparison with RNA and DNA (CpG)₁₂ duplexes¹

Abstract

The structural and dynamic properties of the water and ion first coordination shell of the r(A-U) and d(A-T) base-pairs embedded within the r(UpA)₁₂and d(TpA)₁₂duplexes are described on the basis of two 2.4 ns molecular dynamics simulations performed in a neutralizing aqueous environment with 0.25 M added KCl. The results are compared to previous molecular dynamics simulations of the r(CpG)₁₂and d(CpG)₁₂structures performed under similar conditions. It can be concluded that: (i) RNA helices are more rigid than DNA helices of identical sequence, as reflected by the fact that RNA duplexes keep their initial A-form shape while DNA duplexes adopt more sequence-specific shapes. (ii) Around these base-pairs, the water molecules occupy 21 to 22 well-defined hydration sites, some of which are partially occupied by potassium ions. (iii) These hydration sites are occupied by an average of 21.9, 21.0, 20.1, and 19.8 solvent molecules (water and ions) around the r(G=C), r(A-U), d(G=C), and d(A-T) pairs, respectively. (iv) From a dynamic point of view, the stability of the hydration shell is the strongest for the r(G=C) pairs and the weakest for the d(A-T) pairs. (v) For RNA, the observed long-lived hydration patterns are essentially non-sequence dependent and involve water bridges located in the deep groove and linking OR atoms of adjacent phosphate groups. Maximum lifetimes are close to 400 ps. (vi) In contrast, for DNA, long-lived hydration patterns are sequence dependent and located in the minor groove. For d(CpG)₁₂, water bridges linking the (G)N3 and (C)O2 with the O4′ atoms of adjacent nucleotides with 400 ps maximum lifetimes are characterized while no such bridges are observed for d(TpA)₁₂. (vii) Potassium ions are observed to bind preferentially to deep/major groove atoms at RpY steps, essentially d(GpC), r(GpC), and r(ApU), by forming ion-bridges between electronegative atoms of adjacent base-pairs. On average, about half an ion is observed per base-pair. Positive ion-binding determinants are related to the proximity of two or more electronegative atoms. Negative binding determinants are associated with the electrostatic and steric hindrance due to the proximity of electropositive amino groups and neutral methyl groups. Potassium ions form only transient contacts with phosphate groups.

Introduction

A large number of molecular dynamics (MD) simulations of RNA and DNA regular helical structures generated with several independently parameterized force-fields Cornell et al 1995, Langley 1998, Cheatham et al 1999, Foloppe and MacKerell 2000 and efficient methods to treat the long-range electrostatic interactions Darden et al 1999, Sagui and Darden 1999 are now available Cheatham and Kollman 1996, Cheatham and Kollman 1997, Duan et al 1997, Young et al 1997b, Bonvin et al 1998, Cheatham et al 1998, Flatters and Lavery 1998, Lyubartsev and Laaksonen 1998, Young and Beveridge 1998, Bostock-Smith et al 1999, Cheatham et al 1999, Sherer et al 1999, Sprous et al 1999, Auffinger and Westhof 2000, Castrignano et al 2000, Hamelberg et al 2000, MacKerell and Banavali 2000, Steff and Koca 2000, Trantirek et al 2000. For RNA, a consensual view emerges indicating that MD techniques describe accurately the structural and dynamic properties of helical structures. RNA Watson-Crick helices display only slight environmental-dependent behaviors, although the situation seems more complex for the simulation of larger RNA structures involving intricate tertiary motifs Hermann et al 1998, Auffinger et al 1999, Schneider and Suhnel 1999, the folding of which is strongly related, among other factors, to the mono and divalent ionic strength. For DNA, the concept of a force-field-dependent polymorphism has been proposed (Auffinger & Westhof, 1998c), essentially on the basis of MD simulations of identical structures with the AMBER (Cornell et al., 1995) and CHARMM (MacKerell et al., 1995) force-fields which displayed a tendency to move either toward B or A-DNA helical structures, respectively Feig and Pettitt 1997, Feig and Pettitt 1998b, Feig and Pettitt 1999a. Besides, DNA helices are much more prone to environmental and sequence-dependent polymorphism Saenger 1984, Dickerson 1999 than RNA helices, and several experimental data support the idea of a structural continuum existing between the well-characterized A and B-DNA conformations (Ng et al., 2000). Thus, the increasing number of DNA shapes leads to a new challenge to reproduce and understand the complex physicochemical properties of these systems in order to deconvolute structural and environmental issues from force-field-dependent effects.

This aim cannot be achieved without a careful, complete, and systematic description of the structure and dynamics of the hydration shells and of the ionic atmosphere which surround nucleic acids as a function of their dependence on sequence and environment Clementi 1983, Saenger 1984, Westhof 1988, Westhof and Beveridge 1990, Jeffrey and Saenger 1991, Westhof 1993, Hummer et al 1995, Hummer et al 1996, Feig and Pettitt 1998a, Auffinger and Westhof 1999. Additionally, the structural and functional characteristics of the numerous non-canonical base-pairs found in all natural RNA molecules cannot be completely understood without a comparison with sound data gathered from theoretical and experimental work on the basic Watson-Crick base-pairs.

Here, we present data extracted from two 2.4 ns MD simulations of the r(UpA)₁₂and d(TpA)₁₂duplexes in an aqueous environment with 0.25 M KCl added. The results are described and compared with respect to those gathered for G=C pairs which were extracted from MD simulations of the r(CpG)₁₂and d(CpG)₁₂duplexes performed under similar conditions (Auffinger & Westhof, 2000). These simulations should provide further clues to the role played by the two single chemical modifications which differentiate RNA from DNA, namely the presence or absence of a 2′-OH (all nucleotides) and the methyl group, present only on DNA thymine bases Wang and Kool 1995, Cheatham and Kollman 1997, Auffinger and Westhof 2000. The choice of K⁺over the more frequently used Na⁺has been dictated by the fact that K⁺is a dominant ion in the intracellular media and by the increasing number of reports describing, beside the major role played by magnesium cations, the essential structural and functional roles played by these ions Gluick et al 1997a, Gluick et al 1997b, Basu et al 1998, Klosterman et al 1999, Batey et al 2000, Shiman and Draper 2000. It is worth noting that a K⁺-binding site has been uncovered in the ribosome peptidyl transferase active site (Nissen et al., 2000). Most of these sites are ion-type specific, as are similar monovalent ion-binding sites occurring in DNA (reviewed by McFail-Isom et al., 1999). From the methodological point of view, potassium ions are more adapted to the time-scales accessible to current MD studies in the sense that the residence times of water molecules in the first hydration shell of K⁺is shorter than that of water molecules around Na⁺. Thus, K⁺can be dehydrated more easily than Na⁺and the relaxation time of the formation of direct ion/nucleic acid interactions is shorter.

Here, several structural characteristics of the r(UpA)₁₂and d(TpA)₁₂duplexes will be described. Then, the first coordination shells surrounding the r(A-U) and d(A-T) base-pairs will be characterized in terms of the number of binding sites and the occupancy factors for water molecules and potassium ions. Next, the dynamics of water molecules and ions present in the first coordination shell will be analyzed in order to obtain estimates of the residence times of the solvent molecules in the various coordination sites.