A “Hydrat-Ion” Spine in a B-DNA Minor Groove

Abstract

The minor groove hydration spine is a key feature of the crystal structure of the B-DNA dodecamer duplex [d(CGCGAATTCGCG)]2. At the floor of the groove, water molecules bridge bases from opposite strands by hydrogen bonding to N3 and O2 atoms of adenine and thymine, respectively. However, the interpretation that the series of electron density peaks lining the groove represents indeed water molecules, while generally agreed upon, remains an assumption. The limited resolutions of dodecamer crystal structures have thus far made it impossible to reliably distinguish between water and monovalent metal cations, such as Na+, normally present in the crystallization buffer. Using X-ray diffraction data to near-atomic resolution of dodecamer crystals grown in the presence of either Rb+ or Cs+ cacodylate, we have tested the possibility of alkali metal ion coordination in the minor groove. The structural data are consistent with a single Rb+ intruding the hydration spine at the central ApT step. The ion has partial occupancy and replaces the water molecule that links the keto oxygens of thymines from opposite strands. The observed dimensions of the binding site suggest preferred binding of Rb+ or K+, while Na+ or Cs+ may be prevented from binding stably. Therefore, minor groove ion coordination appears to be an isolated event, highly sequence dependent and unlikely to significantly affect the particular geometry of the A-tract in the Dickerson−Drew dodecamer. In addition to allowing a distinction between water and alkali metal ions, the high-resolution crystal structures provide a more complete picture of the minor groove water structure: four fused water hexagons dissect the central portion of the minor groove, with the inner corners of the hexagons coinciding with the original spine water positions. Thus, it may be more appropriate to refer to this arrangement as a ribbon of hydration instead of a spine of hydration.

DNA A-tract bending in three dimensions: Solving the dA 4 T 4 vs. dT 4 A 4 conundrum

“…The magnitude of the effect is consistent with previous experimental results on the extent and location of NH 4 ϩ binding to A4T4, T4A4, and GCA5CG (53). The ApT step represents a unique and species-dependent tight binding site for monovalent cations, which can coordinate to the two opposing T carbonyls (41,(49)(50)(51)(52)(53)55). We propose that the specific minor groove widthdependent binding of monovalent cations at the ApT step contributes to the global bend observed for A4T4.…”

“…X-ray crystallography (49,50), molecular dynamics (51), capillary electrophoresis (52), and NMR (53) studies of DNA have shown that, in addition to waters, monovalent cations can bind specifically in the minor groove of A-tracts, although the relative occupancies remain unresolved (54). In our previous NMR studies of A4T4 and T4A4, NH 4 ϩ were found to localize in the narrowest parts of the minor grooves, resulting in a very different distribution of cation localization for the two molecules that was proposed to contribute to A-tract bending (53).…”

Aromaticity of H-bonded and metal complexes of guanine tautomers

“…Such interactions between metal cations and nucleobases can be direct or solvent-mediated [21]. However, in the case of alkali metals, the X-ray investigations [22,23] and MD simulations [24] support mostly direct interactions between nucleobases and partially dehydrated metal ions [25]. Interactions with active centers of guanine located in major groove of DNA (N7 and O at C6 atom) have been discussed for years [26][27][28][29][30][31].…”

Curvature and Deformation of Nucleic Acids: Overview

“…Since GC-rich sequences preferentially localize cations in the major groove (111)(112)(113)(114)(115)(116)(117) and undergo the B-to Α-form structural transition relatively easily (118)(119)(120)(121)(122), and Α-tract DNAs preferentially bind cations in the minor groove (57,58,107,109,(123)(124)(125) and have the relatively rigid B'-DNA structure (40, 41), Hud and coworkers (110) have proposed that DNA conformation is determined by the relative proportion of counterions preferentially localized in the major and minor grooves of GC-rich and Α-tract sequences, respectively. While much experimental data can be correlated by this hypothesis, it is possible that the ionophore concept may be more applicable to DNA and RNA structures that require counterion binding for stability.…”

“…It is well known that DNA hydration is sequence dependent (126,127), although it is not often remembered that Aform DNA is stable up to 98% relative humidity and B-form DNA is stable down to 66% relative humidity (3). The "spine of hydration" on the floor of the DNA minor groove (9) appears to be covered by one or more layers of relatively well-ordered water molecules (57,58,106,116,124,128,129). The transient localization of cations on the floor of the minor groove must disrupt this ordered water structure, although how it happens is not clear (130).…”