X‐ray Crystal Structure of a Metalled Double‐Helix Generated by Infinite and Consecutive C*‐Ag^I‐C* (C*:N¹‐Hexylcytosine) Base Pairs through Argentophilic and Hydrogen Bond Interactions

Abstract

The synthesis of a metalled double-helix containing exclusively silver-mediated C*-C* base pairs is reported herein (C*=N hexylcytosine). Remarkably, it is the first crystal structure containing infinite and consecutive C*-Ag -C* base pairs that form a double helix. The Ag ion occupies the center between two C* residues with N(3)-Ag bond lengths of 2.1 Å and short Ag -Ag distances (3.1 Å) suggesting an interesting argentophilic attraction as a stabilization source of the helical disposition. The solid-state structure is further stabilized by metal-mediated base-pairs, hydrogen bonding and π-stacking interactions. Moreover, the angle N(3)-Ag-N(3) is almost linear in the [Ag(N hexylcytosine) ] motif and the bases are not coplanar, thus generating a double-strand helical aggregate in the solid state. The noncovalent and argentophilic interactions have been rationalized based on DFT calculations.

Addressing the properties of “Metallo-DNA” with a Ag(i)-mediated supramolecular duplex

“…For comparison, the intermetallic distances in [(Ag 11 -(dodecacamer) 2 )] are 3.2-3.4Å; and 3.162-3.235Å in [Ag(I)-N3-(N1-hexylcytosine) 2 ]. 35 Interestingly, the recently reported [Ag(1-Me-cytosine) 2 ] + complex features similarly short Ag/Ag distances (2.902-3.088(2)Å) as 1. 36 This nding indicates that the ribose moiety of the nucleoside does not impose additional steric hinderance to inter-complex interactions allowing short argentophilic bonding.…”

“…A similar pattern of inter base-pair hydrogen bonding between silver-mediated base pairs is observed by Kondo et al 22 in a metallo-DNA [(Ag 11 -(dodecacamer) 2 )] and in the organo-soluble complex [Ag(I)-N3-(N1-hexylcytosine) 2 ]. 35 However, in 1 the argentophilic interactions are stronger as indicated by the shorter Ag/Ag distances in the range 2.982(2)-3.055(2)Å, close to the metallic radius of 2.88Å. For comparison, the intermetallic distances in [(Ag 11 -(dodecacamer) 2 )] are 3.2-3.4Å; and 3.162-3.235Å in [Ag(I)-N3-(N1-hexylcytosine) 2 ].…”

“…Analogous arrays of Ag(I) ions have recently been shown to be a feature in the solid state structure of simple nucleobase complexes of the form [Ag(I)-(N3alkyl-cytosine) 2 ] + isolated from organic solvent. 35,36 Such metallo-DNA systems are frequently considered as molecular or nano-wires 22,37,38 on account of the contiguous linear array of metal ions produced. However, studies on their electrical properties are rather scant [39][40][41][42] and only one, reported while our manuscript was under review, is for a crystallographically characterised material.…”

Anomeric 2′‐Deoxycytidines and Silver Ions: Hybrid Base Pairs with Greatly Enhanced Stability and Efficient DNA Mismatch Detection with α‐dC

“…In the past, the molecular structure of the silver‐mediated dC–dC pair was established; however, nothing was known about the silver‐mediated α‐dC–β‐dC hybrid pair. In fact, in the covalently linked dC residues and the crystal of the 1‐methylcytosine performed by Marzilli, the two nucleobases are aligned transoid , whereas in the crystal structure of a RNA duplex the orientation of the base pairs are cisoid . The same binding mode was confirmed for DNA by NMR spectroscopy .…”

A DNA Structure Containing AgI‐Mediated G:G and C:C Base Pairs

“…In addition to the common stacking interactions, the larger propeller angles of the G7‐Ag I ‐G7* and C8‐Ag I ‐C8* pairs also lead to four direct H‐bond interactions (Figure a): two between the N4 and O6 atoms of C8 and G7* (or C8* and G7), and two between the N4 and O2P atoms of C8 and G7 (or C8* and G7*); as suggested by the average distance (2.82 Å), these H‐bonds are very stable. Two direct H‐bonds are also formed between the neighboring C4‐Ag I ‐C4* and C8‐Ag I ‐C8* pairs via their O2 and N4 atoms; the distances are all around 2.80 Å. Hydrogen‐bonding interactions between neighboring nucleobases have been predicted for short DNA duplexes containing consecutive C‐Ag I ‐C pairs and have recently been observed from small‐molecule structures involving N ‐hexylcytosine (C*)‐Ag I interactions . Interestingly, although the free C* lacks both sugar pucker and a phosphate backbone, many C*‐Ag I ‐C* pairs stack together and show almost linear N3‐Ag I ‐N3 bonds with non‐coplanar bases, thereby resulting a duplex‐like conformation in the C*‐Ag I crystal lattice, which is different from the nonhelical folding of our DNA1‐Ag I complex.…”