Crystal structure of the nucleoside 2′-deoxyguanosine dimethyl sulfoxide disolvate

The first high-quality crystal structure of unmodified 2′-deoxyguanosine is reported. The isolated crystals are the dimethyl sulfoxide disolvate.


Chemical context
Deoxynucleosides are the building blocks of DNA, the storage place for the genetic information in most organisms.Understanding the properties of DNA is crucial for our knowledge of its reactivity in cellular processes of replication and transcription to yield transfer RNA (Stryer, 1995).Furthermore, mutagenic reagents can irreversibly alter the structure and function of DNA (Wang et al., 1998).In view of all this, it is of upmost importance to know the precise geometric parameters of all the nucleobases.These parameters are needed for techniques such as macromolecular X-ray crystallography in some cases and (NMR restrained) modelling of oligonucleotides (Clowney et al., 1996;Gelbin et al., 1996).Surprisingly, no high-quality crystal structure of unmodified 2 0 -deoxyguanosine has been published to date.In the course of studying the interaction of nucleobases with copper(II) (Santangelo et al., 2007), we obtained single crystals of 2 0 -deoxyguanosine as a solvate with two molecules of dimethyl sulfoxide (DMSO), (I), and characterized it by X-ray diffraction.

Structural commentary
Nucleobase (I) crystallized in the orthorhombic Sohnke space group P2 1 2 1 2 1 , with four formula units per unit cell and one per asymmetric unit (Fig. 1).The sugar conformation at the C3 0 position (C13) is endo.The torsion angle � (Alvarez et al., 2019;Schabert et al., 2021) of O14-C11-N9-C4 is À 165.6 (1) � (Table 1).The freely refined H atoms of the exocyclic atom N2 were found to be in the plane of the latter and the adjacent six-membered aromatic ring, implying an sp 2 hybridization of N2.It is of interest to note that in the ligand database (Ligand Expo;Feng et al., 2004) of the Protein Database (Burley et al., 2023) an incorrect Lewis structure of 2 0 -deoxyguanosine (identifier GNG) is present (Fig. S1 in the supporting information).

Supramolecular features
The hydrogen bonds are listed in Table 2.The hydrogen bonding among the guanine nucleobases is a reverse Hoogsteen pairing (Johnson et al., 1992), generating an R 2 2 (9) graph set (Bernstein et al., 1995) (Fig. 2).A very similar hydrogenbonding motif was found for guanine monohydrate (Thewalt et al., 1971) and guanosine dihydrate (Thewalt et al., 1970).Atom O21 of one DMSO molecule is hydrogen bonded to the secondary alcohol group of 2 0 -deoxyguanosine, while atom O22 of the other DMSO molecule is hydrogen bonded both to the exocyclic amino group of one 2 0 -deoxyguanosine molecule and to the primary -OH group of another 2 0 -deoxyguanosine molecule.Analysis of the fingerprint plots of the Hirshfeld surface around the 2 0 -deoxyguanosine molecule calculated by CrystalExplorer (Spackman et al., 2021) (Fig. 3) indicates that H� � �H contacts account for 38.3% of the surface contacts, O� � �H/H� � �O contacts for 28.4%, N� � �H/H� � �N for 16.5% and C� � �H/H� � �C for 9.9%.
2004).Only one of them was recorded at low temperature (Baruah et al., 2004).Still, even for the latter structure, the average C-C bond distance was determined with a rather low precision of 0.009 A ˚.The present structure, (I), is the only purine nucleoside solvate in the CSD (Groom et al., 2016) with two DMSO molecules per host molecule.

Synthesis and crystallization
Single crystals of (I) were obtained upon slow evaporation of 2 0 -deoxyguanosine (product number D0052, TCI) from DMSO.

Refinement
Crystal data, data collection and structure refinement details are summarized in

Special details
Geometry.All esds (except the esd in the dihedral angle between two l.s.planes) are estimated using the full covariance matrix.The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry.An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s.planes.

Table 3 .
(Altomare et al., 1999)d by direct methods with the program SIR97(Altomare et al., 1999).All C-bonded H atoms were placed in ideal positions, with C-H bond lengths of 0.95 A ˚for aromatic, 1.00 A ˚for methine, 0.99 A ˚for methylene and 0.98 A ˚for methyl C atoms, and refined as riding atoms, except those of methyl group C23H 3 of one DMSO molecule, which makes a relatively close contact to O6.The latter H atoms and those attached to non-C atoms were freely refined.The U (Parsons et al., 2013)t at 1.2 times (for CH, NH, NH 2 and CH 2 units) or 1.5 times (for methyl and OH groups) the U eq value of the parent atom.The Flack parameter x was À 0.00 (6) by classical fit to all intensities and 0.022 (14) by Parsons' method(Parsons et al., 2013), from 2107 selected quotients.

Table 3
Experimental details.