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

Bernhard Spingler

doi:10.1107/S2056989023007405

. 2023 Aug 30;79(Pt 9):852–855. doi: 10.1107/S2056989023007405

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

Bernhard Spingler ^a,^*

Editor: A S Batsanov^b

PMCID: PMC10483554 PMID: 37693671

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

Keywords: crystal structure, nucleoside, guanine, guanosine, purine

Abstract

The title compound, C₁₀H₁₃N₅O₄·2C₂H₆OS, which is of interest with respect to its biological activity, at 183 K has orthorhombic (P2₁2₁2₁) crystal symmetry. The structure displays a network of intermolecular N—H⋯N, N—H⋯O and O—H⋯O hydrogen bonds. 2′-Deoxyguanosine molecules are linked to each other and to the two dimethyl sulfoxide solvent molecules by hydrogen bonding.

1. 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′-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′-deoxyguanosine as a solvate with two molecules of dimethyl sulfoxide (DMSO), (I), and characterized it by X-ray diffraction.

2. Structural commentary

Nucleobase (I) crystallized in the orthorhombic Sohnke space group P2₁2₁2₁, with four formula units per unit cell and one per asymmetric unit (Fig. 1 ▸). The sugar conformation at the C3′ position (C13) is endo. The torsion angle χ (Alvarez et al., 2019 ▸; Schabert et al., 2021 ▸) of O14—C11—N9—C4 is −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′-deoxyguanosine (identifier GNG) is present (Fig. S1 in the supporting information).

Displacement ellipsoid plot (50% probability) of (I).

Table 1. Sugar conformations in 2′-deoxyguanosine, its supramolecular complexes and guanosine.

Compound	Space group	Sugar conformation	χ (O4′—C1′—N1—C6) (°)	Reference
2′-Deoxyguanosine·2(DMSO)	P2₁2₁2₁	Envelope, C3′-endo	−165.6 (1)	This work
(Actinomycin D)·2(2′-deoxyguanosine)·12H₂O	P2₁2₁2₁	Envelope, C3′-endo; Twisted, C1′-exo/C2′-endo	−86.5; −90.6	Jain & Sobell (1972 ▸)
(7-Bromoactinomycin D)·2(2′-deoxyguanosine)·11H₂O	P2₁2₁2₁	Twisted, C2′-exo/C3′-endo; Twisted, C1′-exo/C2′-endo	−86.5; −88.9	Jain & Sobell (1972 ▸)
(2′-Deoxyguanosine)·(5-bromo-2′-deoxycytidine)	P2₁2₁2	Envelope, C2′-endo	56.7	Haschemeyer et al. (1965 ▸)
(Guanosine)₂·4H₂O	P2₁	Envelope, C2′-endo; Twisted, C1′-exo/C2′-endo	−58.1; −137.2	Thewalt et al. (1970 ▸)

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3. 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 Inline graphic (9) graph set (Bernstein et al., 1995 ▸) (Fig. 2 ▸). A very similar hydrogen-bonding 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′-deoxyguanosine, while atom O22 of the other DMSO molecule is hydrogen bonded both to the exocyclic amino group of one 2′-deoxyguanosine molecule and to the primary –OH group of another 2′-deoxyguanosine molecule. Analysis of the fingerprint plots of the Hirshfeld surface around the 2′-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%.

Table 2. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C23—H23B⋯O6ⁱ	0.96 (3)	2.35 (3)	3.239 (3)	153 (2)
N1—H1⋯N7ⁱⁱ	0.87 (2)	2.09 (2)	2.962 (2)	173 (2)
N2—H2A⋯O22	0.83 (2)	2.09 (2)	2.902 (2)	168 (2)
N2—H2B⋯O6ⁱⁱ	0.83 (2)	2.24 (2)	3.012 (2)	155 (2)
O13—H13A⋯O21	0.87 (3)	1.88 (4)	2.738 (3)	169 (3)
O15—H15⋯O22ⁱⁱⁱ	0.89 (3)	1.91 (3)	2.752 (2)	159 (3)

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Symmetry codes: (i) Inline graphic ; (ii) ; (iii) .

Hydrogen-bonding pattern of (I). Displacement ellipsoids are drawn at the 50% probability level.

Fingerprint plots of (a) the entire Hirshfeld surface of 2′-deoxyguanosine within 2′-deoxyguanosine·2(DMSO), (b) H⋯H contacts, (c) O⋯H/H⋯O contacts, (d) N⋯H/H⋯N contacts and (e) C⋯H/H⋯C contacts.

4. Database survey

The search of the Cambridge Structural Database (CSD, Version 5.44, April 2023; Groom et al., 2016 ▸) was made with ConQuest (Version 2023.1.0; Bruno et al., 2002 ▸). The first structure containing 2′-deoxyguanosine (CSD refcode DGUBCY, a cocrystal with 5-bromo-2′-deoxycytidine) was published by Haschemeyer et al. (1965 ▸). However, in the corresponding CSD entry, the Lewis diagram of the 2′-deoxyguanosine is wrong (Fig. S2), showing a 2-aminopyrimidin-4-ol moiety, which should be redrawn as a 2-aminopyrimidin-4(3H)-one. The cocrystal structures of (actinomycin D)·2(2′-deoxyguanosine)·12H₂O (ACTDGU) and (7-bromoactinomycin)·2(2′-deoxyguanosine)·11H₂O (BRAXGU) at room temperature were also reported (Sobell et al., 1971 ▸; Jain & Sobell, 1972 ▸). In addition, the X-ray structures of four metal complexes containing 2′-deoxyguanosine are known (WEWKEO, UKISEM, WUNXIM and EWOBIN; Shionoya et al., 1994 ▸; Ito et al., 2002 ▸; Aoki & Salam, 2002 ▸; Baruah et al., 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 Å. The present structure, (I), is the only purine nucleoside solvate in the CSD (Groom et al., 2016 ▸) with two DMSO molecules per host molecule.

5. Synthesis and crystallization

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

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3 ▸. The structure was solved 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 Å for aromatic, 1.00 Å for methine, 0.99 Å for methylene and 0.98 Å for methyl C atoms, and refined as riding atoms, except those of methyl group C23H₃ 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 _iso(H) values were set at 1.2 times (for CH, NH, NH₂ and CH₂ units) or 1.5 times (for methyl and OH groups) the U _eq value of the parent atom. The Flack parameter x was −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.

Crystal data
Chemical formula	C₁₀H₁₃N₅O₄·2C₂H₆OS
M _r	423.51
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	183
a, b, c (Å)	9.7590 (1), 11.7951 (2), 16.7553 (2)
V (Å³)	1928.68 (4)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.32
Crystal size (mm)	0.44 × 0.24 × 0.17

Data collection
Diffractometer	Oxford Diffraction Xcalibur Ruby
Absorption correction	Multi-scan (CrysAlis RED; Oxford Diffraction, 2008 ▸)
T _min, T _max	0.909, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	19896, 5874, 5295
R _int	0.024
(sin θ/λ)_max (Å⁻¹)	0.714

Refinement
R[F ² > 2σ(F ²)], wR(F ²), S	0.030, 0.073, 1.01
No. of reflections	5874
No. of parameters	271
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.30, −0.27
Absolute structure	Flack x determined using 2107 quotients [(I ⁺) − (I ⁻)]/[(I ⁺) + (I ⁻)] (Parsons et al., 2013 ▸)
Absolute structure parameter	0.022 (14)

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Computer programs: CrysAlis CCD (Oxford Diffraction, 2008 ▸), CrysAlis RED (Oxford Diffraction, 2008 ▸), SIR97 (Altomare et al., 1999 ▸), SHELXL2018 (Sheldrick, 2015 ▸) and OLEX2 (Dolomanov et al., 2009 ▸).

7. Computational details

The sugar conformations (Table 1 ▸) were analysed with PLATON (Spek, 2020 ▸), using the published description of such conformations by Saenger (1984 ▸). For older structures, where the CSD does not contain H atoms, these were added using OLEX2 (Dolomanov et al., 2009 ▸) with default parameters.

Supplementary Material

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S2056989023007405/zv2028sup1.cif

e-79-00852-sup1.cif^{(703.6KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989023007405/zv2028Isup2.hkl

e-79-00852-Isup2.hkl^{(467.2KB, hkl)}

Figures S1 and S2. DOI: 10.1107/S2056989023007405/zv2028sup3.pdf

e-79-00852-sup3.pdf^{(119.8KB, pdf)}

CCDC reference: 2290127

Additional supporting information: crystallographic information; 3D view; checkCIF report

supplementary crystallographic information

Crystal data

C₁₀H₁₃N₅O₄·2C₂H₆OS	D_x = 1.459 Mg m⁻³
M_r = 423.51	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P2₁2₁2₁	Cell parameters from 11856 reflections
a = 9.7590 (1) Å	θ = 2.4–32.7°
b = 11.7951 (2) Å	µ = 0.32 mm⁻¹
c = 16.7553 (2) Å	T = 183 K
V = 1928.68 (4) Å³	Needle, colourless
Z = 4	0.44 × 0.24 × 0.17 mm
F(000) = 896

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Data collection

Oxford Diffraction Xcalibur Ruby diffractometer	5874 independent reflections
Radiation source: Enhance (Mo) X-ray Source	5295 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.024
Detector resolution: 10.4498 pixels mm^-1	θ_max = 30.5°, θ_min = 2.4°
ω scans	h = −13→13
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2008)	k = −14→16
T_min = 0.909, T_max = 1.000	l = −22→23
19896 measured reflections

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Refinement

Refinement on F²	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F² > 2σ(F²)] = 0.030	w = 1/[σ²(F_o²) + (0.045P)²] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.073	(Δ/σ)_max < 0.001
S = 1.01	Δρ_max = 0.30 e Å⁻³
5874 reflections	Δρ_min = −0.27 e Å⁻³
271 parameters	Absolute structure: Flack x determined using 2107 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
0 restraints	Absolute structure parameter: 0.022 (14)
Primary atom site location: structure-invariant direct methods

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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.

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Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²)

	x	y	z	U_iso*/U_eq
C2	0.35188 (19)	0.60776 (14)	0.66640 (9)	0.0159 (3)
C4	0.31935 (18)	0.42499 (14)	0.64001 (9)	0.0157 (3)
C5	0.40248 (18)	0.38572 (15)	0.70072 (10)	0.0163 (3)
C6	0.47568 (18)	0.46616 (14)	0.74730 (10)	0.0183 (3)
C8	0.32641 (18)	0.23836 (15)	0.64098 (10)	0.0184 (3)
H8	0.308547	0.161923	0.626466	0.022*
C11	0.17747 (19)	0.33364 (15)	0.53323 (10)	0.0192 (3)
H11	0.101178	0.388127	0.543999	0.023*
C12	0.2513 (2)	0.36613 (16)	0.45639 (10)	0.0242 (4)
H12A	0.190773	0.410232	0.420577	0.029*
H12B	0.334890	0.410942	0.467733	0.029*
C13	0.2870 (2)	0.25191 (18)	0.42025 (10)	0.0243 (4)
H13	0.370902	0.219466	0.445824	0.029*
C14	0.16057 (19)	0.18386 (15)	0.44271 (11)	0.0212 (4)
H14	0.084806	0.204527	0.405249	0.025*
C15	0.1745 (2)	0.05766 (16)	0.44360 (13)	0.0296 (4)
H15A	0.088134	0.023128	0.462851	0.035*
H15B	0.191768	0.029894	0.388760	0.035*
C23	0.0397 (2)	0.63289 (18)	0.47584 (13)	0.0280 (4)
H23A	0.093 (3)	0.593 (2)	0.5123 (15)	0.042*
H23B	0.010 (3)	0.585 (2)	0.4328 (16)	0.042*
H23C	−0.038 (3)	0.668 (2)	0.4972 (15)	0.042*
C24	0.2803 (3)	0.6683 (2)	0.40425 (16)	0.0438 (6)
H24A	0.248599	0.617530	0.361775	0.066*
H24B	0.319500	0.623323	0.447802	0.066*
H24C	0.350235	0.719659	0.382971	0.066*
N1	0.44138 (16)	0.57763 (13)	0.72580 (8)	0.0173 (3)
H1	0.483 (2)	0.6326 (19)	0.7512 (13)	0.021*
N2	0.32939 (19)	0.71824 (13)	0.65567 (9)	0.0218 (3)
H2A	0.281 (3)	0.737 (2)	0.6175 (13)	0.026*
H2B	0.367 (3)	0.771 (2)	0.6808 (13)	0.026*
N3	0.28910 (16)	0.53300 (12)	0.61976 (8)	0.0169 (3)
N7	0.40557 (16)	0.26752 (12)	0.70054 (8)	0.0187 (3)
N9	0.27173 (15)	0.33028 (12)	0.60156 (8)	0.0168 (3)
O6	0.56048 (15)	0.44860 (12)	0.80073 (7)	0.0270 (3)
O13	0.3041 (2)	0.26086 (16)	0.33678 (8)	0.0432 (4)
H13A	0.363 (4)	0.215 (3)	0.3158 (18)	0.065*
O14	0.12431 (14)	0.22319 (10)	0.52196 (7)	0.0219 (3)
O15	0.28382 (17)	0.02499 (13)	0.49400 (10)	0.0385 (4)
H15	0.275 (3)	−0.048 (3)	0.5060 (16)	0.058*
O21	0.50822 (19)	0.11673 (15)	0.28913 (10)	0.0440 (4)
O22	0.19120 (17)	0.80671 (12)	0.51554 (8)	0.0318 (3)
S22	0.13986 (5)	0.74863 (4)	0.44083 (3)	0.02532 (11)
S21	0.53507 (5)	0.01236 (4)	0.24068 (3)	0.02556 (11)
C22	0.4129 (2)	0.0115 (2)	0.16179 (12)	0.0362 (5)
H22A	0.431974	0.074434	0.125214	0.054*
H22B	0.320604	0.020153	0.183990	0.054*
H22C	0.418952	−0.060392	0.132742	0.054*
C21	0.4665 (3)	−0.1037 (2)	0.29503 (13)	0.0396 (5)
H21A	0.371508	−0.087110	0.309943	0.059*
H21B	0.521108	−0.116028	0.343349	0.059*
H21C	0.469085	−0.172052	0.261807	0.059*

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Atomic displacement parameters (Å²)

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C2	0.0194 (8)	0.0140 (8)	0.0144 (7)	0.0000 (6)	0.0000 (6)	−0.0005 (6)
C4	0.0175 (8)	0.0146 (8)	0.0150 (7)	−0.0013 (6)	0.0000 (6)	−0.0009 (6)
C5	0.0184 (8)	0.0146 (8)	0.0158 (7)	0.0009 (6)	−0.0004 (6)	0.0015 (6)
C6	0.0216 (8)	0.0172 (8)	0.0160 (7)	0.0014 (7)	0.0003 (7)	0.0009 (6)
C8	0.0208 (8)	0.0115 (8)	0.0231 (8)	−0.0016 (7)	0.0007 (6)	0.0026 (6)
C11	0.0211 (9)	0.0129 (8)	0.0235 (8)	0.0001 (6)	−0.0063 (7)	−0.0033 (6)
C12	0.0327 (10)	0.0191 (9)	0.0207 (8)	−0.0027 (8)	−0.0048 (7)	0.0022 (7)
C13	0.0301 (9)	0.0238 (9)	0.0189 (7)	0.0038 (8)	−0.0012 (7)	0.0018 (7)
C14	0.0247 (9)	0.0165 (9)	0.0224 (8)	0.0042 (7)	−0.0097 (7)	−0.0051 (7)
C15	0.0368 (11)	0.0169 (9)	0.0350 (10)	0.0027 (8)	−0.0101 (9)	−0.0059 (8)
C23	0.0255 (10)	0.0275 (11)	0.0310 (10)	−0.0040 (9)	0.0012 (9)	−0.0017 (8)
C24	0.0400 (13)	0.0350 (13)	0.0564 (14)	−0.0071 (11)	0.0217 (11)	−0.0083 (11)
N1	0.0228 (8)	0.0124 (7)	0.0166 (6)	−0.0014 (6)	−0.0055 (6)	−0.0015 (5)
N2	0.0317 (9)	0.0118 (7)	0.0218 (7)	−0.0004 (6)	−0.0091 (7)	−0.0011 (6)
N3	0.0208 (7)	0.0127 (7)	0.0171 (6)	0.0010 (6)	−0.0035 (5)	−0.0001 (5)
N7	0.0223 (7)	0.0125 (7)	0.0212 (7)	0.0005 (6)	0.0001 (6)	0.0032 (5)
N9	0.0191 (7)	0.0120 (7)	0.0195 (6)	−0.0018 (6)	−0.0031 (5)	−0.0003 (5)
O6	0.0339 (8)	0.0236 (7)	0.0234 (6)	0.0003 (6)	−0.0129 (6)	0.0019 (5)
O13	0.0663 (12)	0.0431 (10)	0.0201 (7)	0.0143 (9)	0.0066 (7)	0.0027 (7)
O14	0.0225 (6)	0.0156 (6)	0.0275 (6)	−0.0048 (5)	−0.0010 (5)	−0.0059 (5)
O15	0.0365 (8)	0.0198 (8)	0.0592 (10)	0.0036 (7)	−0.0145 (7)	0.0086 (7)
O21	0.0483 (11)	0.0361 (9)	0.0477 (10)	0.0013 (8)	−0.0043 (8)	−0.0179 (7)
O22	0.0463 (9)	0.0188 (7)	0.0302 (7)	−0.0004 (7)	−0.0144 (7)	−0.0014 (5)
S22	0.0316 (2)	0.0205 (2)	0.0239 (2)	−0.0008 (2)	−0.00666 (18)	0.00218 (18)
S21	0.0255 (2)	0.0264 (3)	0.0248 (2)	−0.00201 (19)	−0.00031 (19)	−0.00260 (17)
C22	0.0353 (11)	0.0424 (13)	0.0310 (10)	−0.0071 (10)	−0.0079 (9)	0.0039 (9)
C21	0.0464 (14)	0.0379 (13)	0.0345 (11)	−0.0042 (11)	0.0051 (11)	0.0076 (9)

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Geometric parameters (Å, º)

C2—N1	1.371 (2)	C15—H15A	0.9900
C2—N2	1.334 (2)	C15—H15B	0.9900
C2—N3	1.328 (2)	C15—O15	1.414 (2)
C4—C5	1.381 (2)	C23—H23A	0.93 (3)
C4—N3	1.351 (2)	C23—H23B	0.96 (3)
C4—N9	1.371 (2)	C23—H23C	0.94 (3)
C5—C6	1.421 (2)	C23—S22	1.778 (2)
C5—N7	1.395 (2)	C24—H24A	0.9800
C6—N1	1.404 (2)	C24—H24B	0.9800
C6—O6	1.237 (2)	C24—H24C	0.9800
C8—H8	0.9500	C24—S22	1.775 (2)
C8—N7	1.308 (2)	N1—H1	0.87 (2)
C8—N9	1.377 (2)	N2—H2A	0.83 (2)
C11—H11	1.0000	N2—H2B	0.83 (2)
C11—C12	1.525 (2)	O13—H13A	0.87 (3)
C11—N9	1.469 (2)	O15—H15	0.89 (3)
C11—O14	1.415 (2)	O21—S21	1.4978 (17)
C12—H12A	0.9900	O22—S22	1.5124 (14)
C12—H12B	0.9900	S21—C22	1.780 (2)
C12—C13	1.518 (3)	S21—C21	1.775 (2)
C13—H13	1.0000	C22—H22A	0.9800
C13—C14	1.520 (3)	C22—H22B	0.9800
C13—O13	1.412 (2)	C22—H22C	0.9800
C14—H14	1.0000	C21—H21A	0.9800
C14—C15	1.495 (3)	C21—H21B	0.9800
C14—O14	1.450 (2)	C21—H21C	0.9800

N2—C2—N1	117.13 (15)	H23A—C23—H23B	111 (2)
N3—C2—N1	123.30 (15)	H23A—C23—H23C	115 (2)
N3—C2—N2	119.57 (16)	H23B—C23—H23C	108 (2)
N3—C4—C5	129.01 (15)	S22—C23—H23A	107.2 (17)
N3—C4—N9	125.20 (15)	S22—C23—H23B	111.7 (15)
N9—C4—C5	105.78 (15)	S22—C23—H23C	103.7 (16)
C4—C5—C6	118.42 (16)	H24A—C24—H24B	109.5
C4—C5—N7	110.26 (15)	H24A—C24—H24C	109.5
N7—C5—C6	131.13 (16)	H24B—C24—H24C	109.5
N1—C6—C5	111.38 (14)	S22—C24—H24A	109.5
O6—C6—C5	128.47 (16)	S22—C24—H24B	109.5
O6—C6—N1	120.15 (15)	S22—C24—H24C	109.5
N7—C8—H8	123.6	C2—N1—C6	125.52 (14)
N7—C8—N9	112.82 (15)	C2—N1—H1	117.2 (14)
N9—C8—H8	123.6	C6—N1—H1	117.3 (15)
C12—C11—H11	110.1	C2—N2—H2A	117.4 (17)
N9—C11—H11	110.1	C2—N2—H2B	125.9 (17)
N9—C11—C12	111.64 (15)	H2A—N2—H2B	116 (2)
O14—C11—H11	110.1	C2—N3—C4	112.18 (14)
O14—C11—C12	106.99 (14)	C8—N7—C5	104.58 (15)
O14—C11—N9	107.98 (14)	C4—N9—C8	106.55 (13)
C11—C12—H12A	111.2	C4—N9—C11	123.81 (14)
C11—C12—H12B	111.2	C8—N9—C11	129.61 (14)
H12A—C12—H12B	109.1	C13—O13—H13A	116 (2)
C13—C12—C11	102.84 (15)	C11—O14—C14	109.10 (14)
C13—C12—H12A	111.2	C15—O15—H15	109 (2)
C13—C12—H12B	111.2	C24—S22—C23	97.37 (11)
C12—C13—H13	110.9	O22—S22—C23	104.88 (9)
C12—C13—C14	100.59 (15)	O22—S22—C24	105.77 (12)
C14—C13—H13	110.9	O21—S21—C22	106.85 (11)
O13—C13—C12	110.84 (16)	O21—S21—C21	106.85 (11)
O13—C13—H13	110.9	C21—S21—C22	97.15 (12)
O13—C13—C14	112.36 (17)	S21—C22—H22A	109.5
C13—C14—H14	108.4	S21—C22—H22B	109.5
C15—C14—C13	117.04 (17)	S21—C22—H22C	109.5
C15—C14—H14	108.4	H22A—C22—H22B	109.5
O14—C14—C13	104.83 (14)	H22A—C22—H22C	109.5
O14—C14—H14	108.4	H22B—C22—H22C	109.5
O14—C14—C15	109.36 (16)	S21—C21—H21A	109.5
C14—C15—H15A	109.6	S21—C21—H21B	109.5
C14—C15—H15B	109.6	S21—C21—H21C	109.5
H15A—C15—H15B	108.1	H21A—C21—H21B	109.5
O15—C15—C14	110.24 (16)	H21A—C21—H21C	109.5
O15—C15—H15A	109.6	H21B—C21—H21C	109.5
O15—C15—H15B	109.6

C4—C5—C6—N1	4.3 (2)	N3—C4—C5—C6	−4.4 (3)
C4—C5—C6—O6	−175.47 (17)	N3—C4—C5—N7	−179.94 (17)
C4—C5—N7—C8	0.2 (2)	N3—C4—N9—C8	−179.89 (17)
C5—C4—N3—C2	0.6 (3)	N3—C4—N9—C11	−1.5 (3)
C5—C4—N9—C8	0.69 (18)	N7—C5—C6—N1	178.83 (18)
C5—C4—N9—C11	179.13 (15)	N7—C5—C6—O6	−1.0 (3)
C5—C6—N1—C2	−1.6 (2)	N7—C8—N9—C4	−0.6 (2)
C6—C5—N7—C8	−174.68 (18)	N7—C8—N9—C11	−178.96 (16)
C11—C12—C13—C14	36.85 (17)	N9—C4—C5—C6	175.04 (15)
C11—C12—C13—O13	155.88 (17)	N9—C4—C5—N7	−0.55 (19)
C12—C11—N9—C4	77.0 (2)	N9—C4—N3—C2	−178.67 (16)
C12—C11—N9—C8	−104.9 (2)	N9—C8—N7—C5	0.3 (2)
C12—C11—O14—C14	0.18 (18)	N9—C11—C12—C13	93.88 (17)
C12—C13—C14—C15	−159.00 (16)	N9—C11—O14—C14	−120.12 (15)
C12—C13—C14—O14	−37.66 (16)	O6—C6—N1—C2	178.24 (16)
C13—C14—C15—O15	55.1 (2)	O13—C13—C14—C15	83.1 (2)
C13—C14—O14—C11	23.95 (18)	O13—C13—C14—O14	−155.58 (16)
C15—C14—O14—C11	150.21 (15)	O14—C11—C12—C13	−24.05 (18)
N1—C2—N3—C4	2.6 (2)	O14—C11—N9—C4	−165.65 (15)
N2—C2—N1—C6	178.46 (17)	O14—C11—N9—C8	12.4 (2)
N2—C2—N3—C4	−178.00 (16)	O14—C14—C15—O15	−63.8 (2)
N3—C2—N1—C6	−2.1 (3)

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Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C23—H23B···O6ⁱ	0.96 (3)	2.35 (3)	3.239 (3)	153 (2)
N1—H1···N7ⁱⁱ	0.87 (2)	2.09 (2)	2.962 (2)	173 (2)
N2—H2A···O22	0.83 (2)	2.09 (2)	2.902 (2)	168 (2)
N2—H2B···O6ⁱⁱ	0.83 (2)	2.24 (2)	3.012 (2)	155 (2)
O13—H13A···O21	0.87 (3)	1.88 (4)	2.738 (3)	169 (3)
O15—H15···O22ⁱⁱⁱ	0.89 (3)	1.91 (3)	2.752 (2)	159 (3)

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Symmetry codes: (i) −x+1/2, −y+1, z−1/2; (ii) −x+1, y+1/2, −z+3/2; (iii) x, y−1, z.

Funding Statement

Funding for this research was provided by: University of Zurich.

References

Altomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115–119.
Alvarez, R., Schabert, G., Soydemir, A., Wick, L., Spitz, U. & Spingler, B. (2019). Cryst. Growth Des. 19, 4019–4028.
Aoki, K. & Salam, M. A. (2002). Inorg. Chim. Acta, 339, 427–437.
Baruah, H., Day, C. S., Wright, M. W. & Bierbach, U. (2004). J. Am. Chem. Soc. 126, 4492–4493. [DOI] [PubMed]
Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N. L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573.
Bruno, I. J., Cole, J. C., Edgington, P. R., Kessler, M., Macrae, C. F., McCabe, P., Pearson, J. & Taylor, R. (2002). Acta Cryst. B58, 389–397. [DOI] [PubMed]
Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chao, H., Chen, L., Craig, P. A., Crichlow, G. V., Dalenberg, K., Duarte, J. M., Dutta, S., Fayazi, M., Feng, Z., Flatt, J. W., Ganesan, S., Ghosh, S., Goodsell, D. S., Green, R. K., Guranovic, V., Henry, J., Hudson, B. P., Khokhriakov, I., Lawson, C. L., Liang, Y., Lowe, R., Peisach, E., Persikova, I., Piehl, D. W., Rose, Y., Sali, A., Segura, J., Sekharan, M., Shao, C., Vallat, B., Voigt, M., Webb, B., Westbrook, J. D., Whetstone, S., Young, J. Y., Zalevsky, A. & Zardecki, C. (2023). Nucleic Acids Res. 51, D488–D508. [DOI] [PMC free article] [PubMed]
Clowney, L., Jain, S. C., Srinivasan, A. R., Westbrook, J., Olson, W. K. & Berman, H. M. (1996). J. Am. Chem. Soc. 118, 509–518.
Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341.
Feng, Z., Chen, L., Maddula, H., Akcan, O., Oughtred, R., Berman, H. M. & Westbrook, J. (2004). Bioinformatics, 20, 2153–2155. [DOI] [PubMed]
Gelbin, A., Schneider, B., Clowney, L., Hsieh, S.-H., Olson, W. K. & Berman, H. M. (1996). J. Am. Chem. Soc. 118, 519–529.
Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179. [DOI] [PMC free article] [PubMed]
Haschemeyer, A. E. V. & Sobell, H. M. (1965). Acta Cryst. 19, 125–130. [DOI] [PubMed]
Ito, K., Somazawa, R., Matsunami, J. & Matsumoto, K. (2002). Inorg. Chim. Acta, 339, 292–296.
Jain, S. C. & Sobell, H. M. (1972). J. Mol. Biol. 68, 1–20. [DOI] [PubMed]
Johnson, K. H., Durland, R. H. & Hogan, M. E. (1992). Nucleic Acids Res. 20, 3859–3864. [DOI] [PMC free article] [PubMed]
Oxford Diffraction (2008). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, Oxfordshire, England.
Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249–259. [DOI] [PMC free article] [PubMed]
Saenger, W. (1984). Principles of Nucleic Acid Structure, 1^st ed., p. 556. New York: Springer.
Santangelo, M. G., Medina-Molner, A., Schweiger, A., Mitrikas, G. & Spingler, B. (2007). J. Biol. Inorg. Chem. 12, 767–775. [DOI] [PubMed]
Schabert, G., Haase, R., Parris, J., Pala, L., Hery-Barranco, A., Spingler, B. & Spitz, U. (2021). Molecules, 26, 2729. [DOI] [PMC free article] [PubMed]
Sheldrick, G. M. (2015). Acta Cryst. C71, 3–8.
Shionoya, M., Ikeda, T., Kimura, E. & Shiro, M. (1994). J. Am. Chem. Soc. 116, 3848–3859.
Sobell, H. M., Jain, S. C., Sakore, T. D. & Nordman, C. E. (1971). Nature New Biol. 231, 200–205. [DOI] [PubMed]
Spackman, P. R., Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Jayatilaka, D. & Spackman, M. A. (2021). J. Appl. Cryst. 54, 1006–1011. [DOI] [PMC free article] [PubMed]
Spek, A. L. (2020). Acta Cryst. E76, 1–11. [DOI] [PMC free article] [PubMed]
Stryer, L. (1995). Biochemistry, 4^th revised ed., p. 1100. New York: W. H. Freeman and Company.
Thewalt, U., Bugg, C. E. & Marsh, R. E. (1970). Acta Cryst. B26, 1089–1101. [DOI] [PubMed]
Thewalt, U., Bugg, C. E. & Marsh, R. E. (1971). Acta Cryst. B27, 2358–2363.
Wang, D., Kreutzer, D. A. & Essigmann, J. M. (1998). Mutat. Res./Fundam. Mol. Mech. Mutagen. 400, 99–115. [DOI] [PubMed]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S2056989023007405/zv2028sup1.cif

e-79-00852-sup1.cif^{(703.6KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989023007405/zv2028Isup2.hkl

e-79-00852-Isup2.hkl^{(467.2KB, hkl)}

Figures S1 and S2. DOI: 10.1107/S2056989023007405/zv2028sup3.pdf

e-79-00852-sup3.pdf^{(119.8KB, pdf)}

CCDC reference: 2290127

Additional supporting information: crystallographic information; 3D view; checkCIF report

[bb1] Altomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115–119.

[bb2] Alvarez, R., Schabert, G., Soydemir, A., Wick, L., Spitz, U. & Spingler, B. (2019). Cryst. Growth Des. 19, 4019–4028.

[bb3] Aoki, K. & Salam, M. A. (2002). Inorg. Chim. Acta, 339, 427–437.

[bb4] Baruah, H., Day, C. S., Wright, M. W. & Bierbach, U. (2004). J. Am. Chem. Soc. 126, 4492–4493. [DOI] [PubMed]

[bb5] Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N. L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573.

[bb6] Bruno, I. J., Cole, J. C., Edgington, P. R., Kessler, M., Macrae, C. F., McCabe, P., Pearson, J. & Taylor, R. (2002). Acta Cryst. B58, 389–397. [DOI] [PubMed]

[bb7] Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chao, H., Chen, L., Craig, P. A., Crichlow, G. V., Dalenberg, K., Duarte, J. M., Dutta, S., Fayazi, M., Feng, Z., Flatt, J. W., Ganesan, S., Ghosh, S., Goodsell, D. S., Green, R. K., Guranovic, V., Henry, J., Hudson, B. P., Khokhriakov, I., Lawson, C. L., Liang, Y., Lowe, R., Peisach, E., Persikova, I., Piehl, D. W., Rose, Y., Sali, A., Segura, J., Sekharan, M., Shao, C., Vallat, B., Voigt, M., Webb, B., Westbrook, J. D., Whetstone, S., Young, J. Y., Zalevsky, A. & Zardecki, C. (2023). Nucleic Acids Res. 51, D488–D508. [DOI] [PMC free article] [PubMed]

[bb8] Clowney, L., Jain, S. C., Srinivasan, A. R., Westbrook, J., Olson, W. K. & Berman, H. M. (1996). J. Am. Chem. Soc. 118, 509–518.

[bb9] Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341.

[bb10] Feng, Z., Chen, L., Maddula, H., Akcan, O., Oughtred, R., Berman, H. M. & Westbrook, J. (2004). Bioinformatics, 20, 2153–2155. [DOI] [PubMed]

[bb11] Gelbin, A., Schneider, B., Clowney, L., Hsieh, S.-H., Olson, W. K. & Berman, H. M. (1996). J. Am. Chem. Soc. 118, 519–529.

[bb12] Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179. [DOI] [PMC free article] [PubMed]

[bb13] Haschemeyer, A. E. V. & Sobell, H. M. (1965). Acta Cryst. 19, 125–130. [DOI] [PubMed]

[bb14] Ito, K., Somazawa, R., Matsunami, J. & Matsumoto, K. (2002). Inorg. Chim. Acta, 339, 292–296.

[bb15] Jain, S. C. & Sobell, H. M. (1972). J. Mol. Biol. 68, 1–20. [DOI] [PubMed]

[bb16] Johnson, K. H., Durland, R. H. & Hogan, M. E. (1992). Nucleic Acids Res. 20, 3859–3864. [DOI] [PMC free article] [PubMed]

[bb17] Oxford Diffraction (2008). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, Oxfordshire, England.

[bb18] Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249–259. [DOI] [PMC free article] [PubMed]

[bb19] Saenger, W. (1984). Principles of Nucleic Acid Structure, 1^st ed., p. 556. New York: Springer.

[bb20] Santangelo, M. G., Medina-Molner, A., Schweiger, A., Mitrikas, G. & Spingler, B. (2007). J. Biol. Inorg. Chem. 12, 767–775. [DOI] [PubMed]

[bb21] Schabert, G., Haase, R., Parris, J., Pala, L., Hery-Barranco, A., Spingler, B. & Spitz, U. (2021). Molecules, 26, 2729. [DOI] [PMC free article] [PubMed]

[bb22] Sheldrick, G. M. (2015). Acta Cryst. C71, 3–8.

[bb23] Shionoya, M., Ikeda, T., Kimura, E. & Shiro, M. (1994). J. Am. Chem. Soc. 116, 3848–3859.

[bb24] Sobell, H. M., Jain, S. C., Sakore, T. D. & Nordman, C. E. (1971). Nature New Biol. 231, 200–205. [DOI] [PubMed]

[bb25] Spackman, P. R., Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Jayatilaka, D. & Spackman, M. A. (2021). J. Appl. Cryst. 54, 1006–1011. [DOI] [PMC free article] [PubMed]

[bb26] Spek, A. L. (2020). Acta Cryst. E76, 1–11. [DOI] [PMC free article] [PubMed]

[bb27] Stryer, L. (1995). Biochemistry, 4^th revised ed., p. 1100. New York: W. H. Freeman and Company.

[bb28] Thewalt, U., Bugg, C. E. & Marsh, R. E. (1970). Acta Cryst. B26, 1089–1101. [DOI] [PubMed]

[bb29] Thewalt, U., Bugg, C. E. & Marsh, R. E. (1971). Acta Cryst. B27, 2358–2363.

[bb30] Wang, D., Kreutzer, D. A. & Essigmann, J. M. (1998). Mutat. Res./Fundam. Mol. Mech. Mutagen. 400, 99–115. [DOI] [PubMed]

PERMALINK

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

Bernhard Spingler

Roles

Abstract

1. Chemical context

2. Structural commentary

Figure 1.

Table 1. Sugar conformations in 2′-deoxyguanosine, its supramolecular complexes and guanosine.