Crystal structure of a nucleoside model for the interstrand cross-link formed by the reaction of 2′-deoxyguanosine and an abasic site in duplex DNA

Crystallographic analysis of a nucleoside analog of the 2′-deoxyguanosine/abasic site cross-link is presented. This structure corroborates an earlier two-dimensional NMR analysis, concluding that the 2-deoxyribose unit attached at the exocyclic N 2-amino group of the guanine residue exists in the cyclic aminoglycoside form.


Chemical context
Recent work has characterized a structurally novel set of interstrand DNA-DNA cross-links involving reaction of the ubiquitous DNA abasic lesion with a nucleobase on the opposing strand of the double helix Dutta et al., 2007;Gamboa Varela & Gates, 2015;Johnson et al., 2013;Price et al., 2014Price et al., , 2015Yang et al., 2015;Zhang et al., 2015). Evidence indicates that the covalent attachment is forged between the anomeric carbon of the abasic sugar and the exocyclic amino group of either a guanine, adenine, or N 4aminocytosine residue Dutta et al., 2007;Gamboa Varela & Gates, 2015;Johnson et al., 2013;Price et al., 2014Price et al., , 2015Yang et al., 2015). This type of glycosidic linkage involving the exocyclic amino group of a nucleobase is reminiscent of that found in the natural products anicemycin, spicamycin, and septacidin (Acton et al., 1977;Igarashi et al., 2005;Suzuki et al., 2002).
Here we present single crystal X-ray crystallographic analysis of a nucleoside analog, (I), of the 2 0 -deoxyguanosine/ abasic site cross-link. This structure corroborates an earlier two-dimensional NMR analysis  ISSN  concluding that the 2-deoxyribose unit attached at the exocyclic N 2 -amino group of the guanine residue exists in the cyclic aminoglycoside form.

Structural commentary
The two independent molecules (A and B) of (I) are shown in Fig. 1 as they are oriented in the crystal, while Fig. 2 shows an overlay to illustrate the differences in orientation and conformation of the furanose rings. Ring puckering analysis, after Cremer & Pople as calculated using PLATON (Spek, 2009) indicates the furanose rings attached to N4 positions in the two molecules to be half-chairs in both molecules, but with the maximum variance from planarity occurring between C7 and C8 in molecule A and C6 and C7 in molecule B [Q(2) = 0.367 (2), È(2) = 88.0 (4) for molecule A and Q(2) = 0.347 (2), È(2) = 60.6 (4) for molecule B]. The disposition of these furanose rings relative to the purine rings can be described by the torsion angle C2-N4-C6-O2, which is 70.9 (3) in molecule A and 61.7 (3) in molecule B. The furanose ring attached to the N5 position in molecule A is again a half-chair, with the maximum deviation from planarity between C11A and C12A [Q(2) = 3.41 (2), È(2) = 62.2 (3) ], while this furanose ring in molecule B is an envelope with C11B at the flap [Q(2) = 0.422 (2), È(2) = 45.4 (3) ]. The disposition of these furanose rings relative to the purine rings can be described by the angle C1-N5-C11-O5, which is À87.4 (2) in molecule A and À93.7 (2) in molecule B.

Supramolecular features
In the crystal, the two molecules form infinite ribbons along the a-c diagonal of the unit cell, with the A molecules on one The molecular structure of (I) showing 50% displacement ellipsoids.

Figure 2
Overlay plot of the two molecules in (I). A molecule in orange and B molecule in blue. side of the ribbon and the B molecules on the other. The molecules are staggered such that each A molecule forms hydrogen bonds to two B molecules and each B molecule forms hydrogen bonds (Table 1) to two A molecules, fully involving the N1, N3, N5 and O1 atoms. These ribbons are then stacked to form slabs propagating in the ac plane and one half the b dimension in thickness. The deoxyribose moieties occupy the outsides of these slabs and are linked via hydrogen bonds to twofold screw-related slabs, resulting in a herringbone pattern in the three-dimensional structure as seen in Fig. 3.

Database survey
A search of the Cambridge Structural Database (CSD, Version 5.36, update February 2015;Groom & Allen, 2014) for deoxyguanosine analogues with exocyclic amine substitution revealed three crystal structures (Morr et al., 1991;Fujino et al., 2010). In all these crystal structures, the five-membered 2deoxyribofuranose rings have envelope conformations, as in the title compound.  Table 1 Hydrogen-bond geometry (Å , ).

Figure 3
The packing in (I) along the c axis showing the formation of hydrogen-bonded chains (A molecules green, B molecules blue). chloromethane) to yield 36 mg (12% yield) of the title compound as a colorless oil. The precursor 3,5-bis-O-methyl-2-deoxy-d-ribofuranose was synthesized according to previously reported procedures (Deriaz et al., 1949;Olsson et al., 1998). The title compound was crystallized by vapour diffusion, a 2 ml vial containing the title compound in methanol being placed in a 20 ml vial containing hexanes at room temperature for several days.

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 2. H atoms were placed geometrically (C-H = 0.95 or 0.98 Å ) and refined as riding with U iso (H) = 1.2U eq (C).

Computing details
Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXS2013 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2015); molecular graphics: X-SEED, Barbour, 2001; software used to prepare material for publication: CIFTAB (Sheldrick, 2008).   (5) 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.