Section 23.3.4.1.1. Minor groove width

The simplest and first-noticed sequence-dependent deformability of the B-DNA duplex was variation in minor groove width. The first B-DNA oligomer to be solved, C-G-C-G-A-A-T-T-C-G-C-G (B1–B6), had a narrow minor groove in the central A-A-T-T region, with only ca 3.5 Å of free space between opposing phosphates and sugar rings. (It has become conventional to define the free space between phosphates as the measured minimal P–P separation across the groove, less 5.8 Å to represent two phosphate-group radii. Similarly, the measured distance between sugar oxygens is decreased by 2.8 Å, representing two oxygen van der Waals radii.) The C-G-C-G ends of the helix had the 6–7 Å opening expected for ideal B-DNA, but the situation was clouded, because the outermost two base pairs at each end of the helix interlocked minor grooves with neighbours in the crystal. Hence, the wider ends could possibly be only an artifact of crystal packing.

After 1991, the situation was clarified by the structures of several decamers [Table A23.3.1.2, Part I(c)], which stack on top of one another without the interlocking of grooves. The normal minor groove opening is ca 7 Å. Regions of four or more AT base pairs can exhibit a significantly narrowed minor groove, although such narrowing is not mandatory. This behaviour is seen with the B-DNA decamer, C-A-A-A-G-A-A-A-A-G, in Fig. 23.3.4.1. The narrowing arises mainly from the larger allowable propeller twist in AT base pairs, which displaces C1′ atoms at opposite ends of the pair in different directions, and moves the backbone chains in such a way as to partially close the groove (Fig. 23.3.4.2).

Figure 23.3.4.1| top | pdf | Structure of C-A-A-A-G-A-A-A-A-G (B107). The lower half of the helix, with -A-A-A-A-G, exhibits the narrow minor groove commonly associated with the AT region of the helix and a single zigzag spine of hydration, as was first seen in C-G-C-G-A-A-T-T-C-G-C-G (B1–B6). The upper half, with C-A-A-A-G-, has the wider minor groove of general-sequence B-DNA and two separate rows of hydrating water molecules along the two walls of the wider groove.

Figure 23.3.4.2| top | pdf | Relationship between minor groove width and propeller twist. (a) View into the minor groove of B-DNA, with base pairs seen on edge and with the sugar–phosphate backbones shown schematically as inclined ladder uprights. (b) Consequences of propeller twisting the base pairs. Glycosyl bonds connected to sugar C1′ atoms are all displaced upward in the right strand and downward in the left strand. This shifts the backbone chains as indicated by the arrows. Hence, the gap between the chains is decreased, and the minor groove is narrowed.

This is an excellent example of the concept of sequence-dependent helix deformability, rather than simple deformation. The two hydrogen bonds of an AT base pair allow a larger propeller twist but do not require it. Hence, AT regions of helix permit a narrowing of the minor groove but do not demand it. Indeed, this lesson was brought home in the most dramatic way when Pelton & Wemmer (1989, 1990) showed via NMR that a 2:1 complex of distamycin with C-G-C-A-A-A-T-T-G-G-C or C-G-C-A-A-A-T-T-T-G-C-G could exist, in which two drug molecules sat side-by-side within an enlarged central minor groove. Fig. 23.3.4.3 shows a narrow minor groove with a single netropsin molecule, and Fig. 23.3.4.4 shows a wide minor groove enclosing two di-imidazole lexitropsins side-by-side. In summary, an AT-rich region of minor groove is capable of narrowing but is not inevitably narrow, in contrast to GC-rich regions where the third hydrogen bond tends to keep the base pairs flat and the minor groove wide. The AT minor groove is potentially deformable without being inevitably deformed.

Figure 23.3.4.3| top | pdf | Structure of the 1:1 complex of netropsin with C-G-C-G-A-A-T-T-C-G-C-G (B11, B12, B87). The drug binds to the central -A-A-T-T- region of the minor groove, which is barely wide enough to enclose the nearly planar polyamide molecule. The netropsin structure can be represented by where Py is a five-membered methylpyrrole ring. An even more compact representation, useful when comparing other polyamide netropsin analogues or lexitropsins, is +=Py=Py=+, where the common cationic tails are indicated only by a plus sign, and = represents a —CONH— amide.

Figure 23.3.4.4| top | pdf | Structure of the 2:1 complex of a di-imidazole lexitropsin with C-A-T-G-G-C-C-A-T-G (B108). The drug now is represented by where Im is a five-membered imidazole ring, or again more compactly by 0=Im=Im=+. The uncharged leading amide group, characteristic of distamycins, is identified by 0. Distamycin itself would be represented in this shorthand notation by 0=Py=Py=Py=+. Reprinted from B108, copyright (1977), with permission from Excerpta Medica Inc.