Bound Compound, Interfacial Water, and Phenyl Ring Rotation Dynamics of a Compound in the DNA Minor Groove

Abstract

DB2277, a heterocyclic diamidine, is a successful design for mixed base pair (bp) DNA sequence recognition. The compound has a central aza-benzimidazole group that forms two H-bonds with a GC bp that has flanking AT bps. The nuclear magnetic resonance structure of the DB2277-DNA complex with an AAGATA recognition site sequence was determined, and here we report extended molecular dynamics (MD) simulations of the structure. DB2277 has two terminal phenyl-amidine groups, one of which is directly linked to the DB2277 heterocyclic core and the other through a flexible -OCH₂- group. The flexibly linked phenyl is too far from the minor groove floor to make direct H-bonds but is linked to an AT bp through water-mediated H-bonds. The flexibly linked phenyl-amidine with water-mediated H-bonds to the bases at the floor of the minor groove suggested that it might rotate in time spans accessible in MD. To test this idea, we conducted multimicrosecond MD simulations to determine if these phenyl rotations could be observed for a bound compound. In a 3 μs simulation, highly dynamic torsional motions were observed for the -OCH₂-linked phenyl but not for the other phenyl. The dynamics periodically reached a level to allow 180° rotation of the phenyl while it was still bound in the minor groove. This is the first observation of rotation of a phenyl bound to DNA, and the results provide mechanistic details about how a rotation can occur as well as how mixed bp recognition can occur for monomer compounds bound to the minor groove.

Figure 1.

Graphic of the molecular structure of DB2277 with the target DNA sequence. Abbreviations for aromatic rings are listed along with their torsion angles. Brown lines represent the NOE interactions of DB2277 protons with specific DNA protons in the minor groove. Broken lines illustrates the H-bond interaction of amidines with T-O2 in the minor groove of DNA.

Figure 2.

Minor groove views of the DB2277-DNA complex are shown in panel A and B. Ø1 and α1 torsion angles are shown at several key times (frame-number on top-left) along with water-mediated H-bonds (yellow) (Å). Panel A shows larger twists for α1 and Ø1, compare 1218-frame with the orthogonal position of Ph1 relative to other aromatic groups of bound DB2277 in frame 1238. Starting at frame 1218 with C1 and C2 pointed out in panel A and end at the frame 2700 with C3 and C4 pointed out in Panel B. The DNA backbone is represented in orange-colored-stick with khaki-colored-space fill. The DB2277 molecule is shown in stick (green-C). Water molecules in ball and stick.

Figure 3.

A) Minor groove views of the DB2277-DNA complex with reported Ø2 and α2 torsion angles of Phenyl Ph2 and amidine Am2 respectively, for the initial frame and the end frame for 1 ns trajectory of Ph1 flip. Colors as in Figure 2. B) Torsion angle plot of Ø2 and α2 angles of Ph2 in the bound DB2277 molecule for 1 ns trajectory. The time interval for each frame in the plot is 0.25 ps of 1 ns trajectory (1020-1021 ns of 3 μs MD simulation).

Figure 4.

Torsion angle plot of Ø1 and α1 angles of Phenyl Ph1 and amidine Am1 respectively, of the bound DB2277 molecule for 1 ns trajectory of Ph1 flip. Major transitions of Ø1 and α1 torsions are highlighted and illustrated in time frames in Figures 2 and 5. The time interval for each frame in the plot is 0.25 ps of 1 ns trajectory (1020-1021 ns of 3 μs MD simulation).

Figure 5.

Minor groove views of the DB2277-DNA complex capturing the concerted motions of water molecules and Am1 twist to facilitate the Ph1-flip within few ps (3238-3248-frames). Flipped Ph1 in complex with C3 and C4 atoms pointed out of the minor groove. Water-mediated H-bond network of Am1 group with the minor groove of DNA helps to stabilize the structure in 3248-frame as it approaches the minimum energy compared to other frames. Water-mediated H-bonds (yellow) between T16-O2 and –NH of Am1 at the floor of the minor groove are reported in Å in different frames. Ø1 and α1 torsion angles are also reported. Colors as in Figure 2.