Consecutive non-natural PZ nucleobase pairs in DNA impact helical structure as seen in 50 μs molecular dynamics simulations

Abstract

Little is known about the influence of multiple consecutive ‘non-standard’ (Z, 6-amino-5-nitro-2(1H)-pyridone, and P, 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one) nucleobase pairs on the structural parameters of duplex DNA. P:Z nucleobase pairs follow standard rules for Watson–Crick base pairing but have rearranged hydrogen bonding donor and acceptor groups. Using the X-ray crystal structure as a starting point, we have modeled the motions of a DNA duplex built from a self-complementary oligonucleotide (5΄-CTTATPPPZZZATAAG-3΄) in water over a period of 50 μs and calculated DNA local parameters, step parameters, helix parameters, and major/minor groove widths to examine how the presence of multiple, consecutive P:Z nucleobase pairs might impact helical structure. In these simulations, the PZ-containing DNA duplex exhibits a significantly wider major groove and greater average values of stagger, slide, rise, twist and h-rise than observed for a ‘control’ oligonucleotide in which P:Z nucleobase pairs are replaced by G:C. The molecular origins of these structural changes are likely associated with at least two differences between P:Z and G:C. First, the electrostatic properties of P:Z differ from G:C in terms of density distribution and dipole moment. Second, differences are seen in the base stacking of P:Z pairs in dinucleotide steps, arising from energetically favorable stacking of the nitro group in Z with π–electrons of the adjacent base.

Toward an Expanded Genome: Structural and Computational Characterization of an Artificially Expanded Genetic Information System

“…8), which we have termed “slide” and “shift” conformers because one of the two nucleobase pairs is displaced along the axis corresponding to slide or shift, respectively. 21 Comparison with X-ray crystal structures shows that the slide conformer is similar to what is observed for the stacking of PP/ZZ dinucleotides in A-form DNA while the shift conformer resembles that observed in B-form DNA. The calculated energy difference between the two structures (1.5 kcal/mol) suggests that the “slide” conformer, which features “staggered” stacking of the nitro groups (Fig.…”

“…38 We, and others, 14,15 have therefore used these methods to demonstrate that stacking P:Z nucleobase pairs is energetically preferred to stacking G:C nucleobase pairs by approximately 2.0 kcal/mol, 21 primarily because of favorable electrostatic interactions between the electron-deficient Z ring and the π-electrons of the adjacent P nucleobase (Fig. 2).…”

“…To date, QM calculations have only been reported for the P:Z nucleobase pair. 14,15,21 Although high-level ab initio calculations suggest that the free energy of hydrogen bonding in the P:Z nucleobase pair is less favorable (1.4 kcal/mol) than for G:C in the gas-phase, 21 calculations that include the effects of solvation indicate that the presence of the Z-nitro group decreases the enthalpy of the hydrogen bonds in P:Z relative to those in G:C by 0.6 kcal/mol. 15,21 This finding is supported by recent biophysical studies in which the P:Z hydrogen bonding interactions were found to be stronger than natural or mispaired interactions involving either P or Z .…”

“…2), 21 which can potentially be exploited in re-engineering the specificity of transcription factors and restriction endonucleases. 22 …”

“…2). 14,21 Perhaps more importantly for duplex stability and conformational properties for DNA containing multiple consecutive P:Z nucleobase pairs, high-level QM calculations suggest that the PP/ZZ dinucleotide (i.e. two consecutive P:Z pairs) can adopt two different structural forms (Fig.…”