Conformational Morphing by a DNA Analogue Featuring 7‑Deazapurines and 5‑Halogenpyrimidines and the Origins of Adenine-Tract Geometry

Several efforts are currently directed at the creation
and cellular
implementation of alternative genetic systems composed of pairing
components that are orthogonal to the natural dA/dT and dG/dC base
pairs. In an alternative approach, Watson–Crick-type pairing
is conserved, but one or all of the four letters of the A, C, G, and
T alphabet are substituted by modified components. Thus, all four
nucleobases were altered to create halogenated deazanucleic acid (DZA):
dA was replaced by 7-deaza-2′-deoxyadenosine (dzA), dG by 7-deaza-2′-deoxyguanosine
(dzG), dC by 5-fluoro-2′-deoxycytidine (FdC), and dT by 5-chloro-2′-deoxyuridine
(CldU). This base-pairing system was previously shown to retain function
in Escherichia coli. Here, we analyze
the stability, hydration, structure, and dynamics of a DZA Dickerson–Drew
Dodecamer (DDD) of sequence 5′-FdC-dzG-FdC-dzG-dzA-dzA-CldU-CldU-FdC-dzG-FdC-dzG-3′.
Contrary to similar stabilities of DDD and DZA-DDD, osmotic stressing
revealed a dramatic loss of hydration for the DZA-DDD relative to
that for the DDD. The parent DDD 5′-d(CGCGAATTCGCG)-3′
features an A-tract, a run of adenosines uninterrupted by a TpA step,
and exhibits a hallmark narrow minor groove. Crystal structuresin
the presence of RNase Hand MD simulations show increased conformational
plasticity (“morphing”) of DZA-DDD relative to that
of the DDD. The narrow dzA-tract minor groove in one structure widens
to resemble that in canonical B-DNA in a second structure. These changes
reflect an indirect consequence of altered DZA major groove electrostatics
(less negatively polarized compared to that in DNA) and hydration
(reduced compared to that in DNA). Therefore, chemical modifications
outside the minor groove that lead to collapse of major groove electrostatics
and hydration can modulate A-tract geometry.