Sequence-Selective Minor Groove Recognition of a DNA Duplex Containing Synthetic Genetic Components.

Giacomo Padroni,Andrea Taladriz-Sender,Linus F Reichenbach,John A Parkinson,Jamie M Withers,Glenn A Burley

doi:10.1021/jacs.8b12444

Giacomo Padroni, Andrea Taladriz-Sender + Show 4 more

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https://doi.org/10.1021/jacs.8b12444

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Abstract

The structural basis of minor groove recognition of a DNA duplex containing synthetic genetic information by hairpin pyrrole-imidazole polyamides is described. Hairpin polyamides induce a higher melting stabilization of a DNA duplex containing the unnatural P·Z base-pair when an imidazole unit is aligned with a P nucleotide. An NMR structural study showed that the incorporation of two isolated P·Z pairs enlarges the minor groove and slightly narrows the major groove at the site of this synthetic genetic information, relative to a DNA duplex consisting entirely of Watson-Crick base-pairs. Pyrrole-imidazole polyamides bind to a P·Z-containing DNA duplex to form a stable complex, effectively mimicking a G·C pair. A structural hallmark of minor groove recognition of a P·Z pair by a polyamide is the reduced level of allosteric distortion induced by binding of a polyamide to a DNA duplex. Understanding the molecular determinants that influence minor groove recognition of DNA containing synthetic genetic components provides the basis to further develop unnatural base-pairs for synthetic biology applications.

Highlights

Fundamental to all living organisms is the storage and transmission of genetic information in the form of a fourletter nucleic acid code
The P·Z pair is the most prominent exemplar of these artificially expanded genetic information systems (AEGIS), where the mode of selective recognition is via a three hydrogen-bond arrangement not present in either a G·C or an A·T pair (Figure 1a).[5−8] This strategy is distinct from other artificial base-pairs (e.g., Romesberg’s dNAM·dTPT39 pair and Hirao’s Ds·Pa10,11 pair) as P·Z pairing is more closely aligned with Watson−
Crick pairs[37,38,40,43−47] rendered Pyrrole-imidazole polyamides (PIPs) excellent candidates to investigate whether the N3 atom of an N-methyl imidazole (Im) unit hydrogen bonds with the exocyclic amine (N2) of P, much akin to hydrogen bonding observed with the cognate N2 amine of G

Summary

Introduction

Fundamental to all living organisms is the storage and transmission of genetic information in the form of a fourletter nucleic acid code. The distinct structural differences of P·Z compared to G·C pairs could influence sequence-selective recognition These structural differences include inversion of the central hydrogen bond, the absence of a major groove hydrogen-bond acceptor in the P nucleotide (i.e., PC7 versus GN7), and the presence of an electron-withdrawing nitro group (Z-NO2) projecting into the major groove.[16,17] a key challenge in the further development of unnatural basepairs for synthetic biology applications[6,8,11,12,18−28] is understanding how auxiliary molecular recognition interactions, such as major/minor groove recognition, are influenced by these structural differences.[29,30]

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