Crystal structures of ‘ALternative Isoinformational ENgineered’ DNA in B-form

Abstract

The first structural model of duplex DNA reported in 1953 by Watson & Crick presented the double helix in B-form, the form that genomic DNA exists in much of the time. Thus, artificial DNA seeking to mimic the properties of natural DNA should also be able to adopt B-form. Using a host–guest system in which Moloney murine leukemia virus reverse transcriptase serves as the host and DNA as the guests, we determined high-resolution crystal structures of three complexes including 5′-CTT BPPBBSSZZS AAG, 5′-CTT SSPBZPSZBB AAG and 5′-CTT ZZPBSBSZPP AAG with 10 consecutive unnatural nucleobase pairs in B-form within self-complementary 16 bp duplex oligonucleotides. We refer to this ALternative Isoinformational ENgineered (ALIEN) genetic system containing two nucleobase pairs ( P:Z , pairing 2-amino-imidazo-[1,2- a ]-1,3,5-triazin-(8 H )-4-one with 6-amino-5-nitro-(1 H )-pyridin-2-one, and B:S , 6-amino-4-hydroxy-5-(1 H )-purin-2-one with 3-methyl-6-amino-pyrimidin-2-one) as ALIEN DNA. We characterized both position- and sequence-specific helical, nucleobase pair and dinucleotide step parameters of P:Z and B:S pairs in the context of B-form DNA. We conclude that ALIEN DNA exhibits structural features that vary with sequence. Further, Z can participate in alternative stacking modes within a similar sequence context as captured in two different structures. This finding suggests that ALIEN DNA may have a larger repertoire of B-form structures than natural DNA. This article is part of the theme issue ‘Reactivity and mechanism in chemical and synthetic biology’.