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Hachimoji DNA and RNA: A genetic system with eight building blocks

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Science  22 Feb 2019:
Vol. 363, Issue 6429, pp. 884-887
DOI: 10.1126/science.aat0971
  • Fig. 1 The eight nucleotides of hachimoji DNA and hachimoji RNA are designed to form four size- and hydrogen bond-complementary pairs.

    Hydrogen bond donor atoms involved in pairing are blue; hydrogen bond acceptor atoms are red. The left two pairs in each set are formed from the four standard nucleotides (note missing hydrogen-bonding group in the A:T pair, a peculiarity of standard terran DNA and RNA). The right two pairs in each set are formed from the four new nonstandard nucleotides. Notice the absence of electron density in the minor groove of S, which has a NH (green) moiety.

  • Fig. 2 Thermodynamics of hachimoji DNA duplexes.

    (A) Plot of experimental versus predicted free energy changes (∆G°37) for 94 SBZP-containing hachimoji DNA duplexes (tables S3, S6, and S9). (B) Plot of experimental versus predicted melting temperatures Tm of 94 SBZP-containing hachimoji DNA duplexes (tables S3, S6, and S9). The outlier is a sequence embedded in the PP guest (Fig. 3E).

  • Fig. 3 Crystal structures of PB, PC, and PP hachimoji DNA.

    (A) The host-guest complex with two N-terminal fragments from Moloney murine leukemia virus reverse transcriptase (in green and cyan) bound to a 16-mer PP hachimoji DNA; in the duplex sphere model, Z:P pairs are green and S:B pairs are magenta. The asymmetric unit includes one protein molecule and half of the 16-mer DNA, as indicated by the line. (B) Hachimoji DNA structures PB (green), PC (red), and PP (blue) are superimposed with GC DNA (gray). (C) Structure of hachimoji DNA with self-complementary duplex 5′-CTTATPBTASZATAAG (“PB”). (D) Structure of hachimoji DNA with self-complementary duplex 5′-CTTAPCBTASGZTAAG (“PC”). (E) Structure of hachimoji DNA with self-complementary duplex with six consecutive nonstandard 5′-CTTATPPSBZZATAAG (PP) components. DNA structures are shown as stick models with P:Z pairs (carbon atoms, green), B:S pairs (carbon atoms, magenta), and natural pairs (carbon atoms, gray). (F to I) Examples of largest differences in detailed structures. The Z:P pair from the PB structure (F) is more buckled than the corresponding G:C pair (G). The S:B pair from the PB structure (H) exhibits a propeller angle similar to that in the corresponding G:C pair (I).

  • Fig. 4 Structure and fluorescent properties of hachimoji RNA molecules.

    (A) Schematic showing the full hachimoji spinach variant aptamer; additional nucleotide components of the hachimoji system are shown as black letters at positions 8, 10, 76, and 78 (B, Z, P, and S, respectively). The fluor binds in loop L12 (25). (B to E) Fluorescence of various species in equal amounts as determined by UV. Fluorescence was visualized under a blue light (470 nm) with an amber (580 nm) filter. (B) Control with fluor only, lacking RNA. (C) Hachimoji spinach with the sequence shown in (A). (D) Native spinach aptamer with fluor. (E) Fluor and spinach aptamer containing Z at position 50, replacing the A:U pair at positions 53:29 with G:C to restore the triple observed in the crystal structure. This places the quenching Z chromophore near the fluor; CD spectra suggest that this variant had the same fold as native spinach (fig. S8).

Supplementary Materials

  • Hachimoji DNA and RNA: A genetic system with eight building blocks

    Shuichi Hoshika, Nicole A. Leal, Myong-Jung Kim, Myong-Sang Kim, Nilesh B. Karalkar, Hyo-Joong Kim, Alison M. Bates, Norman E. Watkins Jr., Holly A. SantaLucia, Adam J. Meyer, Saurja DasGupta, Joseph A. Piccirilli, Andrew D. Ellington, John SantaLucia Jr., Millie M. Georgiadis, Steven A. Benner

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

    Download Supplement
    • Materials and Methods 
    • Figs. S1 to S16
    • Tables S1 to S13
    • References 

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