Structural basis for a six nucleotide genetic alphabet

Millie Georgiadis, Isha Singh, Whitney F. Kellett, Shuichi Hoshika, Steven A. Benner, Nigel G J Richards

Research output: Contribution to journalArticle

48 Citations (Scopus)

Abstract

Expanded genetic systems are most likely to work with natural enzymes if the added nucleotides pair with geometries that are similar to those displayed by standard duplex DNA. Here, we present crystal structures of 16-mer duplexes showing this to be the case with two nonstandard nucleobases (Z, 6-amino-5-nitro-2(1H)-pyridone and P, 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)one) that were designed to form a Z:P pair with a standard edge on Watson-Crick geometry, but joined by rearranged hydrogen bond donor and acceptor groups. One duplex, with four Z:P pairs, was crystallized with a reverse transcriptase host and adopts primarily a B-form. Another contained six consecutive Z:P pairs; it crystallized without a host in an A-form. In both structures, Z:P pairs fit canonical nucleobase hydrogen-bonding parameters and known DNA helical forms. Unique features include stacking of the nitro group on Z with the adjacent nucleobase ring in the A-form duplex. In both B- and A-duplexes, major groove widths for the Z:P pairs are approximately 1 Å wider than those of comparable G:C pairs, perhaps to accommodate the large nitro group on Z. Otherwise, ZP-rich DNA had many of the same properties as CG-rich DNA, a conclusion supported by circular dichroism studies in solution. The ability of standard duplexes to accommodate multiple and consecutive Z:P pairs is consistent with the ability of natural polymerases to biosynthesize those pairs. This, in turn, implies that the GACTZP synthetic genetic system can explore the entire expanded sequence space that additional nucleotides create, a major step forward in this area of synthetic biology.

Original languageEnglish
Pages (from-to)6947-6955
Number of pages9
JournalJournal of the American Chemical Society
Volume137
Issue number21
DOIs
StatePublished - Jun 3 2015

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Nucleotides
DNA
Hydrogen bonds
Synthetic Biology
Pyridones
Geometry
RNA-Directed DNA Polymerase
Dichroism
Hydrogen Bonding
Circular Dichroism
Hydrogen
Enzymes
Crystal structure

ASJC Scopus subject areas

  • Chemistry(all)
  • Catalysis
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

Georgiadis, M., Singh, I., Kellett, W. F., Hoshika, S., Benner, S. A., & Richards, N. G. J. (2015). Structural basis for a six nucleotide genetic alphabet. Journal of the American Chemical Society, 137(21), 6947-6955. https://doi.org/10.1021/jacs.5b03482

Structural basis for a six nucleotide genetic alphabet. / Georgiadis, Millie; Singh, Isha; Kellett, Whitney F.; Hoshika, Shuichi; Benner, Steven A.; Richards, Nigel G J.

In: Journal of the American Chemical Society, Vol. 137, No. 21, 03.06.2015, p. 6947-6955.

Research output: Contribution to journalArticle

Georgiadis, M, Singh, I, Kellett, WF, Hoshika, S, Benner, SA & Richards, NGJ 2015, 'Structural basis for a six nucleotide genetic alphabet', Journal of the American Chemical Society, vol. 137, no. 21, pp. 6947-6955. https://doi.org/10.1021/jacs.5b03482
Georgiadis, Millie ; Singh, Isha ; Kellett, Whitney F. ; Hoshika, Shuichi ; Benner, Steven A. ; Richards, Nigel G J. / Structural basis for a six nucleotide genetic alphabet. In: Journal of the American Chemical Society. 2015 ; Vol. 137, No. 21. pp. 6947-6955.
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