26
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

      Hachimoji DNA and RNA. A Genetic System with Eight Building Blocks

      research-article

      Read this article at

      ScienceOpenPublisherPMC
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Reported here are DNA and RNA-like systems built from eight (hachi-) nucleotide letters (-moji) that form four orthogonal pairs. This synthetic genetic biopolymer meets the structural requirements needed to support Darwinism, including a polyelectrolyte backbone, predictable thermodynamic stability, and stereoregular building blocks that fit a Schrödinger aperiodic crystal. Measured thermodynamic parameters predict the stability of hachimoji duplexes, allowing hachimoji DNA to double the information density of natural terran DNA. Three crystal structures show that the synthetic building blocks do not perturb the aperiodic crystal seen in the DNA double helix. Hachimoji DNA was then transcribed to give hachimoji RNA in the form of a functioning fluorescent hachimoji aptamer. These results expand the scope of molecular structures that might support life, including life throughout the cosmos.

          One Sentence Summary:

          DNA with eight nucleotide letters forms four orthogonal pairs with predictable thermodynamics, supports transcription to give a functioning 8-letter fluorescent RNA aptamer, and creates double helices that fit the Schrödinger aperiodic crystal needed for Darwinism, presumed to be universally necessary for life in the cosmos.

          Related collections

          Most cited references26

          • Record: found
          • Abstract: found
          • Article: not found

          A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics.

          A unified view of polymer, dumbbell, and oligonucleotide nearest-neighbor (NN) thermodynamics is presented. DNA NN DeltaG degrees 37 parameters from seven laboratories are presented in the same format so that careful comparisons can be made. The seven studies used data from natural polymers, synthetic polymers, oligonucleotide dumbbells, and oligonucleotide duplexes to derive NN parameters; used different methods of data analysis; used different salt concentrations; and presented the NN thermodynamics in different formats. As a result of these differences, there has been much confusion regarding the NN thermodynamics of DNA polymers and oligomers. Herein I show that six of the studies are actually in remarkable agreement with one another and explanations are provided in cases where discrepancies remain. Further, a single set of parameters, derived from 108 oligonucleotide duplexes, adequately describes polymer and oligomer thermodynamics. Empirical salt dependencies are also derived for oligonucleotides and polymers.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Generation of high-affinity DNA aptamers using an expanded genetic alphabet.

            DNA aptamers produced with natural or modified natural nucleotides often lack the desired binding affinity and specificity to target proteins. Here we describe a method for selecting DNA aptamers containing the four natural nucleotides and an unnatural nucleotide with the hydrophobic base 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds). We incorporated up to three Ds nucleotides in a random sequence library, which is expected to increase the chemical and structural diversity of the DNA molecules. Selection experiments against two human target proteins, vascular endothelial cell growth factor-165 (VEGF-165) and interferon-γ (IFN-γ), yielded DNA aptamers that bind with KD values of 0.65 pM and 0.038 nM, respectively, affinities that are >100-fold improved over those of aptamers containing only natural bases. These results show that incorporation of unnatural bases can yield aptamers with greatly augmented affinities, suggesting the potential of genetic alphabet expansion as a powerful tool for creating highly functional nucleic acids.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Thermodynamics and NMR of internal G.T mismatches in DNA.

              Thermodynamics of 39 oligonucleotides with internal G.T mismatches dissolved in 1 M NaCl were determined from UV absorbance versus temperature profiles. These data were combined with literature values of six sequences to derive parameters for 10 linearly independent trimer and tetramer sequences with G.T mismatches and Watson-Crick base pairs. The G.T mismatch parameters predict DeltaG degrees 37, DeltaH degrees , DeltaS degrees , and TM with average deviations of 5.1%, 7.5%, 8.0%, and 1.4 degrees C, respectively. These predictions are within the limits of what can be expected for a nearest-neighbor model. The data show that the contribution of a single G.T mismatch to helix stability is context dependent and ranges from +1.05 kcal/mol for AGA/TTT to -1.05 kcal/mol for CGC/GTG. Several tests of the applicability of the nearest-neighbor model to G.T mismatches are described. Analysis of imino proton chemical shifts show that structural perturbations from the G.T mismatches are highly localized. One-dimensional NOE difference spectra demonstrate that G.T mismatches form stable hydrogen-bonded wobble pairs in diverse contexts. Refined nearest-neighbor parameters for Watson-Crick base pairs are also presented.
                Bookmark

                Author and article information

                Journal
                0404511
                7473
                Science
                Science
                Science (New York, N.Y.)
                0036-8075
                1095-9203
                7 March 2019
                22 February 2019
                22 February 2020
                : 363
                : 6429
                : 884-887
                Affiliations
                [1 ]Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, No. 17, Alachua FL 32615, United States
                [2 ]Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua FL 32615, United States
                [3 ]Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
                [4 ]DNA Software, Ann Arbor, Michigan 48104, United States
                [5 ]Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78703, United States
                [6 ]Department of Biochemistry & Molecular Biology and Department of Chemistry, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
                Author notes
                [†]

                Contributed equally to this work

                Author contributions: S.H. synthesized and purified all of the hachimoji oligonucleotides and the hachimoji 3’-phosphates, and synthesized hachimoji RNA derivatives needed to support the label shift analyses. N.A.L. performed all the studies involving enzymatic reactions, including preparation of various RNA transcripts; she also developed the hachimoji RNA analytical chemistry, including its 2D-TLC strategies. M.J.K., M.S.K., N.B.K., and H.J.K. synthesized all of the hachimoji phosphoramidites and triphosphates. N.E.W., H.A.S., and J.S.L. designed the hachimoji DNA oligonucleotides, performed the melting temperature studies, and interpreted the melting temperature data. S.D. and J.A.P. performed the biophysical studies on the Z-variant of the spinach aptamer. A.M.B. and M.M.G. performed all of the crystallographic studies and analyzed the three crystal structures containing hachimoji DNA. A.J.M. and A.D.E. prepared variants of T7 RNA polymerase. M.M.G., J.S.L. and S.A.B. further directed the research and prepared the manuscript, with the help of the other co-authors.

                [* ]Corresponding author ( manuscripts@ 123456ffame.org )
                Article
                PMC6413494 PMC6413494 6413494 nihpa1016131
                10.1126/science.aat0971
                6413494
                30792304
                54ea93fe-82a6-46f3-9a75-536216f081f0
                History
                Categories
                Article

                Comments

                Comment on this article