"Skinny" and "Fat" DNA: Two New Double Helices

Journal of the American Chemical Society
Shuichi HoshikaSteven A Benner

Abstract

According to the iconic model, the Watson-Crick double helix exploits nucleobase pairs that are both size complementary (big purines pair with small pyrimidines) and hydrogen bond complementary (hydrogen bond donors pair with hydrogen bond acceptors). Using a synthetic biology strategy, we report here the discovery of two new DNA-like systems that appear to support molecular recognition with the same proficiency as standard Watson-Crick DNA. However, these both violate size complementarity (big pairs with small), retaining hydrogen bond complementarity (donors pair with acceptors) as their only specificity principle. They exclude mismatches as well as standard Watson-Crick DNA excludes mismatches. In crystal structures, these "skinny" and "fat" systems form the expected hydrogen bonds, while conferring novel minor groove properties to the resultant duplex regions of the DNA oligonucleotides. Further, computational tools, previously tested primarily on natural DNA, appear to work well for these two new molecular recognition systems, offering a validation of the power of modern computational biology. These new molecular recognition systems may have application in materials science and synthetic biology, and in developing our unde...Continue Reading

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Citations

Jun 20, 2019·Chembiochem : a European Journal of Chemical Biology·Fabienne Levi-AcobasMarcel Hollenstein
Sep 6, 2019·Angewandte Chemie·Aaron JohnsonNathan W Luedtke
Sep 24, 2019·Chemistry : a European Journal·Andreas Marx, Karin Betz
Sep 25, 2020·Biopolymers·Shiqin MiaoDennis Bong
May 6, 2020·Acta Crystallographica. Section C, Structural Chemistry·Dasharath KondhareFrank Seela
Apr 16, 2020·Chembiochem : a European Journal of Chemical Biology·Rami Koskinen
Jun 7, 2019·Nucleic Acids Research·Lynnette N JacksonJohn C Chaput
Mar 22, 2021·The Journal of Biological Chemistry·Stephen Neidle
May 24, 2021·Journal of Materials Chemistry. B, Materials for Biology and Medicine·Bin LiuKai Liu
Mar 4, 2020·Journal of Chemical Theory and Computation·Lukas EberleinNigel G J Richards
May 24, 2019·Journal of the American Chemical Society·Giacomo PadroniGlenn A Burley
Aug 28, 2021·Journal of the American Chemical Society·Kunihiko MorihiroAkimitsu Okamoto
Aug 13, 2021·Chemistry : a European Journal·Rebekah J KaradeemaRamanarayanan Krishnamurthy

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