"Skinny" and "fat" DNA

Two New Double Helices

Shuichi Hoshika, Isha Singh, Christopher Switzer, Robert W. Molt, Nicole A. Leal, Myong Jung Kim, Myong Sang Kim, Hyo Joong Kim, Millie Georgiadis, Steven A. Benner

Research output: Contribution to journalArticle

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 understanding of alternative ways that genetic information might be stored and transmitted.

Original languageEnglish (US)
Pages (from-to)11655-11660
Number of pages6
JournalJournal of the American Chemical Society
Volume140
Issue number37
DOIs
StatePublished - Sep 19 2018

Fingerprint

Oils and fats
Hydrogen
Hydrogen bonds
DNA
Molecular recognition
Fats
Synthetic Biology
Pair Bond
Pyrimidines
Purines
Oligonucleotides
Materials science
Computational Biology
Crystal structure

ASJC Scopus subject areas

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

Cite this

Hoshika, S., Singh, I., Switzer, C., Molt, R. W., Leal, N. A., Kim, M. J., ... Benner, S. A. (2018). "Skinny" and "fat" DNA: Two New Double Helices. Journal of the American Chemical Society, 140(37), 11655-11660. https://doi.org/10.1021/jacs.8b05042

"Skinny" and "fat" DNA : Two New Double Helices. / Hoshika, Shuichi; Singh, Isha; Switzer, Christopher; Molt, Robert W.; Leal, Nicole A.; Kim, Myong Jung; Kim, Myong Sang; Kim, Hyo Joong; Georgiadis, Millie; Benner, Steven A.

In: Journal of the American Chemical Society, Vol. 140, No. 37, 19.09.2018, p. 11655-11660.

Research output: Contribution to journalArticle

Hoshika, S, Singh, I, Switzer, C, Molt, RW, Leal, NA, Kim, MJ, Kim, MS, Kim, HJ, Georgiadis, M & Benner, SA 2018, '"Skinny" and "fat" DNA: Two New Double Helices', Journal of the American Chemical Society, vol. 140, no. 37, pp. 11655-11660. https://doi.org/10.1021/jacs.8b05042
Hoshika S, Singh I, Switzer C, Molt RW, Leal NA, Kim MJ et al. "Skinny" and "fat" DNA: Two New Double Helices. Journal of the American Chemical Society. 2018 Sep 19;140(37):11655-11660. https://doi.org/10.1021/jacs.8b05042
Hoshika, Shuichi ; Singh, Isha ; Switzer, Christopher ; Molt, Robert W. ; Leal, Nicole A. ; Kim, Myong Jung ; Kim, Myong Sang ; Kim, Hyo Joong ; Georgiadis, Millie ; Benner, Steven A. / "Skinny" and "fat" DNA : Two New Double Helices. In: Journal of the American Chemical Society. 2018 ; Vol. 140, No. 37. pp. 11655-11660.
@article{2aad2aebad704e828a912314ab9fcd44,
title = "{"}Skinny{"} and {"}fat{"} DNA: Two New Double Helices",
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 understanding of alternative ways that genetic information might be stored and transmitted.",
author = "Shuichi Hoshika and Isha Singh and Christopher Switzer and Molt, {Robert W.} and Leal, {Nicole A.} and Kim, {Myong Jung} and Kim, {Myong Sang} and Kim, {Hyo Joong} and Millie Georgiadis and Benner, {Steven A.}",
year = "2018",
month = "9",
day = "19",
doi = "10.1021/jacs.8b05042",
language = "English (US)",
volume = "140",
pages = "11655--11660",
journal = "Journal of the American Chemical Society",
issn = "0002-7863",
publisher = "American Chemical Society",
number = "37",

}

TY - JOUR

T1 - "Skinny" and "fat" DNA

T2 - Two New Double Helices

AU - Hoshika, Shuichi

AU - Singh, Isha

AU - Switzer, Christopher

AU - Molt, Robert W.

AU - Leal, Nicole A.

AU - Kim, Myong Jung

AU - Kim, Myong Sang

AU - Kim, Hyo Joong

AU - Georgiadis, Millie

AU - Benner, Steven A.

PY - 2018/9/19

Y1 - 2018/9/19

N2 - 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 understanding of alternative ways that genetic information might be stored and transmitted.

AB - 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 understanding of alternative ways that genetic information might be stored and transmitted.

UR - http://www.scopus.com/inward/record.url?scp=85053327161&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85053327161&partnerID=8YFLogxK

U2 - 10.1021/jacs.8b05042

DO - 10.1021/jacs.8b05042

M3 - Article

VL - 140

SP - 11655

EP - 11660

JO - Journal of the American Chemical Society

JF - Journal of the American Chemical Society

SN - 0002-7863

IS - 37

ER -