Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: Supramolecular polymerization of a prebiotic nucleoside provides insights into the creation of sequence-controlled polymers

Abstract

The self-assembly of a nucleoside on Au(111) was studied to ascertain whether polymerization on well-defined substrates constitutes a promising approach for making sequence-controlled polymers. Scanning tunneling microscopy and density functional theory were used to investigate the self-assembly on Au(111) of (RS)-N9-(2,3-dihydroxypropyl)adenine (DHPA), a plausibly prebiotic nucleoside analog of adenosine. It is found that DHPA molecules self-assemble into a hydrogen-bonded polymer that grows almost exclusively along the herringbone reconstruction pattern, has a two component sequence that is repeated over hundreds of nanometers, and is erasable with electron-induced excitation. Although the sequence is simple, more complicated ones are envisioned if two or more nucleoside types are combined. Because polymerization occurs on a substrate in a dry environment, the success of each combination can be gauged with high-resolution imaging and accurate modeling techniques. The resulting characteristics make nucleoside self-assembly on a substrate an attractive approach for designing sequence-controlled polymers. Moreover, by choosing plausibly prebiotic nucleosides, insights may be provided into how nature created the first sequence-controlled polymers capable of storing information. Such insights, in turn, can inspire new ways of synthesizing sequence-controlled polymers.

Authors:
 [1];  [1];  [2];  [2];  [2];  [3];  [1];  [1];  [4];  [1];  [1]
+ Show Author Affiliations
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  2. Universidad Autonoma del Estado de Hidalgo, Mexico; Autonomous Univ. of the State of Hidalgo (Mexico)
  3. Tokyo Inst. of Technology (Japan); Inst. for Advanced Study, Princeton, NJ (United States); Blue Marble Space Inst. of Science, Washington, DC (United States); Georgia Inst. of Technology, Atlanta, GA (United States)
  4. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Huazhong Univ. of Science and Technology, Wuhan (China)
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Sciences (CNMS)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1238003
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 6; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Wang, Jun, Bonnesen, Peter V, Rangel, E., Vallejo, E., Sanchez-Castillo, Ariadna, Cleaves, II, H. James, Baddorf, Arthur P, Sumpter, Bobby G, Pan, Minghu, Maksymovych, Petro, and Fuentes-Cabrera, Miguel A. Supramolecular polymerization of a prebiotic nucleoside provides insights into the creation of sequence-controlled polymers. United States: N. p., 2016. Web. doi:10.1038/srep18891.
Copy to clipboard
Wang, Jun, Bonnesen, Peter V, Rangel, E., Vallejo, E., Sanchez-Castillo, Ariadna, Cleaves, II, H. James, Baddorf, Arthur P, Sumpter, Bobby G, Pan, Minghu, Maksymovych, Petro, & Fuentes-Cabrera, Miguel A. Supramolecular polymerization of a prebiotic nucleoside provides insights into the creation of sequence-controlled polymers. United States. https://doi.org/10.1038/srep18891
Copy to clipboard
Wang, Jun, Bonnesen, Peter V, Rangel, E., Vallejo, E., Sanchez-Castillo, Ariadna, Cleaves, II, H. James, Baddorf, Arthur P, Sumpter, Bobby G, Pan, Minghu, Maksymovych, Petro, and Fuentes-Cabrera, Miguel A. Mon . "Supramolecular polymerization of a prebiotic nucleoside provides insights into the creation of sequence-controlled polymers". United States. https://doi.org/10.1038/srep18891. https://www.osti.gov/servlets/purl/1238003.
Copy to clipboard
@article{osti_1238003,
title = {Supramolecular polymerization of a prebiotic nucleoside provides insights into the creation of sequence-controlled polymers},
author = {Wang, Jun and Bonnesen, Peter V and Rangel, E. and Vallejo, E. and Sanchez-Castillo, Ariadna and Cleaves, II, H. James and Baddorf, Arthur P and Sumpter, Bobby G and Pan, Minghu and Maksymovych, Petro and Fuentes-Cabrera, Miguel A},
abstractNote = {The self-assembly of a nucleoside on Au(111) was studied to ascertain whether polymerization on well-defined substrates constitutes a promising approach for making sequence-controlled polymers. Scanning tunneling microscopy and density functional theory were used to investigate the self-assembly on Au(111) of (RS)-N9-(2,3-dihydroxypropyl)adenine (DHPA), a plausibly prebiotic nucleoside analog of adenosine. It is found that DHPA molecules self-assemble into a hydrogen-bonded polymer that grows almost exclusively along the herringbone reconstruction pattern, has a two component sequence that is repeated over hundreds of nanometers, and is erasable with electron-induced excitation. Although the sequence is simple, more complicated ones are envisioned if two or more nucleoside types are combined. Because polymerization occurs on a substrate in a dry environment, the success of each combination can be gauged with high-resolution imaging and accurate modeling techniques. The resulting characteristics make nucleoside self-assembly on a substrate an attractive approach for designing sequence-controlled polymers. Moreover, by choosing plausibly prebiotic nucleosides, insights may be provided into how nature created the first sequence-controlled polymers capable of storing information. Such insights, in turn, can inspire new ways of synthesizing sequence-controlled polymers.},
doi = {10.1038/srep18891},
journal = {Scientific Reports},
number = ,
volume = 6,
place = {United States},
year = {Mon Jan 04 00:00:00 EST 2016},
month = {Mon Jan 04 00:00:00 EST 2016}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1038/srep18891
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 5 works
Citation information provided by
Web of Science
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Sequence-Controlled Polymers
journal, August 2013

Sequence control in polymer synthesis
journal, January 2009

  • Badi, Nezha; Lutz, Jean-François
  • Chemical Society Reviews, Vol. 38, Issue 12
  • DOI: 10.1039/b806413j

Ultra-precise insertion of functional monomers in chain-growth polymerizations
journal, January 2012

  • Zamfir, Mirela; Lutz, Jean-François
  • Nature Communications, Vol. 3, Issue 1
  • DOI: 10.1038/ncomms2151

Design and synthesis of digitally encoded polymers that can be decoded and erased
journal, May 2015

  • Roy, Raj Kumar; Meszynska, Anna; Laure, Chloé
  • Nature Communications, Vol. 6, Issue 1
  • DOI: 10.1038/ncomms8237

Synthesis of Monodisperse Sequence-Coded Polymers with Chain Lengths above DP100
journal, September 2015

Information-containing macromolecules
journal, May 2014

  • Colquhoun, Howard; Lutz, Jean-François
  • Nature Chemistry, Vol. 6, Issue 6
  • DOI: 10.1038/nchem.1958

Electronic Control over Attachment and Self-Assembly of Alkyne Groups on Gold
journal, September 2012

  • Li, Qing; Han, Chengbo; Fuentes-Cabrera, Miguel
  • ACS Nano, Vol. 6, Issue 10
  • DOI: 10.1021/nn303734r

Self-Organized and Cu-Coordinated Surface Linear Polymerization
journal, July 2013

  • Li, Qing; Owens, Jonathan R.; Han, Chengbo
  • Scientific Reports, Vol. 3, Issue 1
  • DOI: 10.1038/srep02102

Nano-architectures by covalent assembly of molecular building blocks
journal, October 2007

  • Grill, Leonhard; Dyer, Matthew; Lafferentz, Leif
  • Nature Nanotechnology, Vol. 2, Issue 11
  • DOI: 10.1038/nnano.2007.346

Conductance of a Single Conjugated Polymer as a Continuous Function of Its Length
journal, February 2009

Controlling on-surface polymerization by hierarchical and substrate-directed growth
journal, January 2012

  • Lafferentz, L.; Eberhardt, V.; Dri, C.
  • Nature Chemistry, Vol. 4, Issue 3
  • DOI: 10.1038/nchem.1242

Influence of Deoxyribose Group on Self-Assembly of Thymidine on Au(111)
journal, September 2009

  • Yang, Bing; Wang, Yeliang; Li, Guo
  • The Journal of Physical Chemistry C, Vol. 113, Issue 41
  • DOI: 10.1021/jp906944c

A Simple Glycol Nucleic Acid
journal, March 2005

  • Zhang, Lilu; Peritz, Adam; Meggers, Eric
  • Journal of the American Chemical Society, Vol. 127, Issue 12
  • DOI: 10.1021/ja042564z

8-Bromo-9-alkyl adenine derivatives as tools for developing new adenosine A2A and A2B receptors ligands
journal, April 2009

  • Lambertucci, Catia; Antonini, Ippolito; Buccioni, Michela
  • Bioorganic & Medicinal Chemistry, Vol. 17, Issue 7
  • DOI: 10.1016/j.bmc.2009.02.030

A new approach to the synthesis of optically active alkylated adenine derivatives
journal, June 2004

  • Zakirova, N. F.; Shipitsyn, A. V.; Belanov, E. F.
  • Bioorganic & Medicinal Chemistry Letters, Vol. 14, Issue 12
  • DOI: 10.1016/j.bmcl.2003.12.107

An Investigation into the Interactions Between Self-Assembled Adenine Molecules and a Au(111) Surface
journal, September 2008

Adenine monolayers on the Au(111) surface: Structure identification by scanning tunneling microscopy experiment and ab initio calculations
journal, January 2009

  • Lukas, Maya; Kelly, Ross E. A.; Kantorovich, Lev N.
  • The Journal of Chemical Physics, Vol. 130, Issue 2
  • DOI: 10.1063/1.3046690

Two-dimensional self-assembled structures of adenine molecules: modeling and simulation
journal, May 2004

Homopairing Possibilities of the DNA Base Adenine
journal, June 2005

  • Kelly, R. E. A.; Lee, Y. J.; Kantorovich, L. N.
  • The Journal of Physical Chemistry B, Vol. 109, Issue 24
  • DOI: 10.1021/jp050962y

Two-Dimensional Self-Assembly of Supramolecular Clusters and Chains
journal, July 1999

  • Böhringer, Matthias; Morgenstern, Karina; Schneider, Wolf-Dieter
  • Physical Review Letters, Vol. 83, Issue 2
  • DOI: 10.1103/PhysRevLett.83.324

Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs
journal, August 2004

  • Šponer, Jiří; Jurečka, Petr; Hobza, Pavel
  • Journal of the American Chemical Society, Vol. 126, Issue 32
  • DOI: 10.1021/ja048436s

Complex self-assembly of pyrimido[4,5-d]pyrimidine nucleoside supramolecular structures
journal, January 2014

  • Zhao, Hang; Guo, Xiurong; He, Shiliang
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms4108

Highly Ordered Assembly of Single-Domain Dichloropentacene over Large Areas on Vicinal Gold Surfaces
journal, February 2011

  • Wang, Jun; Kaur, Irvinder; Diaconescu, Bogdan
  • ACS Nano, Vol. 5, Issue 3
  • DOI: 10.1021/nn102468p

High performance computational chemistry: An overview of NWChem a distributed parallel application
journal, June 2000

Density‐functional thermochemistry. III. The role of exact exchange
journal, April 1993

  • Becke, Axel D.
  • The Journal of Chemical Physics, Vol. 98, Issue 7, p. 5648-5652
  • DOI: 10.1063/1.464913

Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
journal, January 1988

Ab initiomolecular dynamics for liquid metals
journal, January 1993

Generalized Gradient Approximation Made Simple
journal, October 1996

  • Perdew, John P.; Burke, Kieron; Ernzerhof, Matthias
  • Physical Review Letters, Vol. 77, Issue 18, p. 3865-3868
  • DOI: 10.1103/PhysRevLett.77.3865

Projector augmented-wave method
journal, December 1994

Van der Waals Density Functional for General Geometries
journal, June 2004

Chemical accuracy for the van der Waals density functional
journal, December 2009

  • Klimeš, Jiří; Bowler, David R.; Michaelides, Angelos
  • Journal of Physics: Condensed Matter, Vol. 22, Issue 2
  • DOI: 10.1088/0953-8984/22/2/022201

Optimization of parameters for semiempirical methods I. Method
journal, March 1989

Optimization of parameters for semiempirical methods II. Applications
journal, March 1989

Accurate spin-dependent electron liquid correlation energies for local spin density calculations: a critical analysis
journal, August 1980

  • Vosko, S. H.; Wilk, L.; Nusair, M.
  • Canadian Journal of Physics, Vol. 58, Issue 8
  • DOI: 10.1139/p80-159

Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields
journal, November 1994

  • Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.
  • The Journal of Physical Chemistry, Vol. 98, Issue 45, p. 11623-11627
  • DOI: 10.1021/j100096a001

Parallel Nanoimprint Forming of One-Dimensional Chiral Semiconductor for Strain-Engineered Optical Properties
journal, August 2020

Electronic structure of AlFeN films exhibiting crystallographic orientation change from c- to a-axis with Fe concentrations and annealing effect
journal, February 2020

Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
text, January 1988

  • Robert, Parr,; Chengteh, Lee,; Weitao, Yang,
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/zrp0-ry04

Chemical accuracy for the van der Waals density functional
preprint, January 2009

An Investigation into the Interactions Between Self-Assembled Adenine Molecules and a Au(111) Surface
journal, September 2008

A new approach to the synthesis of optically active alkylated adenine derivatives
journal, June 2004

  • Zakirova, N. F.; Shipitsyn, A. V.; Belanov, E. F.
  • Bioorganic & Medicinal Chemistry Letters, Vol. 14, Issue 12
  • DOI: 10.1016/j.bmcl.2003.12.107

A Simple Glycol Nucleic Acid
journal, March 2005

  • Zhang, Lilu; Peritz, Adam; Meggers, Eric
  • Journal of the American Chemical Society, Vol. 127, Issue 12
  • DOI: 10.1021/ja042564z

Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs
journal, August 2004

  • Šponer, Jiří; Jurečka, Petr; Hobza, Pavel
  • Journal of the American Chemical Society, Vol. 126, Issue 32
  • DOI: 10.1021/ja048436s

Highly Ordered Assembly of Single-Domain Dichloropentacene over Large Areas on Vicinal Gold Surfaces
journal, February 2011

  • Wang, Jun; Kaur, Irvinder; Diaconescu, Bogdan
  • ACS Nano, Vol. 5, Issue 3
  • DOI: 10.1021/nn102468p

Electronic Control over Attachment and Self-Assembly of Alkyne Groups on Gold
journal, September 2012

  • Li, Qing; Han, Chengbo; Fuentes-Cabrera, Miguel
  • ACS Nano, Vol. 6, Issue 10
  • DOI: 10.1021/nn303734r

Controlling on-surface polymerization by hierarchical and substrate-directed growth
journal, January 2012

  • Lafferentz, L.; Eberhardt, V.; Dri, C.
  • Nature Chemistry, Vol. 4, Issue 3
  • DOI: 10.1038/nchem.1242

Information-containing macromolecules
journal, May 2014

  • Colquhoun, Howard; Lutz, Jean-François
  • Nature Chemistry, Vol. 6, Issue 6
  • DOI: 10.1038/nchem.1958

Ultra-precise insertion of functional monomers in chain-growth polymerizations
journal, January 2012

  • Zamfir, Mirela; Lutz, Jean-François
  • Nature Communications, Vol. 3, Issue 1
  • DOI: 10.1038/ncomms2151

Complex self-assembly of pyrimido[4,5-d]pyrimidine nucleoside supramolecular structures
journal, January 2014

  • Zhao, Hang; Guo, Xiurong; He, Shiliang
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms4108

Design and synthesis of digitally encoded polymers that can be decoded and erased
journal, May 2015

  • Roy, Raj Kumar; Meszynska, Anna; Laure, Chloé
  • Nature Communications, Vol. 6, Issue 1
  • DOI: 10.1038/ncomms8237

Self-Organized and Cu-Coordinated Surface Linear Polymerization
journal, July 2013

  • Li, Qing; Owens, Jonathan R.; Han, Chengbo
  • Scientific Reports, Vol. 3, Issue 1
  • DOI: 10.1038/srep02102

Sequence control in polymer synthesis
journal, January 2009

  • Badi, Nezha; Lutz, Jean-François
  • Chemical Society Reviews, Vol. 38, Issue 12
  • DOI: 10.1039/b806413j

Adenine monolayers on the Au(111) surface: Structure identification by scanning tunneling microscopy experiment and ab initio calculations
journal, January 2009

  • Lukas, Maya; Kelly, Ross E. A.; Kantorovich, Lev N.
  • The Journal of Chemical Physics, Vol. 130, Issue 2
  • DOI: 10.1063/1.3046690

Conductance of a Single Conjugated Polymer as a Continuous Function of Its Length
journal, February 2009

Sequence-Controlled Polymers
journal, August 2013

Van der Waals Density Functional for General Geometries
text, January 2004

    Sort by:
    [ × clear filter / sort ]

    Works referencing / citing this record:

    Theoretical and experimental evidence of conformational transformation in stereoisomers of nucleoside analogues
    journal, September 2018

    • Hernández-Hernández, Luis Alberto; Yi, Ruiqin; Cleaves, Henderson James
    • International Journal of Quantum Chemistry, Vol. 118, Issue 20
    • DOI: 10.1002/qua.25714
      Sort by:
      [ × clear filter / sort ]

      Similar Records in DOE PAGES and OSTI.GOV collections: