Nucleobase pairing and photodimerization in a biologically derived metal-organic framework nanoreactor
Abstract
Biologically derived metal-organic frameworks (bio-MOFs) are of great importance as they can be used as models for bio-mimicking and in catalysis, allowing us to gain insights into how large biological molecules function. Through rational design, here we report the synthesis of a novel bio-MOF featuring unobstructed Watson-Crick faces of adenine (Ade) pointing towards the MOF cavities. We show, through a combined experimental and computational approach, that thymine (Thy) molecules diffuse through the pores of the MOF and become base-paired with Ade. The Ade-Thy pair binding at 40–45% loading reveals that Thy molecules are packed within the channels in a way that fulfill both the Woodward-Hoffmann and Schmidt rules, and upon UV irradiation, Thy molecules dimerize into Thy<>Thy. This study highlights the utility of accessible functional groups within the pores of MOFs, and their ability to ‘lock’ molecules in specific positions that can be subsequently dimerized upon light irradiation, extending the use of MOFs as nanoreactors for the synthesis of molecules that are otherwise challenging to isolate.
- Authors:
-
[1];
[5];
[1];
[1]
- École Polytechnique Fédérale de Lausanne (EPFL Valais Wallis), Sion (Switzerland)
- Univ. College London, London (United Kingdom)
- École Polytechnique Fédérale de Lausanne (EPFL), Lausanne (Switzerland)
- Univ. of Southampton, Southampton (United Kingdom)
- Univ. of Liverpool, Liverpool (United Kingdom)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1559204
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Anderson, Samantha L., Boyd, Peter G., Gładysiak, Andrzej, Nguyen, Tu N., Palgrave, Robert G., Kubicki, Dominik, Emsley, Lyndon, Bradshaw, Darren, Rosseinsky, Matthew J., Smit, Berend, and Stylianou, Kyriakos C. Nucleobase pairing and photodimerization in a biologically derived metal-organic framework nanoreactor. United States: N. p., 2019.
Web. doi:10.1038/s41467-019-09486-2.
Anderson, Samantha L., Boyd, Peter G., Gładysiak, Andrzej, Nguyen, Tu N., Palgrave, Robert G., Kubicki, Dominik, Emsley, Lyndon, Bradshaw, Darren, Rosseinsky, Matthew J., Smit, Berend, & Stylianou, Kyriakos C. Nucleobase pairing and photodimerization in a biologically derived metal-organic framework nanoreactor. United States. https://doi.org/10.1038/s41467-019-09486-2
Anderson, Samantha L., Boyd, Peter G., Gładysiak, Andrzej, Nguyen, Tu N., Palgrave, Robert G., Kubicki, Dominik, Emsley, Lyndon, Bradshaw, Darren, Rosseinsky, Matthew J., Smit, Berend, and Stylianou, Kyriakos C. Mon .
"Nucleobase pairing and photodimerization in a biologically derived metal-organic framework nanoreactor". United States. https://doi.org/10.1038/s41467-019-09486-2. https://www.osti.gov/servlets/purl/1559204.
@article{osti_1559204,
title = {Nucleobase pairing and photodimerization in a biologically derived metal-organic framework nanoreactor},
author = {Anderson, Samantha L. and Boyd, Peter G. and Gładysiak, Andrzej and Nguyen, Tu N. and Palgrave, Robert G. and Kubicki, Dominik and Emsley, Lyndon and Bradshaw, Darren and Rosseinsky, Matthew J. and Smit, Berend and Stylianou, Kyriakos C.},
abstractNote = {Biologically derived metal-organic frameworks (bio-MOFs) are of great importance as they can be used as models for bio-mimicking and in catalysis, allowing us to gain insights into how large biological molecules function. Through rational design, here we report the synthesis of a novel bio-MOF featuring unobstructed Watson-Crick faces of adenine (Ade) pointing towards the MOF cavities. We show, through a combined experimental and computational approach, that thymine (Thy) molecules diffuse through the pores of the MOF and become base-paired with Ade. The Ade-Thy pair binding at 40–45% loading reveals that Thy molecules are packed within the channels in a way that fulfill both the Woodward-Hoffmann and Schmidt rules, and upon UV irradiation, Thy molecules dimerize into Thy<>Thy. This study highlights the utility of accessible functional groups within the pores of MOFs, and their ability to ‘lock’ molecules in specific positions that can be subsequently dimerized upon light irradiation, extending the use of MOFs as nanoreactors for the synthesis of molecules that are otherwise challenging to isolate.},
doi = {10.1038/s41467-019-09486-2},
journal = {Nature Communications},
number = 1,
volume = 10,
place = {United States},
year = {Mon Apr 08 00:00:00 EDT 2019},
month = {Mon Apr 08 00:00:00 EDT 2019}
}
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Works referenced in this record:
Cyclobutane Thymine Photodimerization Mechanism Revealed by Nonadiabatic Molecular Dynamics
journal, October 2016
- Rauer, Clemens; Nogueira, Juan J.; Marquetand, Philipp
- Journal of the American Chemical Society, Vol. 138, Issue 49
Metal–carboxylato–nucleobase systems: From supramolecular assemblies to 3D porous materials
journal, October 2013
- Beobide, Garikoitz; Castillo, Oscar; Cepeda, Javier
- Coordination Chemistry Reviews, Vol. 257, Issue 19-20
Shape Selectivity by Guest-Driven Restructuring of a Porous Material
journal, March 2014
- Warren, J. E.; Perkins, C. G.; Jelfs, K. E.
- Angewandte Chemie International Edition, Vol. 53, Issue 18
Biologically derived metal organic frameworks
journal, October 2017
- Anderson, Samantha L.; Stylianou, Kyriakos C.
- Coordination Chemistry Reviews, Vol. 349
Generation of a solid Brønsted acid site in a chiral framework
journal, January 2008
- Ingleson, Michael J.; Barrio, Jorge Perez; Bacsa, John
- Chemical Communications, Issue 11
RNA double-helical fragments at atomic resolution: I. The crystal and molecular structure of sodium adenylyl-3′,5′-uridine hexahydrate
journal, June 1976
- Seeman, Nadrian C.; Rosenberg, John M.; Suddath, F. L.
- Journal of Molecular Biology, Vol. 104, Issue 1
Porous metal–organic-framework nanoscale carriers as a potential platform for drug delivery and imaging
journal, December 2009
- Horcajada, Patricia; Chalati, Tamim; Serre, Christian
- Nature Materials, Vol. 9, Issue 2
Metal-adeninate vertices for the construction of an exceptionally porous metal-organic framework
journal, January 2012
- An, Jihyun; Farha, Omar K.; Hupp, Joseph T.
- Nature Communications, Vol. 3, Issue 1
Cage amines in the metal–organic frameworks chemistry
journal, July 2017
- Sapchenko, Sergey A.; Dybtsev, Danil N.; Fedin, Vladimir P.
- Pure and Applied Chemistry, Vol. 89, Issue 8
Kinetics of the Ultraviolet-Induced Dimerization of Thymine in Frozen Solutions
journal, April 1966
- Füchtbauer, Walter; Mazur, Peter
- Photochemistry and Photobiology, Vol. 5, Issue 4
Systematic Design of Pore Size and Functionality in Isoreticular MOFs and Their Application in Methane Storage
journal, January 2002
- Eddaoudi, Mohamed; Kim, Jaheon; Rosi, Nathaniel
- Science, Vol. 295, Issue 5554, p. 469-472
Mapping of Functional Groups in Metal-Organic Frameworks
journal, July 2013
- Kong, X.; Deng, H.; Yan, F.
- Science, Vol. 341, Issue 6148, p. 882-885
UV-induced single-crystal-to-single-crystal conversion from a coordination ladder to a two-dimensional network through an intermolecular carbon–carbon coupling reaction
journal, January 2017
- Chen, Jing-Min; Hou, Yi-Xuan; Zhou, Qian-Kun
- Dalton Transactions, Vol. 46, Issue 30
Side-chain control of porosity closure in single- and multiple-peptide-based porous materials by cooperative folding
journal, February 2014
- Martí-Gastaldo, C.; Antypov, D.; Warren, J. E.
- Nature Chemistry, Vol. 6, Issue 4
A grid-based Bader analysis algorithm without lattice bias
journal, January 2009
- Tang, W.; Sanville, E.; Henkelman, G.
- Journal of Physics: Condensed Matter, Vol. 21, Issue 8
A Guest-Responsive Fluorescent 3D Microporous Metal−Organic Framework Derived from a Long-Lifetime Pyrene Core
journal, March 2010
- Stylianou, Kyriakos C.; Heck, Romain; Chong, Samantha Y.
- Journal of the American Chemical Society, Vol. 132, Issue 12, p. 4119-4130
An Adaptable Peptide-Based Porous Material
journal, August 2010
- Rabone, J.; Yue, Y. - F.; Chong, S. Y.
- Science, Vol. 329, Issue 5995
Applied Topological Analysis of Crystal Structures with the Program Package ToposPro
journal, May 2014
- Blatov, Vladislav A.; Shevchenko, Alexander P.; Proserpio, Davide M.
- Crystal Growth & Design, Vol. 14, Issue 7
Porous materials based on metal–nucleobase systems sustained by coordination bonds and base pairing interactions
journal, January 2015
- Beobide, Garikoitz; Castillo, Oscar; Luque, Antonio
- CrystEngComm, Vol. 17, Issue 16
Systematic modulation and enhancement of CO2 : N2 selectivity and water stability in an isoreticular series of bio-MOF-11 analogues
journal, January 2013
- Li, Tao; Chen, De-Li; Sullivan, Jeanne E.
- Chemical Science, Vol. 4, Issue 4
Biomimicry in metal–organic materials
journal, June 2015
- Zhang, Muwei; Gu, Zhi-Yuan; Bosch, Mathieu
- Coordination Chemistry Reviews, Vol. 293-294
Boronic Acid Decorated Defective Metal-Organic Framework Nanoreactors for High-Efficiency Carbohydrates Separation and Labeling
journal, August 2017
- Chen, Guosheng; Fang, Xu'an; Chen, Qing
- Advanced Functional Materials, Vol. 27, Issue 38
Photosensitised pyrimidine dimerisation in DNA
journal, January 2011
- Cuquerella, M. Consuelo; Lhiaubet-Vallet, Virginie; Bosca, Francisco
- Chemical Science, Vol. 2, Issue 7
Predicting Thymine Dimerization Yields from Molecular Dynamics Simulations
journal, May 2008
- Law, Yu Kay; Azadi, Javad; Crespo-Hernández, Carlos E.
- Biophysical Journal, Vol. 94, Issue 9
PAMAM Dendrimers Undergo pH Responsive Conformational Changes without Swelling
journal, March 2009
- Liu, Yi; Bryantsev, Vyacheslav S.; Diallo, Mamadou S.
- Journal of the American Chemical Society, Vol. 131, Issue 8
Screening and evaluating aminated cationic functional moieties for potential CO2 capture applications using an anionic MOF scaffold
journal, January 2013
- Li, Tao; Rosi, Nathaniel L.
- Chemical Communications, Vol. 49, Issue 97
Metal–Organic Frameworks Encapsulated in Photocleavable Capsules for UV-Light Triggered Catalysis
journal, August 2015
- Deleu, Willem P. R.; Rivero, Guadalupe; Teixeira, Roberto F. A.
- Chemistry of Materials, Vol. 27, Issue 16
Self-Complementary Quadruple Hydrogen-Bonding Motifs as a Functional Principle: From Dimeric Supramolecules to Supramolecular Polymers
journal, December 2001
- Schmuck, Carsten; Wienand, Wolfgang
- Angewandte Chemie International Edition, Vol. 40, Issue 23
Engineering Homochiral Metal-Organic Frameworks by Spatially Separating 1D Chiral Metal-Peptide Ladders: Tuning the Pore Size for Enantioselective Adsorption
journal, June 2015
- Stylianou, Kyriakos C.; Gómez, Laura; Imaz, Inhar
- Chemistry - A European Journal, Vol. 21, Issue 28
A superior fluorescent sensor for Al 3+ and UO 2 2+ based on a Co( ii ) metal–organic framework with exposed pyrimidyl Lewis base sites
journal, January 2017
- Chen, Wen-Miao; Meng, Xiao-Ling; Zhuang, Gui-Lin
- Journal of Materials Chemistry A, Vol. 5, Issue 25
Protecting group and switchable pore-discriminating adsorption properties of a hydrophilic–hydrophobic metal–organic framework
journal, March 2011
- Mohideen, M. Infas H.; Xiao, Bo; Wheatley, Paul S.
- Nature Chemistry, Vol. 3, Issue 4
Opening the Door to Peptide-Based Porous Solids
journal, August 2010
- Wright, P. A.
- Science, Vol. 329, Issue 5995
Metal–biomolecule frameworks (MBioFs)
journal, January 2011
- Imaz, Inhar; Rubio-Martínez, Marta; An, Jihyun
- Chemical Communications, Vol. 47, Issue 26
Photodimerization in the solid state
journal, January 1971
- Schmidt, G. M. J.
- Pure and Applied Chemistry, Vol. 27, Issue 4
Hydrogen Bonding in DNA Base Pairs: Reconciliation of Theory and Experiment
journal, May 2000
- Fonseca Guerra, Célia; Bickelhaupt, F. Matthias; Snijders, Jaap G.
- Journal of the American Chemical Society, Vol. 122, Issue 17
Conservation of orbital symmetry
journal, January 1968
- Hoffmann, Roald; Woodward, Robert B.
- Accounts of Chemical Research, Vol. 1, Issue 1
Thymine Dimerization in DNA Is an Ultrafast Photoreaction
journal, February 2007
- Schreier, W. J.; Schrader, T. E.; Koller, F. O.
- Science, Vol. 315, Issue 5812
Dynamic Photo-Switching in Metal-Organic Frameworks as a Route to Low-Energy Carbon Dioxide Capture and Release
journal, February 2013
- Lyndon, Richelle; Konstas, Kristina; Ladewig, Bradley P.
- Angewandte Chemie International Edition, Vol. 52, Issue 13
Peptide Metal–Organic Frameworks for Enantioselective Separation of Chiral Drugs
journal, March 2017
- Navarro-Sánchez, José; Argente-García, Ana I.; Moliner-Martínez, Yolanda
- Journal of the American Chemical Society, Vol. 139, Issue 12
UV wavelength-dependent DNA damage and human non-melanoma and melanoma skin cancer
journal, January 2012
- Pfeifer, Gerd P.; Besaratinia, Ahmad
- Photochem. Photobiol. Sci., Vol. 11, Issue 1
The crystal structure of thymine
journal, June 1969
- Ozeki, K.; Sakabe, N.; Tanaka, J.
- Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry, Vol. 25, Issue 6
Spatial, Hysteretic, and Adaptive Host-Guest Chemistry in a Metal-Organic Framework with Open Watson-Crick Sites
journal, July 2015
- Cai, Hong; Li, Mian; Lin, Xiao-Rong
- Angewandte Chemie, Vol. 127, Issue 36
Molecular Level Characterization of the Structure and Interactions in Peptide-Functionalized Metal-Organic Frameworks
journal, October 2016
- Todorova, Tanya K.; Rozanska, Xavier; Gervais, Christel
- Chemistry - A European Journal, Vol. 22, Issue 46
Shedding Light on the Protonation States and Location of Protonated N Atoms of Adenine in Metal–Organic Frameworks
journal, February 2018
- Gładysiak, Andrzej; Nguyen, Tu N.; Anderson, Samantha L.
- Inorganic Chemistry, Vol. 57, Issue 4
Dynamic Photo-Switching in Metal-Organic Frameworks as a Route to Low-Energy Carbon Dioxide Capture and Release
journal, February 2013
- Lyndon, Richelle; Konstas, Kristina; Ladewig, Bradley P.
- Angewandte Chemie, Vol. 125, Issue 13
Spatial, Hysteretic, and Adaptive Host-Guest Chemistry in a Metal-Organic Framework with Open Watson-Crick Sites
journal, July 2015
- Cai, Hong; Li, Mian; Lin, Xiao-Rong
- Angewandte Chemie International Edition, Vol. 54, Issue 36
Dynamic Photo-Switching in Metal-Organic Frameworks as a Route to Low-Energy Carbon Dioxide Capture and Release
journal, February 2013
- Lyndon, Richelle; Konstas, Kristina; Ladewig, Bradley P.
- Angewandte Chemie
Shape Selectivity by Guest-Driven Restructuring of a Porous Material
journal, March 2014
- Warren, J. E.; Perkins, C. G.; Jelfs, K. E.
- Angewandte Chemie, Vol. 126, Issue 18
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journal, October 2019
- Carloni, Laure‐Elie; Bezzu, C. Grazia; Bonifazi, Davide
- Chemistry – A European Journal, Vol. 25, Issue 71
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journal, September 2019
- Kourtellaris, Andreas; Moushi, Eleni E.; Spanopoulos, Ioannis
- European Journal of Inorganic Chemistry, Vol. 2019, Issue 38
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journal, January 2020
- Panagiotou, Nikos; Evangelou, Kasiani; Psalti, Athanasia
- Molecular Systems Design & Engineering, Vol. 5, Issue 6
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journal, January 2020
- Zhang, Hongyuan; Jieying, Wang; Zhengji, Liang
- New Journal of Chemistry, Vol. 44, Issue 4
Water-stable 2-D Zr MOFs with exceptional UO 2 2+ sorption capability
journal, January 2020
- Panagiotou, Nikos; Liatsou, Ioanna; Pournara, Anastasia
- Journal of Materials Chemistry A, Vol. 8, Issue 4
A Microporous Co(II)-Based 3-D Metal Organic Framework Built from Magnetic Infinite Rod-Shaped Secondary Building Units
journal, October 2019
- Kourtellaris, Andreas; Moushi, Eleni E.; Spanopoulos, Ioannis
- European Journal of Inorganic Chemistry, Vol. 2019, Issue 38
A Nanoscale Metal–Organic Framework to Mediate Photodynamic Therapy and Deliver CpG Oligodeoxynucleotides to Enhance Antigen Presentation and Cancer Immunotherapy
journal, November 2019
- Ni, Kaiyuan; Luo, Taokun; Lan, Guangxu
- Angewandte Chemie International Edition, Vol. 59, Issue 3