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Furan-oxidation-triggered inducible DNA cross-linking: acyclic versus cyclic furan-containing building blocks-on the benefit of restoring the cyclic sugar backbone

Kristof Stevens UGent, Diederica Claeys UGent, Saron Catak UGent, Sara Figaroli UGent, Michal Hocek, Jan M Tromp, Stefan Schurch, Veronique Van Speybroeck UGent and Annemieke Madder UGent (2011) CHEMISTRY-A EUROPEAN JOURNAL. 17(25). p.6940-6953
abstract
Oligodeoxynucleotides incorporating a reactive functionality can cause irreversible cross-linking to the target sequence and have been widely studied for their potential in inhibition of gene expression or development of diagnostic probes for gene analysis. Reactive oligonucleotides further show potential in a supramolecular context for the construction of nanometer-sized DNA-based objects. Inspired by the cytochrome P450 catalyzed transformation of furan into a reactive enal species, we recently introduced a furan-oxidation-based methodology for cross-linking of nucleic acids. Previous experiments using a simple acyclic building block equipped with a furan moiety for incorporation into oligodeoxynucleotides have shown that cross-linking occurs in a very fast and efficient way and that substantial amounts of stable, site-selectively cross-linked species can be isolated. Given the destabilization of duplexes observed upon introduction of the initially designed furan-modified building block into DNA duplexes, we explore here the potential benefits of two new building blocks featuring an extended aromatic system and a restored cyclic backbone. Thorough experimental analysis of cross-linking reactions in a series of contexts, combined with theoretical calculations, permit structural characterization of the formed species and allow assessment of the origin of the enhanced cross-link selectivity. Our experiments clearly show that the modular nature of the furan-modified building blocks used in the current cross-linking strategy allow for fine tuning of both yield and selectivity of the interstrand cross-linking reaction.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
BINDING ABILITY, MODULAR SYNTHESIS, CELL-PROLIFERATION, C-RIBONUCLEOSIDES, ABASIC SITE, DUPLEX DNA, BASE, OLIGONUCLEOTIDE, NUCLEOSIDES, ADDUCTS, bioorganic chemistry, DNA, molecular modeling, nucleosides, oxidation
journal title
CHEMISTRY-A EUROPEAN JOURNAL
Chem.-Eur. J.
volume
17
issue
25
pages
6940 - 6953
Web of Science type
Article
Web of Science id
000292206600011
JCR category
CHEMISTRY, MULTIDISCIPLINARY
JCR impact factor
5.925 (2011)
JCR rank
18/149 (2011)
JCR quartile
1 (2011)
ISSN
0947-6539
DOI
10.1002/chem.201100067
project
HPC-UGent: the central High Performance Computing infrastructure of Ghent University
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1860846
handle
http://hdl.handle.net/1854/LU-1860846
date created
2011-07-26 08:32:43
date last changed
2013-09-17 10:46:33
@article{1860846,
  abstract     = {Oligodeoxynucleotides incorporating a reactive functionality can cause irreversible cross-linking to the target sequence and have been widely studied for their potential in inhibition of gene expression or development of diagnostic probes for gene analysis. Reactive oligonucleotides further show potential in a supramolecular context for the construction of nanometer-sized DNA-based objects. Inspired by the cytochrome P450 catalyzed transformation of furan into a reactive enal species, we recently introduced a furan-oxidation-based methodology for cross-linking of nucleic acids. Previous experiments using a simple acyclic building block equipped with a furan moiety for incorporation into oligodeoxynucleotides have shown that cross-linking occurs in a very fast and efficient way and that substantial amounts of stable, site-selectively cross-linked species can be isolated. Given the destabilization of duplexes observed upon introduction of the initially designed furan-modified building block into DNA duplexes, we explore here the potential benefits of two new building blocks featuring an extended aromatic system and a restored cyclic backbone. Thorough experimental analysis of cross-linking reactions in a series of contexts, combined with theoretical calculations, permit structural characterization of the formed species and allow assessment of the origin of the enhanced cross-link selectivity. Our experiments clearly show that the modular nature of the furan-modified building blocks used in the current cross-linking strategy allow for fine tuning of both yield and selectivity of the interstrand cross-linking reaction.},
  author       = {Stevens, Kristof and Claeys, Diederica and Catak, Saron and Figaroli, Sara and Hocek, Michal and Tromp, Jan M and Schurch, Stefan and Van Speybroeck, Veronique and Madder, Annemieke},
  issn         = {0947-6539},
  journal      = {CHEMISTRY-A EUROPEAN JOURNAL},
  keyword      = {BINDING ABILITY,MODULAR SYNTHESIS,CELL-PROLIFERATION,C-RIBONUCLEOSIDES,ABASIC SITE,DUPLEX DNA,BASE,OLIGONUCLEOTIDE,NUCLEOSIDES,ADDUCTS,bioorganic chemistry,DNA,molecular modeling,nucleosides,oxidation},
  language     = {eng},
  number       = {25},
  pages        = {6940--6953},
  title        = {Furan-oxidation-triggered inducible DNA cross-linking: acyclic versus cyclic furan-containing building blocks-on the benefit of restoring the cyclic sugar backbone},
  url          = {http://dx.doi.org/10.1002/chem.201100067},
  volume       = {17},
  year         = {2011},
}

Chicago
Stevens, Kristof, Diederica Claeys, Saron Catak, Sara Figaroli, Michal Hocek, Jan M Tromp, Stefan Schurch, Veronique Van Speybroeck, and Annemieke Madder. 2011. “Furan-oxidation-triggered Inducible DNA Cross-linking: Acyclic Versus Cyclic Furan-containing Building Blocks-on the Benefit of Restoring the Cyclic Sugar Backbone.” Chemistry-a European Journal 17 (25): 6940–6953.
APA
Stevens, Kristof, Claeys, D., Catak, S., Figaroli, S., Hocek, M., Tromp, J. M., Schurch, S., et al. (2011). Furan-oxidation-triggered inducible DNA cross-linking: acyclic versus cyclic furan-containing building blocks-on the benefit of restoring the cyclic sugar backbone. CHEMISTRY-A EUROPEAN JOURNAL, 17(25), 6940–6953.
Vancouver
1.
Stevens K, Claeys D, Catak S, Figaroli S, Hocek M, Tromp JM, et al. Furan-oxidation-triggered inducible DNA cross-linking: acyclic versus cyclic furan-containing building blocks-on the benefit of restoring the cyclic sugar backbone. CHEMISTRY-A EUROPEAN JOURNAL. 2011;17(25):6940–53.
MLA
Stevens, Kristof, Diederica Claeys, Saron Catak, et al. “Furan-oxidation-triggered Inducible DNA Cross-linking: Acyclic Versus Cyclic Furan-containing Building Blocks-on the Benefit of Restoring the Cyclic Sugar Backbone.” CHEMISTRY-A EUROPEAN JOURNAL 17.25 (2011): 6940–6953. Print.