Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair.

Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry
Jens Sobek, Ralph Schlapbach

Abstract

To understand the complex fluorescence properties of astraphloxin (CY3)-labelled oligonucleotides, it is necessary to take into account the redox properties of the nucleobases. In oligonucleotide hybrids, we observed a dependence of the fluorescence intensity on the oxidation potential of the neighbouring base pair. For the series I < A < G < 8-oxoG, the extent of fluorescence quenching follows the trend of decreasing oxidation potentials. In a series of 7 nt hybrids, stacking interactions of CY3 with perfect match and mismatch base pairs were found to stabilise the hybrid by 7-8 kJ/mol. The fluorescence measurements can be explained by complex formation resulting in fluorescence quenching that prevails over the steric effect of a reduced excited state trans-cis isomerisation, which was expected to increase the fluorescence efficiency of the dye when stacking to a base pair. This can be explained by the fact that, in a double strand, base pairing and stacking cause a dramatic change in the oxidation potential of the nucleobases. In single-molecule fluorescence measurements, the oxidation of G to 8-oxoG was observed as a result of photoinduced electron transfer and subsequent chemical reactions. Our results demonstrate that cova...Continue Reading

References

Apr 1, 1991·Journal of Photochemistry and Photobiology. B, Biology·T P DevasagayamH Sies
Jan 1, 1987·Annual Review of Biochemistry·P Modrich
Mar 1, 1993·Bioconjugate Chemistry·R B MujumdarA S Waggoner
Jul 15, 1997·Nucleic Acids Research·J B Randolph, A S Waggoner
Dec 6, 2000·Proceedings of the National Academy of Sciences of the United States of America·C WanA H Zewail
Feb 19, 2002·Chemical Reviews·Cynthia J. Burrows, James G. Muller
Apr 4, 2002·Journal of the American Chemical Society·Kiyohiko KawaiTetsuro Majima
May 8, 2002·Analytical Sciences : the International Journal of the Japan Society for Analytical Chemistry·M TorimuraR Kurane
Feb 20, 2003·Journal of the American Chemical Society·Jean-Luc RavanatJean Cadet
Dec 24, 2004·Journal of Fluorescence·Michael CooperRichard West
Oct 27, 2005·Journal of the American Chemical Society·Tonino CarusoAndrea Peluso
Apr 13, 2006·Chemical Research in Toxicology·William L Neeley, John M Essigmann
Feb 14, 2007·The Journal of Physical Chemistry. a·Ke JiaGuoqiang Yang
Apr 24, 2007·The Journal of Physical Chemistry. B·Carlos E Crespo-HernandezJerzy Leszczynski
Aug 28, 2007·The Journal of Physical Chemistry. B·Matthew E SanbornMarcia Levitus
Nov 10, 2007·Journal of the American Chemical Society·Tonino CarusoAndrea Peluso
Jan 30, 2008·The Journal of Physical Chemistry. B·Kiyohiko KawaiTetsuro Majima
Feb 23, 2008·Organic & Biomolecular Chemistry·Avik GhoshJean Cadet
Aug 1, 2008·Accounts of Chemical Research·Jean CadetJean-Luc Ravanat
Aug 5, 2008·Proceedings of the National Academy of Sciences of the United States of America·Asif IqbalDavid M J Lilley
Aug 30, 2008·Nature Methods·Ute Resch-GengerThomas Nann
Oct 31, 2008·Journal of Fluorescence·Billie J Harvey, Marcia Levitus
Nov 22, 2008·Science·John EidStephen Turner
May 28, 2009·Journal of the American Chemical Society·Amitava AdhikaryMichael D Sevilla
May 29, 2009·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Sören DooseMarkus Sauer
Jul 30, 2009·Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society for Photobiology·Billie Jo HarveyMarcia Levitus
Nov 27, 2009·Accounts of Chemical Research·Sriram KanvahUzi Landman
Mar 4, 2010·The Journal of Physical Chemistry. B·Christopher Batchelor-McAuleyRichard G Compton
Mar 6, 2010·Organic & Biomolecular Chemistry·Sriram Kanvah, Gary B Schuster
Mar 11, 2010·Chemical Reviews·Joseph C Genereux, Jacqueline K Barton
Feb 10, 2000·Journal of the American Chemical Society·Kevin M GuckianEric T Kool
Feb 16, 2011·Biophysical Journal·Justin SpiritiArjan van der Vaart
Apr 20, 2011·The Journal of Physical Chemistry. a·Y Paukku, G Hill
Sep 6, 2011·Biophysical Journal·Jonathan OuelletDavid M J Lilley
Dec 14, 2011·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Ingo H SteinPhilip Tinnefeld
Dec 22, 2011·Genome Integrity·Tyson A ClarkJonas Korlach
Feb 15, 2012·Journal of the American Chemical Society·Yekaterina RokhlenkoVladimir Shafirovich
Mar 13, 2012·Annual Review of Physical Chemistry·Taekjip Ha, Philip Tinnefeld

❮ Previous
Next ❯

Citations

Sep 9, 2021·The Journal of Physical Chemistry. a·Mohammed I SorourSpiridoula Matsika

❮ Previous
Next ❯

Methods Mentioned

BETA
chip
NMR

Software Mentioned

BiaEvaluation
RSII

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society for Photobiology
Billie J HarveyMarcia Levitus
© 2021 Meta ULC. All rights reserved