Folding Landscape of a Parallel G-Quadruplex

The Journal of Physical Chemistry Letters
Robert GrayJonathan B Chaires

Abstract

Circular dichroism and stopped-flow UV spectroscopies were used to investigate the thermodynamic stability and the folding pathway of d[TGAG3TG3TAG3TG3TA2] at 25 °C in solutions containing 25 mM KCl. Under these conditions the oligonucleotide adopts a thermally stable, all-parallel G-quadruplex topography containing three stacked quartets. K+-induced folding shows three resolved relaxation times, each with distinctive spectral changes. Folding is complete within 200 s. These data indicate a folding pathway that involves at least two populated intermediates, one of which seems to be an antiparallel structure that rearranges to the final all-parallel conformation. Molecular dynamics reveals a stereochemically plausible folding pathway that does not involve complete unfolding of the intermediate. The rate of unfolding was determined using complementary DNA to trap transiently unfolded states to form a stable duplex. As assessed by 1D-1H NMR and fluorescence spectroscopy, unfolding is extremely slow with only one observable rate-limiting relaxation time.

References

Aug 27, 2002·Proceedings of the National Academy of Sciences of the United States of America·Adam Siddiqui-JainLaurence H Hurley
Mar 27, 2003·Journal of the American Chemical Society·Jeremy J GreenShankar Balasubramanian
Dec 3, 2003·Proceedings of the National Academy of Sciences of the United States of America·Liming YingShankar Balasubramanian
Apr 14, 2004·Proceedings of the National Academy of Sciences of the United States of America·Cory L GrandLaurence H Hurley
Jul 15, 2004·Journal of the American Chemical Society·Anh Tuân PhanDinshaw J Patel
Dec 21, 2005·Proceedings of the National Academy of Sciences of the United States of America·J Y LeeTaekjip Ha
Aug 12, 2006·Nucleosides, Nucleotides & Nucleic Acids·Danzhou Yang, Laurence H Hurley
Dec 16, 2006·Nucleic Acids Research·Julian L Huppert, Shankar Balasubramanian
May 26, 2007·Journal of the American Chemical Society·Pravin S ShirudeShankar Balasubramanian
Jun 10, 2008·Chemical Communications : Chem Comm·Pravin S ShirudeShankar Balasubramanian
Jun 17, 2008·Bioorganic & Medicinal Chemistry·Kenji OkamotoMasahide Terazima
Aug 23, 2008·Nucleic Acids Research·Andrew N LaneJohn O Trent
Feb 5, 2009·Nucleic Acids Research·Jaroslav KyprMichaela Vorlícková
Jul 16, 2009·Chemistry : a European Journal·Susanna LynchKumar Sinniah
Aug 27, 2009·The Journal of Physical Chemistry. B·Robert D GrayJonathan B Chaires
Oct 27, 2009·Nucleic Acids Research·Ron MiloMichael Springer
Dec 17, 2009·Methods in Molecular Biology·Burak Okumus, Taekjip Ha
Jun 4, 2011·Current Protocols in Nucleic Acid Chemistry·Robert D Gray, Jonathan B Chaires
Sep 20, 2011·Angewandte Chemie·Andreas Ioannis KarsisiotisMateus Webba da Silva
Apr 11, 2012·Methods : a Companion to Methods in Enzymology·Jiwook Shim, Li-Qun Gu
Sep 20, 2012·Journal of the American Chemical Society·Robert D GrayJonathan B Chaires
Sep 26, 2012·Physical Review Letters·Michel de MessieresArthur La Porta
Nov 2, 2012·Journal of the American Chemical Society·Amy Y Q Zhang, Shankar Balasubramanian
Jan 30, 2013·Biochemistry·Brittany RauzanAlice A Deckert
Jan 28, 2014·The Journal of Biological Chemistry·Md Ashraful IslamDonald M Miller
Feb 4, 2014·Journal of Molecular Biology·Robert D GrayJonathan B Chaires
Jul 12, 2014·Nucleic Acids Research·Huijuan YouJie Yan
Sep 17, 2014·Proceedings of the National Academy of Sciences of the United States of America·Na AnCynthia J Burrows
Dec 20, 2014·PloS One·Jonathan B ChairesDonald M Miller
Feb 6, 2015·Journal of the American Chemical Society·Huijuan YouJie Yan
Feb 18, 2016·Nucleic Acids Research·Oscar MendozaJean-Louis Mergny
Mar 12, 2016·Cell·Maya ShamirRon Milo
Dec 8, 2016·Nucleic Acids Research·Adrien Marchand, Valérie Gabelica
Dec 17, 2016·Biochimica Et Biophysica Acta. General Subjects·Jiří ŠponerMichal Otyepka
Sep 25, 2017·Biochemical Society Transactions·Markus Sauer, Katrin Paeschke
Aug 31, 2018·Nucleic Acids Research·Marek HavrilaJirí Šponer

❮ Previous
Next ❯

Citations

Aug 29, 2020·International Journal of Molecular Sciences·Klára BednářováDaniel Renčiuk
Feb 2, 2021·Nucleic Acids Research·Martina Lenarčič ŽivkovićLukáš Trantírek
Jan 21, 2021·Nucleic Acids Research·Robert W HarknessAnthony K Mittermaier
Apr 20, 2021·Journal of the American Chemical Society·J Tassilo GrünHarald Schwalbe
Jun 22, 2021·Physical Chemistry Chemical Physics : PCCP·Jussara AmatoBruno Pagano
Jul 20, 2021·The Journal of Physical Chemistry. B·K LaouerF Hache
Jan 11, 2020·The Journal of Physical Chemistry. B·Lutan LiuTigran V Chalikian
Aug 19, 2021·The Journal of Physical Chemistry Letters·Valeria LiberaLucia Comez
Sep 5, 2020·The Journal of Physical Chemistry Letters·Yuanlei ChengHuijuan You
Jun 13, 2020·The Journal of Physical Chemistry. B·Thi Quynh Ngoc NguyenAnh Tuân Phan
Sep 25, 2021·Science Advances·Koichi SatoPuck Knipscheer

❮ Previous
Next ❯

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.