Kinetics of duplex formation for individual DNA strands within a single protein nanopore

Proceedings of the National Academy of Sciences of the United States of America
Stefan HoworkaHagan Bayley

Abstract

A single oligonucleotide was covalently attached to a genetically engineered subunit of the heptameric protein pore, alpha-hemolysin, to allow DNA duplex formation inside the pore lumen. Single-channel current recording was used to study the properties of the modified pore. On addition of an oligonucleotide 8 bases in length and with a sequence complementary to the tethered DNA strand, current blockades with durations of hundreds of milliseconds occurred, representing hybridization events of individual oligonucleotides to the tethered DNA strand. Kinetic constants for DNA duplex formation at the single molecule level were derived and found to be consistent with established literature values for macroscopic duplex formation. The resultant equilibrium constant for duplex formation in the nanopore was found to be close to the experimentally derived constant for duplex formation in solution. A good agreement between the equilibrium constants for duplex formation in the nanopore and in solution was also found for two other oligonucleotide pairs. In addition, the nanopore recordings revealed details of the kinetics difficult to obtain by conventional methods, like surface plasmon resonance, which measure ensemble properties. By inves...Continue Reading

References

Jun 1, 1973·The Journal of General Physiology·A M Woodhull
Apr 28, 1971·Journal of Molecular Biology·F H MartinP Doty
Jun 21, 1994·Proceedings of the National Academy of Sciences of the United States of America·M Eigen, R Rigler
Jan 1, 1995·Bioconjugate Chemistry·D R CoreyA Huang
May 25, 1995·Nucleic Acids Research·M Kinjo, R Rigler
Nov 26, 1996·Proceedings of the National Academy of Sciences of the United States of America·J J KasianowiczD W Deamer
Feb 18, 1997·Proceedings of the National Academy of Sciences of the United States of America·R G SosnowskiM J Heller
Sep 1, 1973·Journal of Neurocytology·C D BucanaJ L Frehn
Jan 1, 1997·Annual Review of Biophysics and Biomolecular Structure·S Nie, R N Zare
Jul 1, 1997·Chemistry & Biology·O BrahaH Bayley
Mar 21, 1998·Proceedings of the National Academy of Sciences of the United States of America·C EggelingC A Seidel
Apr 16, 1998·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·I SzabòM Zoratti
Apr 14, 1999·Nature Structural Biology·M RiefH E Gaub
Jul 1, 1999·Protein Science : a Publication of the Protein Society·S CheleyH Bayley
Sep 29, 1999·Proceedings of the National Academy of Sciences of the United States of America·T StrunzH J Güntherodt
Feb 3, 2000·Proceedings of the National Academy of Sciences of the United States of America·A MellerD Branton
Mar 31, 2000·Trends in Biotechnology·D W Deamer, M Akeson
Jun 22, 2000·Analytical Biochemistry·S Wright Lucas, M M Harding
Sep 27, 2000·Physical Review Letters·S E HenricksonJ J Kasianowicz
Sep 28, 2000·Current Opinion in Chemical Biology·H Clausen-SchaumannH E Gaub
Jan 10, 2001·Proceedings of the National Academy of Sciences of the United States of America·F DumasB Hohn
Apr 28, 2001·Science·J LiphardtC Bustamante
May 1, 2001·Physical Review Letters·A MellerD Branton
Dec 26, 2001·Chemical Reviews·W P AmbroseR A Keller

❮ Previous
Next ❯

Citations

Mar 28, 2008·European Biophysics Journal : EBJ·Mohammad M Mohammad, Liviu Movileanu
Mar 27, 2012·Analytica Chimica Acta·Lajos Höfler, Róbert E Gyurcsányi
Mar 17, 2004·Bioorganic & Medicinal Chemistry·Eric BironNormand Voyer
Apr 15, 2005·Mutation Research·Eugene Y Chan
Aug 15, 2002·Trends in Biotechnology·Christof M Niemeyer
Jun 12, 2012·Biochemistry·Belete R ChenekeLiviu Movileanu
Nov 20, 2012·Chemical Reviews·Joseph E ReinerJohn J Kasianowicz
Jan 9, 2008·Journal of the American Chemical Society·Michael MayerGeorge M Whitesides
Aug 5, 2010·Journal of the American Chemical Society·David J NiedzwieckiLiviu Movileanu
Jun 15, 2010·The Journal of Physical Chemistry. B·Mohammad M Mohammad, Liviu Movileanu
Dec 27, 2011·Nano Letters·Nicholas A W BellUlrich F Keyser
May 15, 2012·Nature Structural & Molecular Biology·Ibrahim I CisseTaekjip Ha
Nov 9, 2006·Physical Chemistry Chemical Physics : PCCP·Youngseon ChoiCharles R Martin
Jul 9, 2010·Molecular BioSystems·Daren J Caruana, Stefan Howorka
Feb 16, 2012·Physical Chemistry Chemical Physics : PCCP·Liping WenLei Jiang
Dec 9, 2008·Proceedings of the National Academy of Sciences of the United States of America·Giovanni MagliaHagan Bayley
Jan 12, 2012·Proceedings of the National Academy of Sciences of the United States of America·Tommaso BelliniNoel A Clark
Sep 11, 2013·Proceedings of the National Academy of Sciences of the United States of America·Silvia BiffiTommaso Bellini
Jul 1, 2011·Journal of the Royal Society, Interface·Ulrich F Keyser
Jun 19, 2002·Protein Science : a Publication of the Protein Society·George MilesStephen Cheley
Dec 23, 2011·BMC Bioinformatics·Stephen Winters-HiltEric Morales
Apr 11, 2013·Biomicrofluidics·Chuanhua DuanQuan Xie
Aug 25, 2007·Nanomedicine·Ken Healy
Aug 23, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jérôme MathéAmit Meller
Feb 10, 2016·Analytical Chemistry·Christopher E AngevineJoseph E Reiner
Jun 5, 2012·Physics of Life Reviews·Meni Wanunu
Jun 22, 2010·Current Opinion in Biotechnology·Sheereen MajdMichael Mayer
Mar 26, 2016·Mikrochimica Acta·Nannan LiuFan Xia
Apr 28, 2009·Trends in Biotechnology·Liviu Movileanu
Oct 9, 2007·Biophysical Journal·Paul L BiancanielloJohn C Crocker
Oct 24, 2007·Biophysical Journal·Debabrata Panja, Gerard T Barkema
Sep 7, 2004·Biophysical Journal·Jérôme MathéAmit Meller
Jul 30, 2003·Biophysical Journal·Liviu MovileanuHagan Bayley
Mar 16, 2011·Biophysical Journal·Brett GyarfasWilliam B Dunbar
Jul 9, 2004·Biophysical Journal·Jonathan NakaneAndre Marziali
Aug 7, 2007·Biophysical Journal·Tom Z ButlerMark Troll

❮ 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.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
Amit MellerDaniel Branton
Physical Review Letters
S E HenricksonJ J Kasianowicz
Proceedings of the National Academy of Sciences of the United States of America
J J KasianowiczDavid W Deamer
© 2021 Meta ULC. All rights reserved