Complex between a Multicrossover DNA Nanostructure, PX-DNA, and T7 Endonuclease I

Biochemistry
Megan E KizerXing Wang

Abstract

Paranemic crossover DNA (PX-DNA) is a four-stranded multicrossover structure that has been implicated in recombination-independent recognition of homology. Although existing evidence has suggested that PX is the DNA motif in homologous pairing (HP), this conclusion remains ambiguous. Further investigation is needed but will require development of new tools. Here, we report characterization of the complex between PX-DNA and T7 endonuclease I (T7endoI), a junction-resolving protein that could serve as the prototype of an anti-PX ligand (a critical prerequisite for the future development of such tools). Specifically, nuclease-inactive T7endoI was produced and its ability to bind to PX-DNA was analyzed using a gel retardation assay. The molar ratio of PX to T7endoI was determined using gel electrophoresis and confirmed by the Hill equation. Hydroxyl radical footprinting of T7endoI on PX-DNA is used to verify the positive interaction between PX and T7endoI and to provide insight into the binding region. Cleavage of PX-DNA by wild-type T7endoI produces DNA fragments, which were used to identify the interacting sites on PX for T7endoI and led to a computational model of their interaction. Altogether, this study has identified a stable...Continue Reading

References

Mar 1, 1979·Nucleic Acids Research·A V VologodskiiM D Frank-Kamenetskii
Jan 1, 1979·Cold Spring Harbor Symposia on Quantitative Biology·M GellertJ Tomizawa
Jan 1, 1979·Proceedings of the National Academy of Sciences of the United States of America·J C Wang
Aug 1, 1979·Proceedings of the National Academy of Sciences of the United States of America·J H Wilson
Nov 17, 1992·Biochemistry·S M DuN C Seeman
Dec 1, 1990·Journal of Biomolecular Structure & Dynamics·N C Seeman
Jan 1, 1990·Annual Review of Genetics·E U Selker
Jan 1, 1990·Methods in Enzymology·F W StudierJ W Dubendorff
Dec 3, 1987·Nature·S M MirkinM D Frank-Kamenetskii
Oct 1, 1985·Proceedings of the National Academy of Sciences of the United States of America·M J Solomon, A Varshavsky
Nov 8, 1985·Science·T D Tullius, B A Dombroski
Jul 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·M E ChurchillN C Seeman
Jan 28, 1971·Journal of Molecular Biology·S McGavin
Nov 21, 1982·Journal of Theoretical Biology·N C Seeman
Jan 1, 1984·Annual Review of Biochemistry·A RichA H Wang
Mar 15, 1994·Experientia·J L Rossignol, G Faugeron
Feb 1, 1994·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·K W Wolf
May 20, 1994·Journal of Molecular Biology·S Zhang, N C Seeman
Apr 6, 1993·Biochemistry·T J Fu, N C Seeman
Sep 2, 1998·Proceedings of the National Academy of Sciences of the United States of America·T R StrickD Bensimon
Oct 3, 1999·Nature Structural Biology·M Ortiz-LombardíaM Coll
Apr 13, 2000·Proceedings of the National Academy of Sciences of the United States of America·B F EichmanP S Ho
Jan 3, 2001·Nature Structural Biology·J M HaddenS E Phillips
Apr 3, 2001·Nature Reviews. Genetics·T Hassold, P Hunt
Jan 10, 2002·Nature·Hao YanNadrian C Seeman
Oct 31, 2002·Journal of the American Chemical Society·Xiaoping ZhangNadrian C Seeman
Feb 12, 2004·Journal of the American Chemical Society·Zhiyong ShenNadrian C Seeman
Dec 18, 2004·Science·Shiping Liao, Nadrian C Seeman
Dec 13, 2006·Science·Baoquan Ding, Nadrian C Seeman
Jan 3, 2007·Biochemistry·Shotaro InoueTakashi Ohyama
Jun 15, 2007·Journal of the American Chemical Society·Xing Wang, Nadrian C Seeman
Sep 18, 2007·Nature·Jonathan M HaddenSimon E V Phillips
Oct 30, 2007·Journal of the American Chemical Society·Chenxiang LinHao Yan
Nov 28, 2007·Nature Reviews. Genetics·Adi Barzel, Martin Kupiec
Jan 10, 2008·The Journal of Physical Chemistry. B·Geoff S BaldwinAlexei A Kornyshev
May 14, 2008·Proceedings of the National Academy of Sciences of the United States of America·Banani ChakrabortyNadrian C Seeman
Oct 18, 2008·Proceedings of the National Academy of Sciences of the United States of America·Chenxiang LinHao Yan
Apr 8, 2009·Nature Nanotechnology·Hongzhou GuNadrian C Seeman
Sep 22, 2009·Proteins·Nelson MaxSilvia Crivelli
Nov 12, 2009·Proceedings of the National Academy of Sciences of the United States of America·C DanilowiczM Prentiss
May 14, 2010·Nature·Hongzhou GuNadrian C Seeman
Jul 10, 2010·Proceedings of the National Academy of Sciences of the United States of America·Xing WangNadrian C Seeman
Jul 24, 2010·Neoplasia : an International Journal for Oncology Research·Kyung ParkMark A Rubin

❮ Previous
Next ❯

Citations

Mar 27, 2020·Journal of the American Chemical Society·Arun Richard ChandrasekaranKen Halvorsen

❮ 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

Methods in Molecular Biology
E ZaychikovH Heumann
Methods in Molecular Biology
P Schickor, H Heumann
Methods in Enzymology
W J DixonT D Tullius
Nucleic Acids Research
Dong NiuNadrian C Seeman
Biochemical Society Transactions
M J Parkinson, David M J Lilley
© 2022 Meta ULC. All rights reserved