Computational Approaches to Nucleic Acid Origami

ACS Combinatorial Science
Hosna JabbariCarlo Montemagno

Abstract

Recent advances in experimental DNA origami have dramatically expanded the horizon of DNA nanotechnology. Complex 3D suprastructures have been designed and developed using DNA origami with applications in biomaterial science, nanomedicine, nanorobotics, and molecular computation. Ribonucleic acid (RNA) origami has recently been realized as a new approach. Similar to DNA, RNA molecules can be designed to form complex 3D structures through complementary base pairings. RNA origami structures are, however, more compact and more thermodynamically stable due to RNA's non-canonical base pairing and tertiary interactions. With all these advantages, the development of RNA origami lags behind DNA origami by a large gap. Furthermore, although computational methods have proven to be effective in designing DNA and RNA origami structures and in their evaluation, advances in computational nucleic acid origami is even more limited. In this paper, we review major milestones in experimental and computational DNA and RNA origami and present current challenges in these fields. We believe collaboration between experimental nanotechnologists and computer scientists are critical for advancing these new research paradigms.

References

Nov 21, 1982·Journal of Theoretical Biology·N C Seeman
Apr 30, 1982·Science·R E DickersonM L Kopka
Apr 6, 1993·Biochemistry·T J Fu, N C Seeman
Aug 26, 1998·Nature·E WinfreeN C Seeman
Feb 2, 1999·Journal of Molecular Biology·E Rivas, S R Eddy
Feb 27, 1999·Nature Structural Biology·J NowakowskiG F Joyce
Apr 27, 1999·Journal of Biomolecular Structure & Dynamics·T E CheathamP A Kollman
Oct 16, 1999·Journal of Molecular Graphics & Modelling·C Massire, E Westhof
Nov 5, 1999·Journal of Molecular Biology·I Tinoco, C Bustamante
Aug 19, 2000·Nature·B YurkeJ L Neumann
Jan 5, 2001·Nucleic Acids Research·L JaegerN B Leontis
Mar 10, 2001·RNA·C FlammM Zehl
Jul 12, 2002·Nature·Carina Dennis
Jun 26, 2003·Nucleic Acids Research·Michael Zuker
Aug 20, 2003·Journal of Computational Chemistry·Robert M Dirks, Niles A Pierce
Feb 13, 2004·Nature·William M ShihGerald F Joyce
Mar 3, 2004·Nucleic Acids Research·Robert M DirksNiles A Pierce
Apr 21, 2004·Journal of Molecular Biology·Mirela AndronescuAnne Condon
Jun 11, 2004·Annual Review of Biochemistry·Gerald F Joyce
Dec 18, 2004·Science·Arkadiusz ChworosLuc Jaeger
Mar 8, 2005·Proceedings of the National Academy of Sciences of the United States of America·Changbong Hyeon, D Thirumalai
Mar 17, 2005·Journal of Computational Chemistry·Thereza A SoaresWilfred F van Gunsteren
Sep 6, 2005·Science·P CarninciUNKNOWN RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group)
Mar 9, 2006·Nucleic Acids Research·Lorena NasaleanLuc Jaeger
Mar 17, 2006·Nature·Paul W K Rothemund
Apr 25, 2006·Journal of Molecular Graphics & Modelling·Jeffrey J BiracNadrian C Seeman
May 3, 2006·Human Molecular Genetics·John S Mattick, Igor V Makunin
May 20, 2006·Bioinformatics·Anke Busch, Rolf Backofen
Feb 3, 2007·BMC Bioinformatics·Rosalía Aguirre-HernándezAnne Condon
Mar 16, 2007·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Bernd Burghardt, Alexander K Hartmann
Sep 7, 2007·RNA·Ebbe S AndersenJan Gorodkin
Jan 8, 2008·Journal of Molecular Biology·Ashesh A SaraiyaPhilip R Cunningham
Jan 19, 2008·Nature·Peng YinNiles A Pierce
Mar 4, 2008·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hosna JabbariShelly Zhao
Mar 7, 2008·Nature·Marc Parisien, François Major
Apr 11, 2008·Journal of Biomolecular Structure & Dynamics·Hugo M MartinezBruce A Shapiro
Jul 3, 2008·Journal of the American Chemical Society·Gregory R BowmanVijay S Pande
Oct 8, 2008·Journal of Molecular Graphics & Modelling·Eckart BindewaldBruce A Shapiro
Nov 26, 2008·Methods in Molecular Biology·Bruce A ShapiroYaroslava Yingling
Feb 12, 2009·ACS Nano·Ebbe S AndersenJørgen Kjems

❮ Previous
Next ❯

Citations

Dec 3, 2015·Analytical Chemistry·Stephen M OjaBo Zhang
Jun 24, 2017·Nature Chemistry·Zhao ZhangChenxiang Lin
Jan 4, 2019·Nucleic Acids Research·Benedict E K SnodinJonathan P K Doye
Apr 25, 2018·Chemical Society Reviews·Pim W J M FrederixSiewert J Marrink
Jun 13, 2017·Chemical Reviews·Fan HongHao Yan
Mar 28, 2020·ACS Combinatorial Science·Deepak Sharma, Manojkumar Ramteke

❮ 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

Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
Meikang QiuPeixuan Guo
Nature Methods
Allison Doerr
Clinical Laboratory Science : Journal of the American Society for Medical Technology
Kathleen Kenwright, Linda L Williford Pifer
© 2021 Meta ULC. All rights reserved