Global and local mechanical properties control endonuclease reactivity of a DNA origami nanostructure.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
21 05 2020
21 05 2020
Historique:
accepted:
29
01
2020
revised:
24
01
2020
received:
05
08
2019
pubmed:
12
2
2020
medline:
9
9
2020
entrez:
12
2
2020
Statut:
ppublish
Résumé
We used coarse-grained molecular dynamics simulations to characterize the global and local mechanical properties of a DNA origami triangle nanostructure. The structure presents two metastable conformations separated by a free energy barrier that is lowered upon omission of four specific DNA staples (defect). In contrast, only one stable conformation is present upon removing eight staples. The metastability is explained in terms of the intrinsic conformations of the three trapezoidal substructures. We computationally modeled the local accessibility to endonucleases, to predict the reactivity of twenty sites, and found good agreement with the experimental data. We showed that global fluctuations affect local reactivity: the removal of the DNA staples increased the computed accessibility to a restriction enzyme, at sites as distant as 40 nm, due to an increase in global fluctuation. These results raise the intriguing possibility of the rational engineering of allosterically modulated DNA origami.
Identifiants
pubmed: 32043111
pii: 5733126
doi: 10.1093/nar/gkaa080
pmc: PMC7229852
doi:
Substances chimiques
DNA
9007-49-2
Endodeoxyribonucleases
EC 3.1.-
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
4672-4680Subventions
Organisme : NIH HHS
ID : S10 OD020095
Pays : United States
Informations de copyright
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
Science. 2009 Aug 7;325(5941):725-30
pubmed: 19661424
ACS Nano. 2014 May 27;8(5):5132-40
pubmed: 24694301
J Enzyme Inhib Med Chem. 2013 Aug;28(4):879-93
pubmed: 22630075
ACS Nano. 2008 Jun;2(6):1213-8
pubmed: 19206339
J Chem Phys. 2015 Jun 21;142(23):234901
pubmed: 26093573
ACS Nano. 2015 Feb 24;9(2):1420-33
pubmed: 25623807
ACS Nano. 2016 Feb 23;10(2):1724-37
pubmed: 26766072
Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):713-8
pubmed: 25561550
ACS Nano. 2018 Jul 24;12(7):6734-6747
pubmed: 29851456
FEBS Lett. 2009 Jun 5;583(11):1692-8
pubmed: 19303011
Nat Commun. 2017 May 31;8:15654
pubmed: 28561045
Nat Methods. 2011 Mar;8(3):221-9
pubmed: 21358626
J Am Chem Soc. 2008 Nov 26;130(47):15754-5
pubmed: 18975864
Nature. 2009 May 21;459(7245):414-8
pubmed: 19458720
Angew Chem Int Ed Engl. 2017 May 8;56(20):5460-5464
pubmed: 28295864
Nature. 2018 Jul;559(7715):593-598
pubmed: 30013119
Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20099-104
pubmed: 24277840
Science. 2015 Mar 27;347(6229):1446-52
pubmed: 25814577
J Chem Phys. 2011 Feb 28;134(8):085101
pubmed: 21361556
Phys Rev Lett. 2010 Apr 30;104(17):178101
pubmed: 20482144
Bioinformatics. 2013 Apr 1;29(7):845-54
pubmed: 23407358
Proc Natl Acad Sci U S A. 2017 Apr 11;114(15):E2991-E2997
pubmed: 28351979
Adv Healthc Mater. 2019 May;8(10):e1801658
pubmed: 30938489
Phys Rev Lett. 2018 May 4;120(18):188003
pubmed: 29775326
Adv Mater. 2019 Jun;31(26):e1806294
pubmed: 30767279
Comput Struct Biotechnol J. 2018 Sep 18;16:342-349
pubmed: 30305885
J Comput Chem. 2019 Nov 5;40(29):2586-2595
pubmed: 31301183
Nucleic Acids Res. 2018 Jan 25;46(2):995-1006
pubmed: 29216375
ACS Nano. 2017 Dec 26;11(12):12426-12435
pubmed: 29083876
Biomater Sci. 2019 Jan 29;7(2):532-541
pubmed: 30534709
J Am Chem Soc. 2009 Nov 4;131(43):15903-8
pubmed: 19807088
Nature. 2016 Jul 21;535(7612):401-5
pubmed: 27398616
Nature. 2006 Mar 16;440(7082):297-302
pubmed: 16541064
Science. 2018 Jan 19;359(6373):296-301
pubmed: 29348232
ACS Nano. 2017 May 23;11(5):4617-4630
pubmed: 28423273
Phys Rev Lett. 1992 Apr 27;68(17):2696-2699
pubmed: 10045464
Eur Phys J E Soft Matter. 2018 May 10;41(5):57
pubmed: 29748779
ACS Nano. 2014 Jul 22;8(7):6633-43
pubmed: 24963790
Rep Prog Phys. 2005 Jan;68(1):237-270
pubmed: 25152542
Angew Chem Int Ed Engl. 2018 Jul 20;57(30):9470-9474
pubmed: 29799663
Nucleic Acids Res. 2018 Sep 6;46(15):7533-7541
pubmed: 29931074
J Am Chem Soc. 2010 Mar 17;132(10):3248-9
pubmed: 20163139
Nucleic Acids Res. 2019 Feb 20;47(3):1585-1597
pubmed: 30605514
Chembiochem. 2019 Nov 18;20(22):2818-2823
pubmed: 31163091
Proc Natl Acad Sci U S A. 2017 Mar 7;114(10):2526-2531
pubmed: 28223497
Science. 2005 Jun 3;308(5727):1424-8
pubmed: 15933191
Nanomedicine (Lond). 2019 Apr;14(7):911-925
pubmed: 30901300
Nucleic Acids Res. 2006 Feb 09;34(3):939-48
pubmed: 16473850
J Chem Phys. 2012 Oct 7;137(13):135101
pubmed: 23039613
Adv Healthc Mater. 2017 Sep;6(18):
pubmed: 28738444
Nucleic Acids Res. 2009 Aug;37(15):5001-6
pubmed: 19531737