Nanofabrication Yields. Hybridization and Click-Fixation of Polycyclic DNA Nanoassemblies

Handle URI:
http://hdl.handle.net/10754/598935
Title:
Nanofabrication Yields. Hybridization and Click-Fixation of Polycyclic DNA Nanoassemblies
Authors:
Lundberg, Erik P.; Plesa, Calin; Wilhelmsson, L. Marcus; Lincoln, Per; Brown, Tom; Nordén, Bengt
Abstract:
We demonstrate the stepwise assembly of a fully addressable polycyclic DNA hexagon nanonetwork for the preparation of a four-ring system, one of the biggest networks yet constructed from tripodal building blocks. We find that the yield exhibits a distinct upper level <100%, a fundamental problem of thermodynamic DNA assembly that appears to have been overlooked in the DNA nanotechnology literature. A simplistic model based on a single step-yield parameter y can quantitatively describe the total yield of DNA assemblies in one-pot reactions as Y = yduplex n, with n the number of hybridization steps. Experimental errors introducing deviations from perfect stoichiometry and the thermodynamics of hybridization equilibria contribute to decreasing the value of yduplex (on average y = 0.96 for our 10 base pair hybridization). For the four-ring system (n = 31), the total yield is thus less than 30%, which is clearly unsatisfactory if bigger nanoconstructs of this class are to be designed. Therefore, we introduced site-specific click chemistry for making and purifying robust building blocks for future modular constructs of larger assemblies. Although the present yield of this robust module was only about 10%, it demonstrates a first step toward a general fabrication approach. Interestingly, we find that the click yields follow quantitatively a binomial distribution, the predictability of which indicates the usefulness of preparing pools of pure and robust building blocks in this way. The binomial behavior indicates that there is no interference between the six simultaneous click reactions but that step-yield limiting factors such as topological constraints and Cu(I) catalyst concentration are local and independent. © 2011 American Chemical Society.
Citation:
Lundberg EP, Plesa C, Wilhelmsson LM, Lincoln P, Brown T, et al. (2011) Nanofabrication Yields. Hybridization and Click-Fixation of Polycyclic DNA Nanoassemblies. ACS Nano 5: 7565–7575. Available: http://dx.doi.org/10.1021/nn202568q.
Publisher:
American Chemical Society (ACS)
Journal:
ACS Nano
Issue Date:
27-Sep-2011
DOI:
10.1021/nn202568q
PubMed ID:
21827213
Type:
Article
ISSN:
1936-0851; 1936-086X
Sponsors:
This research is funded by the European Research Council (ERC grant to B.N.) and King Abdullah University of Science and Technology (KAUST awardee B.N.).
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorLundberg, Erik P.en
dc.contributor.authorPlesa, Calinen
dc.contributor.authorWilhelmsson, L. Marcusen
dc.contributor.authorLincoln, Peren
dc.contributor.authorBrown, Tomen
dc.contributor.authorNordén, Bengten
dc.date.accessioned2016-02-25T13:44:02Zen
dc.date.available2016-02-25T13:44:02Zen
dc.date.issued2011-09-27en
dc.identifier.citationLundberg EP, Plesa C, Wilhelmsson LM, Lincoln P, Brown T, et al. (2011) Nanofabrication Yields. Hybridization and Click-Fixation of Polycyclic DNA Nanoassemblies. ACS Nano 5: 7565–7575. Available: http://dx.doi.org/10.1021/nn202568q.en
dc.identifier.issn1936-0851en
dc.identifier.issn1936-086Xen
dc.identifier.pmid21827213en
dc.identifier.doi10.1021/nn202568qen
dc.identifier.urihttp://hdl.handle.net/10754/598935en
dc.description.abstractWe demonstrate the stepwise assembly of a fully addressable polycyclic DNA hexagon nanonetwork for the preparation of a four-ring system, one of the biggest networks yet constructed from tripodal building blocks. We find that the yield exhibits a distinct upper level <100%, a fundamental problem of thermodynamic DNA assembly that appears to have been overlooked in the DNA nanotechnology literature. A simplistic model based on a single step-yield parameter y can quantitatively describe the total yield of DNA assemblies in one-pot reactions as Y = yduplex n, with n the number of hybridization steps. Experimental errors introducing deviations from perfect stoichiometry and the thermodynamics of hybridization equilibria contribute to decreasing the value of yduplex (on average y = 0.96 for our 10 base pair hybridization). For the four-ring system (n = 31), the total yield is thus less than 30%, which is clearly unsatisfactory if bigger nanoconstructs of this class are to be designed. Therefore, we introduced site-specific click chemistry for making and purifying robust building blocks for future modular constructs of larger assemblies. Although the present yield of this robust module was only about 10%, it demonstrates a first step toward a general fabrication approach. Interestingly, we find that the click yields follow quantitatively a binomial distribution, the predictability of which indicates the usefulness of preparing pools of pure and robust building blocks in this way. The binomial behavior indicates that there is no interference between the six simultaneous click reactions but that step-yield limiting factors such as topological constraints and Cu(I) catalyst concentration are local and independent. © 2011 American Chemical Society.en
dc.description.sponsorshipThis research is funded by the European Research Council (ERC grant to B.N.) and King Abdullah University of Science and Technology (KAUST awardee B.N.).en
dc.publisherAmerican Chemical Society (ACS)en
dc.subjectclick chemistryen
dc.subjectDNA nanostructureen
dc.subjectfixation technologyen
dc.subjectsupramolecular assemblyen
dc.subjectyield analysisen
dc.titleNanofabrication Yields. Hybridization and Click-Fixation of Polycyclic DNA Nanoassembliesen
dc.typeArticleen
dc.identifier.journalACS Nanoen
dc.contributor.institutionChalmers University of Technology, Göteborg, Swedenen
dc.contributor.institutionUniversity of Southampton, Southampton, United Kingdomen

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