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- PDB-7npn: B-brick bare in 5 mM Mg2+ -

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Basic information

Entry
Database: PDB / ID: 7npn
TitleB-brick bare in 5 mM Mg2+
Components
  • (STAPLE STRAND) x 78
  • SCAFFOLD STRAND
KeywordsDNA / DNA Origami
Function / homologyDNA / DNA (> 10) / DNA (> 100) / DNA (> 1000)
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.38 Å
AuthorsBertosin, E. / Stoemmer, P. / Feigl, E. / Wenig, M. / Honemann, M. / Dietz, H.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research Foundation (DFG)Gottfried-Wilhelm-Leibniz Program Germany
European Research Council (ERC)Consolidator Grant (GA #724261) Germany
Max Planck SocietyMax Planck School Matter to Life Germany
German Research Foundation (DFG)SFB863 TPA9 Project ID 111166240 Germany
CitationJournal: ACS Nano / Year: 2021
Title: Cryo-Electron Microscopy and Mass Analysis of Oligolysine-Coated DNA Nanostructures.
Authors: Eva Bertosin / Pierre Stömmer / Elija Feigl / Maximilian Wenig / Maximilian N Honemann / Hendrik Dietz /
Abstract: Cationic coatings can enhance the stability of synthetic DNA objects in low ionic strength environments such as physiological fluids. Here, we used single-particle cryo-electron microscopy (cryo-EM), ...Cationic coatings can enhance the stability of synthetic DNA objects in low ionic strength environments such as physiological fluids. Here, we used single-particle cryo-electron microscopy (cryo-EM), pseudoatomic model fitting, and single-molecule mass photometry to study oligolysine and polyethylene glycol (PEG)-oligolysine-coated multilayer DNA origami objects. The coatings preserve coarse structural features well on a resolution of multiple nanometers but can also induce deformations such as twisting and bending. Higher-density coatings also led to internal structural deformations in the DNA origami test objects, in which a designed honeycomb-type helical lattice was deformed into a more square-lattice-like pattern. Under physiological ionic strength, where the uncoated objects disassembled, the coated objects remained intact but they shrunk in the helical direction and expanded in the direction perpendicular to the helical axis. Helical details like major/minor grooves and crossover locations were not discernible in cryo-EM maps that we determined of DNA origami coated with oligolysine and PEG-oligolysine, whereas these features were visible in cryo-EM maps determined from the uncoated reference objects. Blunt-ended double-helical interfaces remained accessible underneath the coating and may be used for the formation of multimeric DNA origami assemblies that rely on stacking interactions between blunt-ended helices. The ionic strength requirements for forming multimers from coated DNA origami differed from those needed for uncoated objects. Using single-molecule mass photometry, we found that the mass of coated DNA origami objects prior to and after incubation in low ionic strength physiological conditions remained unchanged. This finding indicated that the coating effectively prevented strand dissociation but also that the coating itself remained stable in place. Our results validate oligolysine coatings as a powerful stabilization method for DNA origami but also reveal several potential points of failure that experimenters should watch to avoid working with false premises.
History
DepositionFeb 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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Assembly

Deposited unit
AA: SCAFFOLD STRAND
AB: STAPLE STRAND
AC: STAPLE STRAND
AD: STAPLE STRAND
AE: STAPLE STRAND
AF: STAPLE STRAND
AG: STAPLE STRAND
AH: STAPLE STRAND
AI: STAPLE STRAND
AJ: STAPLE STRAND
AK: STAPLE STRAND
AL: STAPLE STRAND
AM: STAPLE STRAND
AN: STAPLE STRAND
AO: STAPLE STRAND
AP: STAPLE STRAND
AQ: STAPLE STRAND
AR: STAPLE STRAND
AS: STAPLE STRAND
AT: STAPLE STRAND
AU: STAPLE STRAND
AV: STAPLE STRAND
AW: STAPLE STRAND
AX: STAPLE STRAND
AY: STAPLE STRAND
AZ: STAPLE STRAND
Aa: STAPLE STRAND
Ab: STAPLE STRAND
Ac: STAPLE STRAND
Ad: STAPLE STRAND
Ae: STAPLE STRAND
Af: STAPLE STRAND
Ag: STAPLE STRAND
Ah: STAPLE STRAND
Ai: STAPLE STRAND
Aj: STAPLE STRAND
Ak: STAPLE STRAND
Al: STAPLE STRAND
Am: STAPLE STRAND
An: STAPLE STRAND
Ao: STAPLE STRAND
Ap: STAPLE STRAND
Aq: STAPLE STRAND
Ar: STAPLE STRAND
As: STAPLE STRAND
At: STAPLE STRAND
Au: STAPLE STRAND
Av: STAPLE STRAND
Aw: STAPLE STRAND
Ax: STAPLE STRAND
Ay: STAPLE STRAND
Az: STAPLE STRAND
A0: STAPLE STRAND
A1: STAPLE STRAND
A2: STAPLE STRAND
A3: STAPLE STRAND
A4: STAPLE STRAND
A5: STAPLE STRAND
A6: STAPLE STRAND
A7: STAPLE STRAND
A8: STAPLE STRAND
A9: STAPLE STRAND
BA: STAPLE STRAND
BB: STAPLE STRAND
BC: STAPLE STRAND
BD: STAPLE STRAND
BE: STAPLE STRAND
BF: STAPLE STRAND
BG: STAPLE STRAND
BH: STAPLE STRAND
BI: STAPLE STRAND
BJ: STAPLE STRAND
BK: STAPLE STRAND
BL: STAPLE STRAND
BM: STAPLE STRAND
BN: STAPLE STRAND
BO: STAPLE STRAND
BP: STAPLE STRAND
BQ: STAPLE STRAND


Theoretical massNumber of molelcules
Total (without water)1,847,04079
Polymers1,847,04079
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA chain , 79 types, 79 molecules AAABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZAaAbAcAd...

#1: DNA chain SCAFFOLD STRAND


Mass: 887045.500 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain STAPLE STRAND


Mass: 10418.716 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain STAPLE STRAND


Mass: 14620.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain STAPLE STRAND


Mass: 10553.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain STAPLE STRAND


Mass: 12626.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain STAPLE STRAND


Mass: 12544.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain STAPLE STRAND


Mass: 10384.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#8: DNA chain STAPLE STRAND


Mass: 12936.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#9: DNA chain STAPLE STRAND


Mass: 8653.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#10: DNA chain STAPLE STRAND


Mass: 10225.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#11: DNA chain STAPLE STRAND


Mass: 12950.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#12: DNA chain STAPLE STRAND


Mass: 13027.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#13: DNA chain STAPLE STRAND


Mass: 13010.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#14: DNA chain STAPLE STRAND


Mass: 13171.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#15: DNA chain STAPLE STRAND


Mass: 15156.733 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#16: DNA chain STAPLE STRAND


Mass: 15062.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#17: DNA chain STAPLE STRAND


Mass: 8496.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#18: DNA chain STAPLE STRAND


Mass: 8528.485 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#19: DNA chain STAPLE STRAND


Mass: 12940.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#20: DNA chain STAPLE STRAND


Mass: 15842.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#21: DNA chain STAPLE STRAND


Mass: 15233.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#22: DNA chain STAPLE STRAND


Mass: 16036.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#23: DNA chain STAPLE STRAND


Mass: 12950.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#24: DNA chain STAPLE STRAND


Mass: 11535.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#25: DNA chain STAPLE STRAND


Mass: 9476.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#26: DNA chain STAPLE STRAND


Mass: 15065.694 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#27: DNA chain STAPLE STRAND


Mass: 12518.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#28: DNA chain STAPLE STRAND


Mass: 12894.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#29: DNA chain STAPLE STRAND


Mass: 12969.294 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#30: DNA chain STAPLE STRAND


Mass: 10515.767 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#31: DNA chain STAPLE STRAND


Mass: 12489.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#32: DNA chain STAPLE STRAND


Mass: 13030.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#33: DNA chain STAPLE STRAND


Mass: 8592.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#34: DNA chain STAPLE STRAND


Mass: 10400.704 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#35: DNA chain STAPLE STRAND


Mass: 15146.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#36: DNA chain STAPLE STRAND


Mass: 12835.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#37: DNA chain STAPLE STRAND


Mass: 18109.545 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#38: DNA chain STAPLE STRAND


Mass: 12951.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#39: DNA chain STAPLE STRAND


Mass: 12980.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#40: DNA chain STAPLE STRAND


Mass: 12986.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#41: DNA chain STAPLE STRAND


Mass: 8636.563 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#42: DNA chain STAPLE STRAND


Mass: 8598.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#43: DNA chain STAPLE STRAND


Mass: 12565.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#44: DNA chain STAPLE STRAND


Mass: 15904.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#45: DNA chain STAPLE STRAND


Mass: 14889.495 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#46: DNA chain STAPLE STRAND


Mass: 16091.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#47: DNA chain STAPLE STRAND


Mass: 16013.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#48: DNA chain STAPLE STRAND


Mass: 12799.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#49: DNA chain STAPLE STRAND


Mass: 13106.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#50: DNA chain STAPLE STRAND


Mass: 12942.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#51: DNA chain STAPLE STRAND


Mass: 12679.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#52: DNA chain STAPLE STRAND


Mass: 10792.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#53: DNA chain STAPLE STRAND


Mass: 12664.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#54: DNA chain STAPLE STRAND


Mass: 13916.889 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#55: DNA chain STAPLE STRAND


Mass: 10514.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#56: DNA chain STAPLE STRAND


Mass: 12609.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#57: DNA chain STAPLE STRAND


Mass: 12835.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#58: DNA chain STAPLE STRAND


Mass: 9448.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#59: DNA chain STAPLE STRAND


Mass: 8647.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#60: DNA chain STAPLE STRAND


Mass: 10323.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#61: DNA chain STAPLE STRAND


Mass: 10496.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#62: DNA chain STAPLE STRAND


Mass: 13043.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#63: DNA chain STAPLE STRAND


Mass: 10664.894 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#64: DNA chain STAPLE STRAND


Mass: 13718.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#65: DNA chain STAPLE STRAND


Mass: 10907.027 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#66: DNA chain STAPLE STRAND


Mass: 8606.558 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#67: DNA chain STAPLE STRAND


Mass: 8658.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#68: DNA chain STAPLE STRAND


Mass: 12518.994 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#69: DNA chain STAPLE STRAND


Mass: 10735.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#70: DNA chain STAPLE STRAND


Mass: 12993.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#71: DNA chain STAPLE STRAND


Mass: 13095.507 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#72: DNA chain STAPLE STRAND


Mass: 13926.958 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#73: DNA chain STAPLE STRAND


Mass: 9541.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#74: DNA chain STAPLE STRAND


Mass: 12860.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#75: DNA chain STAPLE STRAND


Mass: 15077.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#76: DNA chain STAPLE STRAND


Mass: 12664.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#77: DNA chain STAPLE STRAND


Mass: 12860.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#78: DNA chain STAPLE STRAND


Mass: 10392.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#79: DNA chain STAPLE STRAND


Mass: 11387.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: B-brick bare in 5 mM Mg2+ / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 10.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42209 / Symmetry type: POINT

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