Crystals, resolution and self-assembly - Department of Chemistry ...

Crystals, Resolution and Self-Assembly of DNA Nadrian C. Seeman Department of Chemistry New York University New York, NY 10003, USA ned.seeman@nyu.edu X-ray Crystallography Workshop New York University October 25, 2012

DNA Is a Nanoscale Object DNA BASE PAIRSAT3.4 ÅHHCNCNCHOCCCH 3B-DNA RNCNNCHHNOCCNRHGCHHCNCCOHNCCHRNCNCNHNCNCHNHORH~20 Å

Design of Immobile Branched Junctions: Minimize Sequence Symmetry Seeman, N.C. (1982), J. Theor.Biol. 99, 237-247.

C5-Arm, 6-Arm, 8-Arm and 12-Arm Junctions I IIG •CG •CT •AT •AC • GA • TG •CC • GC • GG • CC • GA • TCG • CG • •AG GA • TT• CT A • •T A G • T• CT • AG • C1 5AG • AG T • • T CT • T • AC• GC • GC G • • A CG • TC • C• CC•GA C • CT • • AA G • GG A • G CG • C• TT • G• • TC G •• AC TAA2 T 4C• AG •G •C G •A CC•G• G T• T• CACA•T •G 3AA•T• C T• C• GG GG • C •A C••G TC G••A TT •CT • AC•C G • GCG • A•TT A• CG•G A •G• CG •C•CGIIII VVIG •CG •CT •AT •AC • GA•TG •CC • GI I CC • GG • • C AG • CG• T•VIGAGT • C•C • GAG • CTG T • • C• CA • TA CG • ATG T •• GA • TT • C AT • •G A •G • TA1 T •C • CC • CC • G 6C A •A • CACG • GT • GG • C C • GA • GG • TC • TT •G •• A• TACA25T GG •• CA • AC • AG • CG •C •• TC • G T • GGC C•A • G C • GC • TC • CG G TA • 3 G•C 4A • GG • AG • CC • GT •C •T • A C TA•TT • AC • CA•TT • TT • GG • AG • AT•AA • GC • AT •G•CC G• C•GCC•GIIIVC G•A•TC•GC G•A • TC • GG• CC•GI VJYL5GJYL6GWang, Y., Mueller, J.E., Kemper, B. & Seeman, N.C. (1991), Biochemistry 30, 5667-5674. Wang, X. & Seeman, N.C. (2007), J. Am. Chem. Soc. 129, 8169-8176.

Sticky-Ended Cohesion: Smart Affinity

Sticky-Ended Cohesion: Structure Qiu, H., Dewan, J.C. & Seeman, N.C. (1997) J. Mol. Biol. 267, 881-898.

The Central Concept of Structural DNA Nanotechnology: Combine Branched DNA with Sticky Ends toMake Objects, Lattices and Devices B 'B'B 'AA'AA'BAA'BBSeeman, N.C. (1982), J. Theor.Biol. 99, 237-247.

OBJECTIVES AND APPLICATIONS FOR OUR LABORATORY ARCHITECTURAL CONTROL AND SCAFFOLDING [1] MACROMOLECULAR CRYSTALLIZATION (PERIODIC IN 2D AND 3D). [2] NANOELECTRONICS ORGANIZATION (PERIODIC IN 2D AND 3D). [3] DNA-BASED COMPUTATION (APERIODIC IN 2D OR 3D). [4] CONTROL OF POLYMER AND MATERIALS COMPOSITION & TOPOLOGY. NANOMECHANICAL DEVICES [1] NANOROBOTICS. [2] NANOFABRICATION. SELF-REPLICABLE SYSTEMS

CURRENT CRYSTALLIZATION PROTOCOLGUESS CONDITIONSDO CRYSTALLOGRAPHYSET UP CRYSTALSPRAY FOR CRYSTALSCRYSTALS?YESNOCHANGE DEITIESGUESS NEW CONDITIONS

A Suggestion for Producing Macromolecular Crystals Seeman, N.C. (1982), J. Theor.Biol. 99, 237-247.

Polyhedral Catenanes Cube: Junghuei Chen

Cube.. Chen, J. & Seeman. N.C. (1991), Nature 350, 631-633..

STRUCTURALASSEMBLIES

ConstructionofCrystallineArrays

REQUIREMENTS FOR LATTICE DESIGN COMPONENTS PREDICTABLE INTERACTIONS PREDICTABLE LOCAL PRODUCT STRUCTURES STRUCTURAL INTEGRITY

DX Isomers Fu, T.-J. & Seeman, N.C. (1993), Biochemistry 32, 3211-3220. Li, X., Yang, X.,Qi, J. & Seeman, N.C. (1996),J. Am. Chem. Soc. 118, 6121-6130. Sa-Ardyen, P., Vologodskii, A.V. & Seeman, N.C. (2003), Biophysical Journal 84, 3829-3837.

2D DX Arrays Erik Winfree (Caltech) Furong Liu Lisa Wenzler

Schematic of a Lattice Containing 1 DX Tile and 1 DX+J Tile 16 nm 16 nm

AFM of a Lattice Containing 1 DX Tile and 1 DX+J Tile Winfree, E., Liu, F., Wenzler, L.A. & Seeman, N.C. (1998), Nature 394, 539-544.

Schematic of a Lattice Containing3 DX Tiles and 1 DX+J Tile

AFM of a Lattice Containing 3 DX Tiles and 1 DX+J Tile Winfree, E., Liu, F., Wenzler, L.A. & Seeman, N.C. (1998), Nature 394, 539-544.

AFM Resolution~70 Å on a Good Day

Three-DimensionalSelf-Assembled Arrays:DESIGNED CRYSTALS! Jianping Zheng, Jens J. Birktoft, Yi Chen (Purdue),Tong Wang, Ruojie Sha, Pam Constantinou, Steve Ginell (Argonne), Chengde Mao (Purdue) Diffraction Data Collected at Brookhaven National Laboratory (NSLS) and Argonne National Laboratory (APS)

A 3D DNA Tensegrity Triangle [D.Liu, M. Wang, Z. Deng, R. Walulu & C.Mao, J. Am. Chem. Soc. 126, 2324-2325 (2004)] X-Ray Diffraction: Predicted Spacings and Rhombohedral Symmetry Resolution: ~10Å Designed 142 A Edges

The Tensegrity Triangle Motif

A Small Threefold Pseudosymmetric DNA Tensegrity Triangle J. Zheng, J.J. Birktoft, Y. Chen, T. Wang, R. Sha,P.E. Constantinou, S.L. Ginell, C. Mao & N.C. Seeman, Nature 461, 74-77 (2009).

Crystal Images J. Zheng, J.J. Birktoft, Y. Chen, T. Wang, R. Sha,P.E. Constantinou, S.L. Ginell, C. Mao & N.C. Seeman, Nature 461, 74-77 (2009).

Crystal Structure of the 2-Turn DNA Tensegrity Triangle J. Zheng, J.J. Birktoft, Y. Chen, T. Wang, R. Sha,P.E. Constantinou, S.L. Ginell, C. Mao & N.C. Seeman, Nature 461, 74-77 (2009).

4 Å Map Perpendicular to a Helix J. Zheng, J.J. Birktoft, Y. Chen, T. Wang, R. Sha,P.E. Constantinou, S.L. Ginell, C. Mao & N.C. Seeman, Nature 461, 74-77 (2009).

Environment of a Single Triangle J. Zheng, J.J. Birktoft, Y. Chen, T. Wang, R. Sha,P.E. Constantinou, S.L. Ginell, C. Mao & N.C. Seeman, Nature 461, 74-77 (2009).

The Rhombohedral Cavity J. Zheng, J.J. Birktoft, Y. Chen, T. Wang, R. Sha,P.E. Constantinou, S.L. Ginell, C. Mao & N.C. Seeman, Nature 461, 74-77 (2009).

Mono View Down 3-Fold Axis R3; a = 68.28 Å; α = 102.44˚ Image Courtesy of David Goodsell J. Zheng, J.J. Birktoft, Y. Chen, T. Wang, R. Sha,P.E. Constantinou, S.L. Ginell, C. Mao & N.C. Seeman, Nature 461, 74-77 (2009).

J. Zheng, J.J. Birktoft, Y. Chen, T. Wang, R. Sha,P.E. Constantinou, S.L. Ginell, C. Mao & N.C. Seeman, Nature 461, 74-77 (2009).

5 Å Calculated Map Perpendicular to a Helix J. Zheng, J.J. Birktoft, Y. Chen, T. Wang, R. Sha,P.E. Constantinou, S.L. Ginell, C. Mao & N.C. Seeman, Nature 461, 74-77 (2009).

10 Å Calculated Map J. Zheng, J.J. Birktoft, Y. Chen, T. Wang, R. Sha,P.E. Constantinou, S.L. Ginell, C. Mao & N.C. Seeman, Nature 461, 74-77 (2009).

Movie Courtesy of Kevin Drew

A Two-Turn Tensegrity Triangle Designed Lattice with Two Components Tong Wang Ruojie Sha Jens Birktoft Jianping Zheng Chengde Mao (Purdue)

Movie of the Rhombohedral Cavity T.Wang, R. Sha, J.J. Birktoft, J. Zheng, C. Mao, N.C. Seeman, J. Am. Chem. Soc., in press (2010).

Covalent Attachment of Fluorescent Dyes to One or Two Triangles in the A•B Crystal Ruojie Sha

Attachment of Cy3 & Cy5 to Triangles T.Wang, R. Sha, J.J. Birktoft, J. Zheng, C. Mao, N.C. Seeman, J. Am. Chem. Soc., 132, 15471-15473 (2010).

Only Watson-Crick Pairs (No Tertiary Interactions) in Designed 3D DNA Crystals Nam Nguyen, Jianping Zheng, Jens J. Birktoft,Yi Chen (Purdue), Tong Wang, Ruojie Sha,Pam Constantinou, Steve Ginell (Argonne),Chengde Mao (Purdue) Diffraction Data Collected at Brookhaven National Laboratory (NSLS)

THE ISSUE:The Self-Assembled Designed3D Crystal Structure of aDNA Tensegrity Triangle SuperficiallyResembles a Duplex Whose CrystalStructure Coheres byTertiary Interactions Involving Cytosine.Are Tertiary Interactions Key in theDesigned DNA Crystal?

Stereoscopic View of 3D Self-Assembled Designed DNA Crystals J. Zheng, J.J. Birktoft, Y. Chen, T. Wang, R. Sha,P.E. Constantinou, S.L. Ginell, C. Mao & N.C. Seeman, Nature 461, 74-77 (2009).

Non-Denaturing Gel Showing Integrity of Triangle (Lanes 5, 6, 7) at Low Concentrations in Contrast to Duplex (Lanes 2, 3, 4) thatCoheres by Tertiary Interactions N. Nguyen, J.J. Birktoft, R. Sha, T. Wang, J. Zheng, P.E. Constantinou, S.L. Ginell, Y. Chen, C. Mao & N.C. Seeman, J. Mol. Recognition 25, 234-237 (2012).

Triangle Lacking the Cytosine Critical for Tertiary Interactions (CG Pair Replaced by TA) N. Nguyen, J.J. Birktoft, R. Sha, T. Wang, J. Zheng, P.E. Constantinou, S.L. Ginell, Y. Chen, C. Mao & N.C. Seeman, J. Mol. Recognition 25, 234-237 (2012).

Crystal Structure of the Triangle Lacking theCytosine Critical for Tertiary Interactions in Stereoscopic Projection N. Nguyen, J.J. Birktoft, R. Sha, T. Wang, J. Zheng, P.E. Constantinou, S.L. Ginell, Y. Chen, C. Mao & N.C. Seeman, J. Mol. Recognition 25, 234-237 (2012).

THE CONCLUSION:The Designed Self-Assembled 3DDNA Crystal is Only Held Together byProgrammable Watson-Crick BasePairing. Tertiary Interactions AreNot Involved.

Organizing 5 and 10 nmGold NanoparticlesJiwen ZhengPam ConstantinouChristine Micheel (Berkeley)Paul Alivisatos (Berkeley)Rick Kiehl (Minnesota)

The 3D-DX Triangle: A DX Version of the Tensegrity 3D Triangle J. Zheng, P.E. Constantinou, C. Micheel, A.P. Alivisatos, R.A. Kiehl & N.C. Seeman, NanoLetters 6, 1502-1504 (2006).

YZ 2D Array of 3D-DX Triangle One Tile Two Tiles J. Zheng, P.E. Constantinou, C. Micheel, A.P. Alivisatos, R.A. Kiehl & N.C. Seeman, NanoLetters 6, 1502-1504 (2006).

Attachment of a Nanoparticle to the 3D-DX Motif J. Zheng, P.E. Constantinou, C. Micheel, A.P. Alivisatos, R.A. Kiehl & N.C. Seeman, NanoLetters 6, 1502-1504 (2006).

Two Motifs Can Organize Nanoparticles J. Zheng, P.E. Constantinou, C. Micheel, A.P. Alivisatos, R.A. Kiehl & N.C. Seeman, NanoLetters 6, 1502-1504 (2006).

Organized 5 nm and 10 nm Particles J. Zheng, P.E. Constantinou, C. Micheel, A.P. Alivisatos, R.A. Kiehl & N.C. Seeman, NanoLetters 6, 1502-1504 (2006).

Extending NanoparticleOrganization to 3DSymmetric and AsymmetricCovalent Gold-11 and Gold-55Xinshuai ZhaoRuojie ShaJens BirktoftChengde Mao

Schematic Views of Gold NanoparticlesOrganized within the Triangle LatticeAsymmetric Symmetric

Anomalous Difference Fourier Maps ofGold-11 Nanoparticles in the Triangle LatticeAsymmetric Symmetric Occupancy ~27% Occupancy ~26%

Anomalous Difference Fourier Maps ofGold-55 Nanoparticles in the Triangle LatticeAsymmetric Symmetric Occupancy ~48% Occupancy ~41%

FrustrationGautham’s 2.5 ÅSelf-Assembled (2+1) D CrystalS. Venkadesh, P.K. Mandal, N. Gautham , B.B.R.C. 407, 548-551 (2011).

Gautham’s Design S. Venkadesh, P.K. Mandal, N. Gautham , B.B.R.C. 407, 548-551 (2011).

Gautham’s 2.5 Å Structure S. Venkadesh, P.K. Mandal, N. Gautham , B.B.R.C. 407, 548-551 (2011).

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