Publications from the Molecular Systems Lab    Dept. Systems Biology Harvard Medical School Wyss Institute for Biologically Inspired Engineering


[50] B. J. Beliveau, J. Y. Kishi, G. Nir, H. M. Sasaki, S. K. Saka, S. C. Nguyen, C.-t. Wu, and P. Yin
OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes
Proc Natl Acad Sci USA, published ahead of print (2018).
DOI: 10.1073/pnas.1714530115 [PDF] [Supplementary Information] [Supplementary Dataset1] [Supplementary Dataset2]

[49] J. Kim, P. Yin*, and A. A. Green*
Ribocomputing: Cellular Logic Computation Using RNA Devices
Biochemistry, Article ASAP DOI: 10.1021/acs.biochem.7b01072 [PDF]


[48] D. Han, X. Qi, C. Myhrvold, B. Wang, M. Dai, S. Jiang, M. Bates, Y. Liu, B. An*, F. Zhang*, H. Yan* and P. Yin*
Single-stranded DNA and RNA origami
Science Vol. 358, Issue 6369, eaao2648 (2017) DOI: 10.1126/science.aao2648 [PDF] [Supplementary Materials] [Supplementary Movies]

[47] L. L. Ong, N. Hanikel, O. K. Yaghi, C. Grun, M. T. Strauss, P. Bron, J. Lai-Kee-Him, F. Schueder, B. Wang, P. Wang, J. Y. Kishi, C.A. Myhrvold, A. Zhu, R. Jungmann, G. Bellot*, Y. Ke*, and P. Yin*
Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components
Nature 552, 72 (2017) doi: 10.1038/nature24648 [PDF] [Supplementary Materials] [Supplementary Data] [Supplementary Movies: SV1, SV2, SV3] [Software: info page, software link] [PhD Thesis: Luvena Ong, 2016]

[46] F. Schueder, J. Lara-Guiterrez, B. Beliveau, S. Saka, H. Sasaki, J. Woehrstein, M. Strauss, H. Grabmayr, P. Yin*, and R. Jungmann*
Multiplexed 3D super-resolution imaging of whole cells using spinning disk confocal microscopy and DNA-PAINT
Nature Communications 8, Article number: 2090 (2017) doi:10.1038/s41467-017-02028-8 [PDF] [Supplementary Materials] [Peer Review File] [Description of Additional Supplementary Files] [Supplementary Movies: 1, 2, 3] [Supplementary Data: 1, 2, 3, 4]

[45] J. Kishi, T. Schaus, N. Gopalkrishnan, F. Xuan, and P. Yin
Programmable autonomous synthesis of single-stranded DNA
Nature Chemistry Advanced Online Publication (2017) doi: 10.1038/nchem.2872 [PDF] [Supplementary Materials]

[44] T. E. Schaus, S. Woo, F. Xuan, X. Chen and P. Yin
A DNA nanoscope via auto-cycling proximity recording
Nature Communications 8, Article number: 696 (2017) doi:10.1038/s41467-017-00542-3 [PDF] [Supplementary Materials]

[43] B. J. Beliveau, A. N. Boettiger, G. Nir, B. Bintu, P. Yin*, X. Zhuang*, C.-t Wu*
In situ super-resolution imaging of genomic DNA with OligoSTORM and OligoDNA-PAINT
In: Erfle H. (eds) Super-Resolution Microscopy.
Methods in Molecular Biology, vol 1663. Humana Press, New York, NY doi:10.1007/978-1-4939-7265-4_19 [PDF]

[42] J. L. Werbin, M. S. Avendano, V. Becker, R. Jungmann, P. Yin*, G. Danuser* and P. K. Sorger*
Multiplexed Exchange-PAINT imaging reveals ligand-dependent EGFR and Met interactions in the plasma membrane
Scientific Reports 7, Article number: 12150 (2017) doi:10.1038/s41598-017-12257-y [PDF] [Supplementary Materials]

[41] A. A. Green, J. Kim, D. Ma, P. A. Silver, J. J. Collins and P. Yin
Complex cellular logic computation using ribocomputing devices
Nature (2017) doi:10.1038/nature23271 [PDF] [Supplementary Materials]

[40] J. B. Woehrstein, M. T. Strauss, L. L. Ong, B. Wei, D. Y. Zhang, R. Jungmann* and P. Yin*
Sub-100-nm metafluorophores with digitally tunable optical properties self-assembled from DNA
Science Advances Vol. 3, no. 6, e1602128, doi: 10.1126/sciadv.1602128 [PDF] [Supplementary Materials]

[39] Y. Wang, J. B. Woehrstein, N. Donoghue, M. Dai, M. S. Avendano, R. C.J. Schackmann, J. Zoeller, S. S. H. Wang, P. W. Tillberg, D. Park, S. W. Lapan, E. S. Boyden, J. S. Brugge, P. S. Kaeser, G. M. Church, S. S. Agasti*, R. Jungmann*, P. Yin*
Rapid sequential in situ multiplexing with DNA-Exchange-Imaging in Neuronal Cells and Tissues
Nano Letters Article ASAP, DOI: 10.1021/acs.nanolett.7b02716 [PDF] [bioRxiv] [Supplementary Materials] [Supplementary Movie] [Supplementary Movie Caption]

  • See a data video:

[38] F. Schueder, M. T. Strauss, D. Hoerl, J. Schnitzbauer, T. Schlichthaerle, S. Strauss, P. Yin, H. Harz, H. Leonhardt and R. Jungmann
Universal super-resolution multiplexing by DNA exchange
Angewandte Chemie 2017, Early View, doi: 10.1002/anie.201611729 [PDF] [Supplementary Materials] [Supplementary Movie]

[37] S. S. Agasti, Y. Wang, F. Schueder, A. Sukumar, R. Jungmann* and P. Yin*
DNA-barcoded labeling probes for highly multiplexed Exchange-PAINT imaging
Chem. Sci. 2017, Advance Article, doi: 10.1039/C6SC05420J [PDF] [Supplementary Materials]

[36] C. Myhrvold, M. Baym, N. Hanikel, L. L. Ong, J. S. Gootenberg and P. Yin
Barcode extension for analysis and reconstruction of structures
Nature Communications 8, Article number: 14698 (2017) doi:10.1038/ncomms14698 [PDF] [Supplementary Materials] [Supplementary Data]

[35] P. Zhan, P. K. Dutta, P. Wang, G. Song, M. Dai, S-X Zhao, Z-G Wang, P. Yin, W. Zhang, B. Ding, and Y. Ke
Reconfigurable three-dimensional gold nanorod plasmonic nanostructures organized on DNA origami tripod
ACS Nano 2017, 11 (2), pp 1172-1179 [PDF] [Supplementary Materials]

[34] C. Tian, H. Kim, W. Sun, Y. Kim, P. Yin, and H. Liu
DNA nanostructures-mediated molecular imprinting lithography
ACS Nano 2017, 11 (1), pp 227-238. [PDF] [Supplementary Materials]


[33] M. Dai, R. Jungmann and P. Yin
Optical imaging of individual biomolecules in densely packed clusters
Nature Nanotechnology, 11, 798-807 (2016), doi:10.1038/nnano.2016.95 [PDF]
[Supplementary Information: S1, Supplementary Table: S2]

[32] R. Jungmann, M. S. Avendano, M. Dai, J. B. Woehrstein, S. S. Agasti, Z. Feiger, A. Rodal and P. Yin
Quantitative super-resolution imaging with qPAINT
Nature Methods, 13, 439-442 (2016), doi:10.1038/nmeth.3804 [PDF]
[Supplementary Materials: S1, Supplementary Videos: V1, V2]

[31] J. Elbaz, P. Yin, and C. Voigt
Genetic encoding of DNA nanostructures and their self-assembly in living bacteria
Nature Communications, 7, Article number: 11179 doi:10.1038/ncomms11179. [PDF] [Supplementary Materials]

[30] F. Zhou, W. Sun, K. B. Ricardo, D. Wang, J. Shen, P. Yin, and H. Liu
Programmably-shaped carbon nanostructure from shape-conserving carbonization of DNA
ACS Nano, 2016, 10 (3), pp 3069-3077, DOI: 10.1021/acsnano.5b05159. [PDF] [Supplementary Materials]


[29] J. B. Knudsen, L. Liu, A. L. B. Kodal, M. Madsen, Q. Li, J. Song, J. B. Woehrstein, S. F. Wickham, M. T. Strauss, F. Schueder, J. Vinther, A. Krissanaprasit, D. Gudnason, A. A. A. Smith, R. Ogaki, A. N. Zelikin, F. Besenbacher, V. Birkedal, P. Yin, W. M. Shih, R. Jungmann, M. Dong and K. V. Gothelf
Routing of individual polymers in designed patterns
Nature Nanotechnology 10, 892-898 (2015). [PDF] [Supplementary Materials]

[28] M. B. Scheible, L. L. Ong, J. B. Woehrstein, R. Jungmann, P. Yin and F. C. Simmel
A compact DNA cube with side length 10 nm
Small 11: 5200-5205 (2015). [PDF] [Supplementary Materials]

[27] C. Grun, J. Werfel, D. Y. Zhang, and P. Yin
DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology
J. R. Soc. Interface 12: 20150580 (2015). [PDF] [Supplementary Materials]

[26] B. J. Beliveau, A. N. Boettiger, M. S. Avendano, R. Jungmann, R. B. McCole, E. F. Joyce, C. Kim-Kiselak, F. Bantignies, C. Y. Fonseka, J. Erceg, M. A. Hannan, H. G. Hoang, D. Colognori, J. T. Lee, W. M. Shih, P. Yin, X. Zhuang & C. Wu
Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes
Nature Communications 6, 7147 (2015). [PDF] [Supplementary Materials]

[25] B. Wei, M. K. Vhudzijena, J. Robaszewski, P. Yin
Self-assembly of complex two-dimensional shapes from single-stranded DNA tiles
J. Vis. Exp. 99, e52486, doi:10.3791/52486 (2015). [link] [Materials List]


[24] W. Sun, E. Boulais, Y. Hakobyan, W. Wang, A. Guan, M. Bathe*, P. Yin*
Casting inorganic structures with DNA molds
Science 346:1258361 (2014). [PDF] [Supplementary Materials]

[23] K. Pardee, A.A. Green, T. Ferrante, E. Cameron, A. DaleyKeyser, P. Yin, and J.J. Collins
Paper-based synthetic gene networks
Cell159:940-954 (2014). [PDF], [Supplementary Materials: S1, Supplementary Data: S1, S2]

[22] A.A. Green, P.A. Silver, J.J. Collins, P. Yin
Toehold switches: de-novo-designed regulators of gene expression
Cell 159: 925-939 (2014). [PDF], [Supplementary Materials: S1, S2, Supplementary Tables: S1, S2, S3, S4, S5, S6, S7]

[21] Y. Ke, L.L. Ong, W. Sun, J. Song, M. Dong, W.M. Shih, P. Yin
DNA brick crystals with prescribed depths
Nature Chemistry 6:994-1002 (2014). [PDF], [Supplementary Materials: S1, S2, S3]

[20] Z. Jin, W. Sun, P. Yin, M. Strano
Nanolithography based on metalized DNA templates for graphene patterning
Current Protocols in Chemical Biology 6:53-64 (2014).

[19] B. Wei, L.L. Ong, J. Chen, A. Jaffe, P. Yin
Complex reconfiguration of DNA nanostructures
Angewandte Chemie 126:7605-7609 (2014). [PDF] [Supplementary Materials]

[18] R. Iinuma, Y. Ke, R. Jungmann, T. Schlichthaerle, J.B. Woehrstein, P. Yin
Polyhedra self-assembled from DNA tripods and characterized with 3D DNA-PAINT
Science 344:65-69 (2014). [PDF] [Supplementary Materials] [Movie 1] [Movie 2]

[17] J. Sadowski, C.R. Calvert, D.Y. Zhang, N.A. Pierce, P. Yin
Developmental self-assembly of a DNA tetrahedron
ACS Nano DOI: 10.1021/nn4038223 (2014). [PDF] [Supplementary Materials]

[16] J. Wu, D. Zhang, P. Yin, F. Vollmer
Ultraspecific and highly sensitive nucleic acid detection by integrating a DNA catalytic network with a label-free microcavity
Small DOI: 10.1002/smll.201303558 (2014).[PDF] [Supplementary Materials]

[15] R. Jungmann, M.S. Avendano, J.B. Woehrstein, M. Dai, W.M. Shih, P. Yin
Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT
Nature Methods11(3):313-318 (2014). [PDF] [Supplementary Materials]


[14] B. Wei, M. Dai, C. Myhrvold, Y. Ke, R. Jungmann, P. Yin
Design space for complex DNA structures
J. Am. Chem. Soc. 135 (48):18080-8 (2013). [PDF], [Supplementary Materials: S1, S2]

[13] L. Hochrein, M. Schwarzkopf, M. Shahgholi, P. Yin, N. Pierce
Conditional Dicer substrate formation via shape and sequence transduction with small conditional RNAs
J. Am. Chem. Soc. 135 (46):17322-30, (2013). [PDF], [Supplementary Materials]

[12] H. Qi, M. Ghodousi, Y. Du, C. Grun, H. Bae, P. Yin*, A. Khademhosseini*.
DNA-directed self-assembly of shape-controlled hydrogels
Nature Communications 4, 2275 (2013). [PDF], [Supplementary Materials]

[11] C. Myhrvold, M. Dai, P.A. Silver, P. Yin.
Isothermal self-assembly of complex DNA structures under diverse and biocompatible conditions
Nano Letters 13(9): 4242-8 (2013). [PDF], [Supplementary Materials: S1, S2]

  • See abstract and summary figure here.

[10] T.E. Schaus, P. Yin.
Molecular computing: In situ computation of cell identity (News and Views)
Nature Nanotechnolgy 155, 546-8 (2013). [PDF]

[9] S. Surwade, F. Zhou, B. Wei, W. Sun, A. Powell, C. O'Donnell, P. Yin*, H. Liu*
Nanoscale growth and patterning of inorganic oxides using DNA nanostructure templates
J. Am. Chem. Soc. 135, 6778-6781 (2013). [PDF] [Supporting Material]

  • See abstract and summary figure here.

[8] Z. Jin, W. Sun, Y. Ke, C.-J. Shih, G. L.C. Paulus, Q. H. Wang, B. Mu, P. Yin*, M. S. Strano*
Metalized DNA nanolithography for encoding and transferring spatial information for graphene patterning
Nature Communications 4, 1663 (2013). [PDF] [Supporting Material]

[7] D. Woods, H.L. Chen, S. Goodfriend, N. Dabby, E. Winfree, P. Yin
Active self-assembly of algorithmic shapes and patterns in polylogarithmic time
Proceedings of the 4th conference on Innovations in Theoretical Computer Science (ITCS) 353-354 (2013). [PDF]. Full article preprint on arXiv arXiv:1301.2626v1. [PDF]

  • See abstract and summary figure here.


[6] Y. Ke, L. Ong, W. Shih, P. Yin
Three-dimensional structures self-assembled from DNA bricks
Science 338, 1177-1183 (2012). [PDF] [Supporting Material]

[5] C. Lin, R. Jungmann, A.M. Leifer, C. Li, D. Levner, G.M. Church, W. Shih*, P. Yin*
Sub-micrometer geometrically encoded fluorescent barcodes self-assembled from DNA
Nature Chemistry 4, 832-839 (2012). [PDF] [Supporting Material]

[4] B. Wei, M. Dai and P. Yin
Complex shapes self-assembled from single-stranded DNA tiles
Nature 485, 623-626 (2012). [PDF] [Supporting material: S1-5, S6, S7, S8]

[3] D.Y. Zhang, S.X. Chen, and P. Yin
Optimizing the specificity of nucleic acid hybridization
Nature Chemistry 4, 208-14 (2012). [PDF] [Supporting material]


[2] P. Yin, R.F. Hariadi, S. Sahu, H.M.T. Choi, S.H. Park, T.H. LaBean, J.H. Reif
Programming DNA tube circumferences
Science 321, 824-826 (2008). [PDF] [Supporting material]

[1] P. Yin, H.M.T. Choi, C.R. Calvert, N.A. Pierce
Programming biomolecular self-assembly pathways
Nature 451, 318-322 (2008). [PDF] [Supporting material]

Old publications (2005 and before) can be found here.