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

2018

[55] J. Y. Kishi, B. J. Beliveau, S. W. Lapan, E. R. West, A. Zhu, H. M. Sasaki, S. K. Saka, Y. Wang, C. L. Cepko*, P. Yin*
SABER enables highly multiplexed and amplified detection of DNA and RNA in cells and tissues
bioRxiv, posted August 27, 2018. DOI: 10.1101/401810 [PDF]
[Supplementary Information]
[Supplementary Table1: experimental conditions]
[Supplementary Table2: detected puncta counts]
[Supplementary Table3: list of sequences]

[54] G. Nir, I. Farabella, C. Perez Estrada, C.G. Ebeling, B.J. Beliveau, H.M. Sasaki, S.H. Lee, S. Nguyen, R.B. McCole, S. Chattoraj, J. Erceg, J. AlHaj Abed, N.C. Martins, H.Q. Nguyen, M.A. Hannan, S. Russell, N.C. Durand, S.P. Rao, J.Y. Kishi, P. Soler-Vila, M. Di Pierro, J.N. Onuchic, S. Callahan, J. Schreiner, J. Stuckey*, P. Yin*, E. Lieberman Aiden*, M.A. Marti-Renom*, C.T. Wu*
Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling
bioRxiv, posted July 28, 2018.
DOI: 10.1101/374058 [PDF] [Supplementary Movie1] [Supplementary Movie2]

[53] X. Qi, F. Zhang, Z. Su, S. Jiang, D. Han, B. Ding, Y. Liu, W. Chiu, P. Yin, H. Yan
Programming molecular topologies from single-stranded nucleic acids
Nature Communications, 9, Article number: 4579 (2018)
DOI: 10.1038/s41467-018-07039-7 [PDF] [Supplementary Information]

[52] W. Xu, P. Yin*, M. Dai*
Super-resolution geometric barcoding for multiplexed miRNA profiling
Angewandte Chemie, Accepted Article, September 5, 2018.
DOI: 10.1002/ange.201807956 [PDF] [Supplementary Information]

[51] T. Lin, J. Yan, L. L. Ong, J. Robaszewski, H. D. Lu, Y. Mi, P. Yin*, and B. Wei*
Hierarchical assembly of DNA nanostructures based on four-way toehold-mediated strand displacement
Nano Lett., 2018, 18 (8), pp 4791-4795
DOI: 10.1021/acs.nanolett.8b01355 [PDF] [Supplementary Information]

[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, March 6, 2018. 115 (10) E2183-E2192
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, 2018, 57 (6), pp 883-885
DOI: 10.1021/acs.biochem.7b01072 [PDF]


2017

[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]


2016

[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]


2015

[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]


2014

[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]


2013

[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.

2012

[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]


2008

[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.