Publications

Li S, Zheng EB, Zhao L, Liu S#. (2019) Nonreciprocal and conditional cooperativity directs the pioneer activity of pluripotency transcription factors. Cell Reports 28:2689-2703.
 
Wasserman MR*, Schauer GD*, O'Donnell ME#, Liu S#. (2019) Replication fork activation is enabled by a single-stranded DNA gate in CMG helicase. Cell 178:600—611.
 
Ju X, Li D, Liu S#. (2019) Full-length RNA profiling reveals pervasive bidirectional transcription terminator in bacteria. Nature Microbiology 4:.
 
Wasserman MRLiu S#. (2019) A tour de force on the double helix: Exploiting DNA mechanics to study DNA-based molecular machines. Biochemistry 58:4667. Review.
 
Wang L, Mo CY, Wasserman MR, Rostol JT, Marraffini LA, Liu S#. (2019) Dynamics of Cas10 govern discrimination between self and non-self in type III CRISPR-Cas immunity. .
 
Liu S*, Chistol G*, Hetherington CL*, Tafoya S, Aathavan K, Schnitzbauer J, Grimes S, Jardine PJ, Bustamante C. (2014) A viral packaging motor varies its DNA rotation and step size to preserve subunit coordination as the capsid fills. Cell 157:702—713.

Liu S*, Chistol G*, Bustamante C. (2014) Mechanical operation and intersubunit coordination of ring-shaped molecular motors: insights from single-molecule studies. Biophys. J. 106:1844—1858. Review.
PDF

Dangkulwanich M*, Ishibashi T*, Liu S*, Kireeva ML, Lubkowska L, Kashlev M, Bustamante C. (2013) Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism. eLife 2:e00971.
PDF
eLife Insight: “On the move”

Chistol G*, Liu S*, Hetherington CL, Moffitt JR, Grimes S, Jardine PJ, Bustamante C. (2012) High degree of coordination and division of labor among subunits in a homomeric ring ATPase. Cell 151:1017—1028.
PDF
F1000Prime Recommendation

Liu S*, Harada BT*, Miller JT, Le Grice SF, Zhuang X. (2010) Initiation complex dynamics direct the transitions between distinct phases of early HIV reverse transcription. Nat. Struct. Mol. Biol. 17:1453—1460.
PDF

Liu S, Abbondanzieri EA, Rausch JW, Le Grice SF, Zhuang X. (2008) Slide into action: dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates. Science 322:1092—1097.
PDF
Science Perspective: “RT slides home…”
HHMI News: “An HIV enzyme with a flair for the acrobatic”
C&EN News: “Acrobatic HIV enzyme caught in action”

Liu S, Bokinsky G, Walter NG, Zhuang X. (2007) Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic “fingerprinting”. Proc. Natl. Acad. Sci. USA 104:12634—12639.
PDF

Zheng Q, Omans ND, Leicher R, Osunsade A, Agustinus AS, Finkin-Groner E, D’Ambrosio H, Liu B, Chandariapaty S, Liu S, David Y. (2019) Reversible histone glycation is associated with disease-related changes in chromatin architecture. Nat. Commun. 10:1289.
PDF

Tafoya S, Large SJ, Liu S, Bustamante C, Sivak DA. (2019) Using a system’s equilibrium behavior to reduce its energy dissipation in nonequilibrium processes. Proc. Natl. Acad. Sci. USA 116:5920—5924.
PDF

Tafoya S, Liu S, Castillo JP, Atz R, Morais MC, Grimes S, Jardine PJ, Bustamante C. (2018) Molecular switch-like regulation enables global subunit coordination in a viral ring ATPase. Proc. Natl. Acad. Sci. USA 115:7961—7966.
PDF

Liu S#, Tafoya S, Bustamante C#. (2017) Deciphering the molecular mechanism of the bacteriophage φ29 DNA packaging motor. Methods Mol. Biol. 1486:343—355. Protocol.
PDF

Cheng B, Wu S, Liu S, Rodriguez-Aliaga P, Yu J, Cui S. (2015) Protein denaturation at a single-molecule level: the effect of nonpolar environments and its implications on the unfolding mechanism by proteases. Nanoscale 7:2970—2977.
PDF

Chung S, Wendeler M, Rausch JW, Beilhartz G, Gotte M, O’Keefe BR, Bermingham A, Beutler JA, Liu S, Zhuang X, Le Grice SF. (2010) Structure-activity analysis of vinylogous urea inhibitors of human immunodeficiency virus-encoded ribonuclease H. Antimicrob. Agents Chemother. 54:3913—3921.
PDF

Rausch JW, Abbondanzieri EA, Liu S, Zhuang X, Le Grice SF. (2010) Retrovirus replication: new perspectives on enzyme and substrate dynamics. In Recent Advances in Human Retroviruses: Principles of Replication and Pathogenesis (eds. Lever A, Jeang KT, Berkhout B. World Scientific) pp. 307—343. Book Chapter.
Web  

Bokinsky G, Nivón LG, Liu S, Chai G, Hong M, Weeks KM, Zhuang X. (2006) Two distinct binding modes of a protein cofactor with its target RNA. J. Mol. Biol. 361:771—784.
PDF

Song Z, Liu S, He H, Hoti N, Wang Y, Feng S, Wu M. (2004) A single amino acid change (Asp53→Ala53) converts Survivin from anti-apoptotic to pro-apoptotic. Mol. Biol. Cell 15:1287—1296.
PDF

 

Featured Publications: Li S, Zheng EB, Zhao L, Liu S#. (2019) Nonreciprocal and conditional cooperativity directs the pioneer activity of pluripotency transcription factors. C