Bio

Bio


William Greenleaf is an Assistant Professor in the Genetics Department at Stanford. Efforts in his lab are split between building new tools to leverage the power of high-throughput sequencing and cutting-edge microscopies, and bringing these new technologies to bear against basic biological questions of genomic and epigenomic variation. Will earned his PhD in the Applied Physics Department at Stanford in the lab of Steve Block investigating the single molecule biophysics of transcription. As a postdoctoral fellow in the lab of Sunney Xie in the Chemistry and Chemical Biology Department at Harvard he was awarded a Damon Runyon Cancer Research Fellowship. He started his lab at Stanford in November 2011, and recently was named a Rita Allen Foundation Scholar.

Academic Appointments


Honors & Awards


  • Graduate Fellowship, National Science Foundation (2003-2005)
  • Gates Cambridge Trust Scholar, Gates Foundation (2002-2003)
  • ARCS Fellowship, ARCS (2006)
  • Damon Runyon Cancer Research Fellowship, Damon Runyon Foundation (2009-2011)
  • Rita Allen Scholar, Rita Allen Foundation (2011-)
  • Baxter Foundation Faculty Fellow, Baxter Foundation

Professional Education


  • Postdoctoral Fellow, Harvard University, Chemistry and Chemical Biology
  • PhD, Stanford University, Applied Physics (2008)
  • Dip Comp Sci, Trinity College, Cambridge University, UK, Computer Science (2003)
  • AB, Harvard University, Physics (2002)

Research & Scholarship

Current Research and Scholarly Interests


Our lab focuses on developing methods to probe the genome and epigenome at the single-cell and single-molecule levels. Our efforts are split between building new tools to leverage the power of high-throughput sequencing and cutting-edge microscopies, and bringing these new technologies to bear against basic biological questions of genomic and epigenomic variation.

Teaching

2016-17 Courses


Stanford Advisees


Graduate and Fellowship Programs


Publications

All Publications


  • Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations. Nature genetics Araya, C. L., Cenik, C., Reuter, J. A., Kiss, G., Pande, V. S., Snyder, M. P., Greenleaf, W. J. 2016; 48 (2): 117-125

    Abstract

    Cancer sequencing studies have primarily identified cancer driver genes by the accumulation of protein-altering mutations. An improved method would be annotation independent, sensitive to unknown distributions of functions within proteins and inclusive of noncoding drivers. We employed density-based clustering methods in 21 tumor types to detect variably sized significantly mutated regions (SMRs). SMRs reveal recurrent alterations across a spectrum of coding and noncoding elements, including transcription factor binding sites and untranslated regions mutated in up to ∼15% of specific tumor types. SMRs demonstrate spatial clustering of alterations in molecular domains and at interfaces, often with associated changes in signaling. Mutation frequencies in SMRs demonstrate that distinct protein regions are differentially mutated across tumor types, as exemplified by a linker region of PIK3CA in which biophysical simulations suggest that mutations affect regulatory interactions. The functional diversity of SMRs underscores both the varied mechanisms of oncogenic misregulation and the advantage of functionally agnostic driver identification.

    View details for DOI 10.1038/ng.3471

    View details for PubMedID 26691984

  • Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions GENOME RESEARCH Schep, A. N., Buenrostro, J. D., Denny, S. K., Schwartz, K., Sherlock, G., Greenleaf, W. J. 2015; 25 (11): 1757-1770
  • Single-cell chromatin accessibility reveals principles of regulatory variation NATURE Buenostro, J. D., Wu, B., Litzenburger, U. M., Ruff, D., Gonzales, M. L., Snyder, M. P., Chang, H. Y., Greenleaf, W. J. 2015; 523 (7561): 486-U264
  • Unraveling the 3D genome: genomics tools for multiscale exploration TRENDS IN GENETICS Risca, V. I., Greenleaf, W. J. 2015; 31 (7): 357-372

    Abstract

    A decade of rapid method development has begun to yield exciting insights into the 3D architecture of the metazoan genome and the roles it may play in regulating transcription. Here we review core methods and new tools in the modern genomicist's toolbox at three length scales, ranging from single base pairs to megabase-scale chromosomal domains, and discuss the emerging picture of the 3D genome that these tools have revealed. Blind spots remain, especially at intermediate length scales spanning a few nucleosomes, but thanks in part to new technologies that permit targeted alteration of chromatin states and time-resolved studies, the next decade holds great promise for hypothesis-driven research into the mechanisms that drive genome architecture and transcriptional regulation.

    View details for DOI 10.1016/j.tig.2015.03.010

    View details for Web of Science ID 000357755700002

  • Transient acquisition of pluripotency during somatic cell transdifferentiation with iPSC reprogramming factors NATURE BIOTECHNOLOGY Maza, I., Caspi, I., Zviran, A., Chomsky, E., Rais, Y., Viukov, S., Geula, S., Buenrostro, J. D., Weinberger, L., Krupalnik, V., Hanna, S., Zerbib, M., Dutton, J. R., Greenleaf, W. J., Massarwa, R., Novershtern, N., Hanna, J. H. 2015; 33 (7): 769-774

    Abstract

    Somatic cells can be transdifferentiated to other cell types without passing through a pluripotent state by ectopic expression of appropriate transcription factors. Recent reports have proposed an alternative transdifferentiation method in which fibroblasts are directly converted to various mature somatic cell types by brief expression of the induced pluripotent stem cell (iPSC) reprogramming factors Oct4, Sox2, Klf4 and c-Myc (OSKM) followed by cell expansion in media that promote lineage differentiation. Here we test this method using genetic lineage tracing for expression of endogenous Nanog and Oct4 and for X chromosome reactivation, as these events mark acquisition of pluripotency. We show that the vast majority of reprogrammed cardiomyocytes or neural stem cells obtained from mouse fibroblasts by OSKM-induced 'transdifferentiation' pass through a transient pluripotent state, and that their derivation is molecularly coupled to iPSC formation mechanisms. Our findings underscore the importance of defining trajectories during cell reprogramming by various methods.

    View details for DOI 10.1038/nbt.3270

    View details for Web of Science ID 000358396100034

  • Assaying the epigenome in limited numbers of cells METHODS Greenleaf, W. J. 2015; 72: 51-56

    Abstract

    Spectacular advances in the throughput of DNA sequencing have allowed genome-wide analysis of epigenetic features such as methylation, nucleosome position and post-translational modification, chromatin accessibility and connectivity, and transcription factor binding. However, for rare or precious biological samples, input requirements of many of these methods limit their application. In this review we discuss recent advances for low-input genome-wide analysis of chromatin immunoprecipitation, methylation, DNA accessibility, and chromatin conformation.

    View details for DOI 10.1016/j.ymeth.2014.10.010

    View details for Web of Science ID 000348410800008

    View details for PubMedID 25461774

  • ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.] Buenrostro, J. D., Wu, B., Chang, H. Y., Greenleaf, W. J. 2015; 109: 21 29 1-9

    Abstract

    This unit describes Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq), a method for mapping chromatin accessibility genome-wide. This method probes DNA accessibility with hyperactive Tn5 transposase, which inserts sequencing adapters into accessible regions of chromatin. Sequencing reads can then be used to infer regions of increased accessibility, as well as to map regions of transcription-factor binding and nucleosome position. The method is a fast and sensitive alternative to DNase-seq for assaying chromatin accessibility genome-wide, or to MNase-seq for assaying nucleosome positions in accessible regions of the genome. © 2015 by John Wiley & Sons, Inc.

    View details for DOI 10.1002/0471142727.mb2129s109

    View details for PubMedID 25559105

  • A Conditional System to Specifically Link Disruption of Protein-Coding Function with Reporter Expression in Mice CELL REPORTS Chiou, S., Kim-Kiselak, C., Risca, V. I., Heimann, M. K., Chuang, C., Burds, A. A., Greenleaf, W. J., Jacks, T. E., Feldser, D. M., Winslow, M. M. 2014; 7 (6): 2078-2086
  • A conditional system to specifically link disruption of protein-coding function with reporter expression in mice. Cell reports Chiou, S., Kim-Kiselak, C., Risca, V. I., Heimann, M. K., Chuang, C., Burds, A. A., Greenleaf, W. J., Jacks, T. E., Feldser, D. M., Winslow, M. M. 2014; 7 (6): 2078-2086

    Abstract

    Conditional gene deletion in mice has contributed immensely to our understanding of many biological and biomedical processes. Despite an increasing awareness of nonprotein-coding functional elements within protein-coding transcripts, current gene-targeting approaches typically involve simultaneous ablation of noncoding elements within targeted protein-coding genes. The potential for protein-coding genes to have additional noncoding functions necessitates the development of novel genetic tools capable of precisely interrogating individual functional elements. We present a strategy that couples Cre/loxP-mediated conditional gene disruption with faithful GFP reporter expression in mice in which Cre-mediated stable inversion of a splice acceptor-GFP-splice donor cassette concurrently disrupts protein production and creates a GFP fusion product. Importantly, cassette inversion maintains physiologic transcript structure, thereby ensuring proper microRNA-mediated regulation of the GFP reporter, as well as maintaining expression of nonprotein-coding elements. To test this potentially generalizable strategy, we generated and analyzed mice with this conditional knockin reporter targeted to the Hmga2 locus.

    View details for DOI 10.1016/j.celrep.2014.05.031

    View details for PubMedID 24931605

  • Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes. Nature biotechnology Buenrostro, J. D., Araya, C. L., Chircus, L. M., Layton, C. J., Chang, H. Y., Snyder, M. P., Greenleaf, W. J. 2014; 32 (6): 562-568

    Abstract

    RNA-protein interactions drive fundamental biological processes and are targets for molecular engineering, yet quantitative and comprehensive understanding of the sequence determinants of affinity remains limited. Here we repurpose a high-throughput sequencing instrument to quantitatively measure binding and dissociation of a fluorescently labeled protein to >10(7) RNA targets generated on a flow cell surface by in situ transcription and intermolecular tethering of RNA to DNA. Studying the MS2 coat protein, we decompose the binding energy contributions from primary and secondary RNA structure, and observe that differences in affinity are often driven by sequence-specific changes in both association and dissociation rates. By analyzing the biophysical constraints and modeling mutational paths describing the molecular evolution of MS2 from low- to high-affinity hairpins, we quantify widespread molecular epistasis and a long-hypothesized, structure-dependent preference for G:U base pairs over C:A intermediates in evolutionary trajectories. Our results suggest that quantitative analysis of RNA on a massively parallel array (RNA-MaP) provides generalizable insight into the biophysical basis and evolutionary consequences of sequence-function relationships.

    View details for DOI 10.1038/nbt.2880

    View details for PubMedID 24727714

  • Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes NATURE BIOTECHNOLOGY Buenrostro, J. D., Araya, C. L., Chircus, L. M., Layton, C. J., Chang, H. Y., Snyder, M. P., Greenleaf, W. J. 2014; 32 (6): 562-?

    View details for DOI 10.1038/nbt.2880

    View details for Web of Science ID 000337233800019

  • A pause sequence enriched at translation start sites drives transcription dynamics in vivo SCIENCE Larson, M. H., Mooney, R. A., Peters, J. M., Windgassen, T., Nayak, D., Gross, C. A., Block, S. M., Greenleaf, W. J., Landick, R., Weissman, J. S. 2014; 344 (6187): 1042-1047

    Abstract

    Transcription by RNA polymerase (RNAP) is interrupted by pauses that play diverse regulatory roles. Although individual pauses have been studied in vitro, the determinants of pauses in vivo and their distribution throughout the bacterial genome remain unknown. Using nascent transcript sequencing, we identified a 16-nucleotide consensus pause sequence in Escherichia coli that accounts for known regulatory pause sites as well as ~20,000 new in vivo pause sites. In vitro single-molecule and ensemble analyses demonstrate that these pauses result from RNAP-nucleic acid interactions that inhibit next-nucleotide addition. The consensus sequence also leads to pausing by RNAPs from diverse lineages and is enriched at translation start sites in both E. coli and Bacillus subtilis. Our results thus reveal a conserved mechanism unifying known and newly identified pause events.

    View details for DOI 10.1126/science.1251871

    View details for Web of Science ID 000336495800049

  • Exome sequencing identifies a DNAJB6 mutation in a family with dominantly-inherited limb-girdle muscular dystrophy NEUROMUSCULAR DISORDERS Couthouis, J., Raphael, A. R., Siskind, C., Findlay, A. R., Buenrostro, J. D., Greenleaf, W. J., Vogel, H., Day, J. W., Flanigan, K. M., Gitler, A. D. 2014; 24 (5): 431-435

    Abstract

    Limb-girdle muscular dystrophy primarily affects the muscles of the hips and shoulders (the "limb-girdle" muscles), although it is a heterogeneous disorder that can present with varying symptoms. There is currently no cure. We sought to identify the genetic basis of limb-girdle muscular dystrophy type 1 in an American family of Northern European descent using exome sequencing. Exome sequencing was performed on DNA samples from two affected siblings and one unaffected sibling and resulted in the identification of eleven candidate mutations that co-segregated with the disease. Notably, this list included a previously reported mutation in DNAJB6, p.Phe89Ile, which was recently identified as a cause of limb-girdle muscular dystrophy type 1D. Additional family members were Sanger sequenced and the mutation in DNAJB6 was only found in affected individuals. Subsequent haplotype analysis indicated that this DNAJB6 p.Phe89Ile mutation likely arose independently of the previously reported mutation. Since other published mutations are located close by in the G/F domain of DNAJB6, this suggests that the area may represent a mutational hotspot. Exome sequencing provided an unbiased and effective method for identifying the genetic etiology of limb-girdle muscular dystrophy type 1 in a previously genetically uncharacterized family. This work further confirms the causative role of DNAJB6 mutations in limb-girdle muscular dystrophy type 1D.

    View details for DOI 10.1016/j.nmd.2014.01.014

    View details for Web of Science ID 000336349400011

  • Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position NATURE METHODS Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., Greenleaf, W. J. 2013; 10 (12): 1213-?

    Abstract

    We describe an assay for transposase-accessible chromatin using sequencing (ATAC-seq), based on direct in vitro transposition of sequencing adaptors into native chromatin, as a rapid and sensitive method for integrative epigenomic analysis. ATAC-seq captures open chromatin sites using a simple two-step protocol with 500-50,000 cells and reveals the interplay between genomic locations of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution. We discovered classes of DNA-binding factors that strictly avoided, could tolerate or tended to overlap with nucleosomes. Using ATAC-seq maps of human CD4(+) T cells from a proband obtained on consecutive days, we demonstrated the feasibility of analyzing an individual's epigenome on a timescale compatible with clinical decision-making.

    View details for DOI 10.1038/NMETH.2688

    View details for Web of Science ID 000327698100025

    View details for PubMedID 24097267

  • Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nature methods Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., Greenleaf, W. J. 2013; 10 (12): 1213-1218

    Abstract

    We describe an assay for transposase-accessible chromatin using sequencing (ATAC-seq), based on direct in vitro transposition of sequencing adaptors into native chromatin, as a rapid and sensitive method for integrative epigenomic analysis. ATAC-seq captures open chromatin sites using a simple two-step protocol with 500-50,000 cells and reveals the interplay between genomic locations of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution. We discovered classes of DNA-binding factors that strictly avoided, could tolerate or tended to overlap with nucleosomes. Using ATAC-seq maps of human CD4(+) T cells from a proband obtained on consecutive days, we demonstrated the feasibility of analyzing an individual's epigenome on a timescale compatible with clinical decision-making.

    View details for DOI 10.1038/nmeth.2688

    View details for PubMedID 24097267

  • Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries AMERICAN JOURNAL OF HUMAN GENETICS Carpenter, M. L., Buenrostro, J. D., Valdiosera, C., Schroeder, H., Allentoft, M. E., Sikora, M., Rasmussen, M., Gravel, S., Guillen, S., Nekhrizov, G., Leshtakov, K., Dimitrova, D., Theodossiev, N., Pettener, D., Luiselli, D., Sandoval, K., Moreno-Estrada, A., Li, Y., Wang, J., Gilbert, M. T., Willerslev, E., Greenleaf, W. J., Bustamante, C. D. 2013; 93 (5): 852-864
  • Digital Polymerase Chain Reaction in an Array of Femtoliter Polydimethylsiloxane Microreactors ANALYTICAL CHEMISTRY Men, Y., Fu, Y., Chen, Z., Sims, P. A., Greenleaf, W. J., Huang, Y. 2012; 84 (10): 4262-4266

    Abstract

    We developed a simple, compact microfluidic device to perform high dynamic-range digital polymerase chain reaction (dPCR) in an array of isolated 36-femtoliter microreactors. The density of the microreactors exceeded 20000/mm(2). This device, made from polydimethylsiloxane (PDMS), allows the samples to be loaded into all microreactors simultaneously. The microreactors are completely sealed through the deformation of a PDMS membrane. The small volume of the microreactors ensures a compact device with high reaction efficiency and low reagent and sample consumption. Future potential applications of this platform include multicolor dPCR and massively parallel dPCR for next generation sequencing library preparation.

    View details for DOI 10.1021/ac300761n

    View details for Web of Science ID 000303965500005

    View details for PubMedID 22482776

  • Fluorogenic DNA sequencing in PDMS microreactors NATURE METHODS Sims, P. A., Greenleaf, W. J., Duan, H., Xie, S. 2011; 8 (7): 575-U84

    Abstract

    We developed a multiplex sequencing-by-synthesis method combining terminal phosphate-labeled fluorogenic nucleotides (TPLFNs) and resealable polydimethylsiloxane (PDMS) microreactors. In the presence of phosphatase, primer extension by DNA polymerase using nonfluorescent TPLFNs generates fluorophores, which are confined in the microreactors and detected. We immobilized primed DNA templates in the microreactors, then sequentially introduced one of the four identically labeled TPLFNs, sealed the microreactors and recorded a fluorescence image after template-directed primer extension. With cycle times of <10 min, we demonstrate 30 base reads with ?99% raw accuracy. Our 'fluorogenic pyrosequencing' offers benefits of pyrosequencing, such as rapid turnaround, one-color detection and generation of native DNA, along with high detection sensitivity and simplicity of parallelization because simultaneous real-time monitoring of all microreactors is not required.

    View details for DOI 10.1038/NMETH.1629

    View details for Web of Science ID 000292194500021

    View details for PubMedID 21666670

  • AN OPTICAL APPARATUS FOR ROTATION AND TRAPPING METHODS IN ENZYMOLOGY, VOL 475: SINGLE MOLECULE TOOLS, PT B Gutierrez-Medina, B., Andreasson, J. O., Greenleaf, W. J., Laporta, A., Block, S. M. 2010; 475: 377-404

    Abstract

    We present details of the design, construction, and testing of a single-beam optical tweezers apparatus capable of measuring and exerting torque, as well as force, on microfabricated, optically anisotropic particles (an "optical torque wrench"). The control of angular orientation is achieved by rotating the linear polarization of a trapping laser with an electro-optic modulator (EOM), which affords improved performance over previous designs. The torque imparted to the trapped particle is assessed by measuring the difference between left- and right-circular components of the transmitted light, and constant torque is maintained by feeding this difference signal back into a custom-designed electronic servo loop. The limited angular range of the EOM (+/-180 degrees ) is extended by rapidly reversing the polarization once a threshold angle is reached, enabling the torque clamp to function over unlimited, continuous rotations at high bandwidth. In addition, we developed particles suitable for rotation in this apparatus using microfabrication techniques. Altogether, the system allows for the simultaneous application of forces (approximately 0.1-100 pN) and torques (approximately 1-10,000 pN nm) in the study of biomolecules. As a proof of principle, we demonstrate how our instrument can be used to study the supercoiling of single DNA molecules.

    View details for DOI 10.1016/S0076-6879(10)75015-1

    View details for Web of Science ID 000280733800015

    View details for PubMedID 20627165

  • Applied force reveals mechanistic and energetic details of transcription termination CELL Larson, M. H., Greenleaf, W. J., Landick, R., Block, S. M. 2008; 132 (6): 971-982

    Abstract

    Transcription termination by bacterial RNA polymerase (RNAP) occurs at sequences coding for a GC-rich RNA hairpin followed by a U-rich tract. We used single-molecule techniques to investigate the mechanism by which three representative terminators (his, t500, and tR2) destabilize the elongation complex (EC). For his and tR2 terminators, loads exerted to bias translocation did not affect termination efficiency (TE). However, the force-dependent kinetics of release and the force-dependent TE of a mutant imply a forward translocation mechanism for the t500 terminator. Tension on isolated U-tracts induced transcript release in a manner consistent with RNA:DNA hybrid shearing. We deduce that different mechanisms, involving hypertranslocation or shearing, operate at terminators with different U-tracts. Tension applied to RNA at terminators suggests that closure of the final 2-3 hairpin bases destabilizes the hybrid and that competing RNA structures modulate TE. We propose a quantitative, energetic model that predicts the behavior for these terminators and mutant variants.

    View details for DOI 10.1016/j.cell.2008.01.027

    View details for Web of Science ID 000254273600016

    View details for PubMedID 18358810

  • Direct observation of hierarchical folding in single riboswitch aptamers SCIENCE Greenleaf, W. J., Frieda, K. L., Foster, D. A., Woodside, M. T., Block, S. M. 2008; 319 (5863): 630-633

    Abstract

    Riboswitches regulate genes through structural changes in ligand-binding RNA aptamers. With the use of an optical-trapping assay based on in situ transcription by a molecule of RNA polymerase, single nascent RNAs containing pbuE adenine riboswitch aptamers were unfolded and refolded. Multiple folding states were characterized by means of both force-extension curves and folding trajectories under constant force by measuring the molecular contour length, kinetics, and energetics with and without adenine. Distinct folding steps correlated with the formation of key secondary or tertiary structures and with ligand binding. Adenine-induced stabilization of the weakest helix in the aptamer, the mechanical switch underlying regulatory action, was observed directly. These results provide an integrated view of hierarchical folding in an aptamer, demonstrating how complex folding can be resolved into constituent parts, and supply further insights into tertiary structure formation.

    View details for DOI 10.1126/science.1151298

    View details for Web of Science ID 000252772000044

    View details for PubMedID 18174398

  • Single-molecule studies of RNA polymerase: Motoring along ANNUAL REVIEW OF BIOCHEMISTRY Herbert, K. M., Greenleaf, W. J., Block, S. M. 2008; 77: 149-176

    Abstract

    Single-molecule techniques have advanced our understanding of transcription by RNA polymerase (RNAP). A new arsenal of approaches, including single-molecule fluorescence, atomic-force microscopy, magnetic tweezers, and optical traps (OTs) have been employed to probe the many facets of the transcription cycle. These approaches supply fresh insights into the means by which RNAP identifies a promoter, initiates transcription, translocates and pauses along the DNA template, proofreads errors, and ultimately terminates transcription. Results from single-molecule experiments complement the knowledge gained from biochemical and genetic assays by facilitating the observation of states that are otherwise obscured by ensemble averaging, such as those resulting from heterogeneity in molecular structure, elongation rate, or pause propensity. Most studies to date have been performed with bacterial RNAP, but work is also being carried out with eukaryotic polymerase (Pol II) and single-subunit polymerases from bacteriophages. We discuss recent progress achieved by single-molecule studies, highlighting some of the unresolved questions and ongoing debates.

    View details for DOI 10.1146/annurev.biochem.77.073106.100741

    View details for Web of Science ID 000257596800008

    View details for PubMedID 18410247

  • Molecule by molecule, the physics and chemistry of life: SMB 2007. Block, S. M., Larson, M. H., Greenleaf, W. J., Herbert, K. M., Guydosh, N. R., Anthony, P. C. 2007: 193-197

    Abstract

    Interdisciplinary work in the life sciences at the boundaries of biology, chemistry and physics is making enormous strides. This progress was showcased at the recent Single Molecule Biophysics conference.

    View details for PubMedID 17372599

  • High-resolution, single-molecule measurements of biomolecular motion ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE Greenleaf, W. J., Woodside, M. T., Block, S. M. 2007; 36: 171-190

    Abstract

    Many biologically important macromolecules undergo motions that are essential to their function. Biophysical techniques can now resolve the motions of single molecules down to the nanometer scale or even below, providing new insights into the mechanisms that drive molecular movements. This review outlines the principal approaches that have been used for high-resolution measurements of single-molecule motion, including centroid tracking, fluorescence resonance energy transfer, magnetic tweezers, atomic force microscopy, and optical traps. For each technique, the principles of operation are outlined, the capabilities and typical applications are examined, and various practical issues for implementation are considered. Extensions to these methods are also discussed, with an eye toward future application to outstanding biological problems.

    View details for DOI 10.1146/annurev.biophys.36.101106.101451

    View details for Web of Science ID 000247773000009

    View details for PubMedID 17328679

  • High-resolution, single-molecule optical trapping measurements of transcription with basepair accuracy: Instrumentation and methods OPTICAL TRAPPING AND OPTICAL MICROMANIPULATION IV Greenleaf, W. J., Frieda, K. L., Abbondanzieri, E. A., Woodside, M. T., Block, S. M. 2007; 6644

    View details for DOI 10.1117/12.739631

    View details for Web of Science ID 000251162100004

  • Single-molecule, motion-based DNA sequencing using RNA polymerase SCIENCE Greenleaf, W. J., Block, S. M. 2006; 313 (5788): 801-801

    Abstract

    We present a method for sequencing DNA that relies on the motion of single RNA polymerase molecules. When a given nucleotide species limits the rate of transcription, polymerase molecules pause at positions corresponding to the rare base. An ultrastable optical trapping apparatus capable of base pair resolution was used to monitor transcription under limiting amounts of each of the four nucleotide species. From the aligned patterns of pauses recorded from as few as four molecules, we determined the DNA sequence. This proof of principle demonstrates that the motion of a processive nucleic acid enzyme may be used to extract sequence information directly from DNA.

    View details for DOI 10.1126/science.1130105

    View details for Web of Science ID 000239671300049

    View details for PubMedID 16902131

  • Direct observation of base-pair stepping by RNA polymerase NATURE Abbondanzieri, E. A., Greenleaf, W. J., Shaevitz, J. W., Landick, R., Block, S. M. 2005; 438 (7067): 460-465

    Abstract

    During transcription, RNA polymerase (RNAP) moves processively along a DNA template, creating a complementary RNA. Here we present the development of an ultra-stable optical trapping system with ångström-level resolution, which we used to monitor transcriptional elongation by single molecules of Escherichia coli RNAP. Records showed discrete steps averaging 3.7 +/- 0.6 A, a distance equivalent to the mean rise per base found in B-DNA. By combining our results with quantitative gel analysis, we conclude that RNAP advances along DNA by a single base pair per nucleotide addition to the nascent RNA. We also determined the force-velocity relationship for transcription at both saturating and sub-saturating nucleotide concentrations; fits to these data returned a characteristic distance parameter equivalent to one base pair. Global fits were inconsistent with a model for movement incorporating a power stroke tightly coupled to pyrophosphate release, but consistent with a brownian ratchet model incorporating a secondary NTP binding site.

    View details for DOI 10.1038/nature04268

    View details for Web of Science ID 000233458200041

    View details for PubMedID 16284617

  • Passive all-optical force clamp for high-resolution laser trapping PHYSICAL REVIEW LETTERS Greenleaf, W. J., Woodside, M. T., Abbondanzieri, E. A., Block, S. M. 2005; 95 (20)

    Abstract

    Optical traps are useful for studying the effects of forces on single molecules. Feedback-based force clamps are often used to maintain a constant load, but the response time of the feedback limits bandwidth and can introduce instability. We developed a novel force clamp that operates without feedback, taking advantage of the anharmonic region of the trapping potential where the differential stiffness vanishes. We demonstrate the utility of such a force clamp by measuring the unfolding of DNA hairpins and the effect of trap stiffness on opening distance and transition rates.

    View details for DOI 10.1103/PhysRevLett.95.208102

    View details for Web of Science ID 000233243500069

    View details for PubMedID 16384102