All Publications


  • A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins MOLECULAR CELL Jarmoskaite, I., Denny, S. K., Vaidyanathan, P. P., Becker, W. R., Andreasson, J. L., Layton, C. J., Kappel, K., Shivashankar, V., Sreenivasan, R., Das, R., Greenleaf, W. J., Herschlag, D. 2019; 74 (5): 966-+
  • Demonstration of protein cooperativity mediated by RNA structure using the human protein PUM2 RNA Becker, W. R., Jarmoskaite, I., Vaidyanathan, P. P., Greenleaf, W. J., Herschlag, D. 2019; 25 (6): 702–12
  • High-Throughput Analysis Reveals Rules for Target RNA Binding and Cleavage by AGO2. Molecular cell Becker, W. R., Ober-Reynolds, B., Jouravleva, K., Jolly, S. M., Zamore, P. D., Greenleaf, W. J. 2019

    Abstract

    Argonaute proteins loaded with microRNAs (miRNAs) or small interfering RNAs (siRNAs) form the RNA-induced silencing complex (RISC), which represses target RNA expression. Predicting the biological targets, specificity, and efficiency of both miRNAs and siRNAs has been hamstrung by an incomplete understanding of the sequence determinants of RISC binding and cleavage. We applied high-throughput methods to measure the association kinetics, equilibrium binding energies, and single-turnover cleavage rates of RISC. We find that RISC readily tolerates insertions of up to 7 nt in its target opposite the central region of the guide. Our data uncover specific guide:target mismatches that enhance the rate of target cleavage, suggesting novel siRNA design strategies. Using these data, we derive quantitative models for RISC binding and target cleavage and show that our in vitro measurements and models predict knockdown in an engineered cellular system.

    View details for DOI 10.1016/j.molcel.2019.06.012

    View details for PubMedID 31324449

  • Biaxial mechanical properties of swine uterosacral and cardinal ligaments BIOMECHANICS AND MODELING IN MECHANOBIOLOGY Becker, W. R., De Vita, R. 2015; 14 (3): 549–60

    Abstract

    Mechanical alterations to pelvic floor ligaments may contribute to the development and progression of pelvic floor disorders. In this study, the first biaxial elastic and viscoelastic properties were determined for uterosacral ligament (USL) and cardinal ligament (CL) complexes harvested from adult female swine. Biaxial stress-stretch data revealed that the ligaments undergo large strains. They are orthotropic, being typically stiffer along their main physiological loading direction (i.e., normal to the upper vaginal wall). Biaxial stress relaxation data showed that the ligaments relax equally in both loading directions and more when they are less stretched. In order to describe the experimental findings, a three-dimensional constitutive law based on the Pipkin-Rogers integral series was formulated. The model accounts for incompressibility, large deformations, nonlinear elasticity, orthotropy, and stretch-dependent stress relaxation. This combined theoretical and experimental study provides new knowledge about the mechanical properties of USLs and CLs that could lead to the development of new preventive and treatment methods for pelvic floor disorders.

    View details for DOI 10.1007/s10237-014-0621-5

    View details for Web of Science ID 000354408100008

    View details for PubMedID 25218641