Professional Education


  • B.S., Sun Yat-sen University (China), Optical Information Science and Technology (2007)
  • Doctor of Philosophy, North Carolina State Univ At Raleigh (2012)

Stanford Advisors


All Publications


  • MutL traps MutS at a DNA mismatch. Proceedings of the National Academy of Sciences of the United States of America Qiu, R., Sakato, M., Sacho, E. J., Wilkins, H., Zhang, X., Modrich, P., Hingorani, M. M., Erie, D. A., Weninger, K. R. 2015

    Abstract

    DNA mismatch repair (MMR) identifies and corrects errors made during replication. In all organisms except those expressing MutH, interactions between a DNA mismatch, MutS, MutL, and the replication processivity factor (β-clamp or PCNA) activate the latent MutL endonuclease to nick the error-containing daughter strand. This nick provides an entry point for downstream repair proteins. Despite the well-established significance of strand-specific nicking in MMR, the mechanism(s) by which MutS and MutL assemble on mismatch DNA to allow the subsequent activation of MutL's endonuclease activity by β-clamp/PCNA remains elusive. In both prokaryotes and eukaryotes, MutS homologs undergo conformational changes to a mobile clamp state that can move away from the mismatch. However, the function of this MutS mobile clamp is unknown. Furthermore, whether the interaction with MutL leads to a mobile MutS-MutL complex or a mismatch-localized complex is hotly debated. We used single molecule FRET to determine that Thermus aquaticus MutL traps MutS at a DNA mismatch after recognition but before its conversion to a sliding clamp. Rather than a clamp, a conformationally dynamic protein assembly typically containing more MutL than MutS is formed at the mismatch. This complex provides a local marker where interaction with β-clamp/PCNA could distinguish parent/daughter strand identity. Our finding that MutL fundamentally changes MutS actions following mismatch detection reframes current thinking on MMR signaling processes critical for genomic stability.

    View details for DOI 10.1073/pnas.1505655112

    View details for PubMedID 26283381

  • Large conformational changes in MutS during DNA scanning, mismatch recognition and repair signalling EMBO JOURNAL Qiu, R., DeRocco, V. C., Harris, C., Sharma, A., Hingorani, M. M., Erie, D. A., Weninger, K. R. 2012; 31 (11): 2528-2540

    Abstract

    MutS protein recognizes mispaired bases in DNA and targets them for mismatch repair. Little is known about the transient conformations of MutS as it signals initiation of repair. We have used single-molecule fluorescence resonance energy transfer (FRET) measurements to report the conformational dynamics of MutS during this process. We find that the DNA-binding domains of MutS dynamically interconvert among multiple conformations when the protein is free and while it scans homoduplex DNA. Mismatch recognition restricts MutS conformation to a single state. Steady-state measurements in the presence of nucleotides suggest that both ATP and ADP must be bound to MutS during its conversion to a sliding clamp form that signals repair. The transition from mismatch recognition to the sliding clamp occurs via two sequential conformational changes. These intermediate conformations of the MutS:DNA complex persist for seconds, providing ample opportunity for interaction with downstream proteins required for repair.

    View details for DOI 10.1038/emboj.2012.95

    View details for Web of Science ID 000304600300011

    View details for PubMedID 22505031

  • Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study NATURE METHODS Hellenkamp, B., Schmid, S., Doroshenko, O., Opanasyuk, O., Kuehnemuth, R., Adariani, S., Ambrose, B., Aznauryan, M., Barth, A., Birkedal, V., Bowen, M. E., Chen, H., Cordes, T., Eilert, T., Fijen, C., Gebhardt, C., Goetz, M., Gouridis, G., Gratton, E., Ha, T., Hao, P., Hanke, C. A., Hartmann, A., Hendrix, J., Hildebrandt, L. L., Hirschfeld, V., Hohlbein, J., Hua, B., Huebner, C. G., Kallis, E., Kapanidis, A. N., Kim, J., Krainer, G., Lamb, D. C., Lee, N., Lemke, E. A., Levesque, B., Levitus, M., McCann, J. J., Naredi-Rainer, N., Nettels, D., Thuy Ngo, Qiu, R., Robb, N. C., Roecker, C., Sanabria, H., Schlierf, M., Schroeder, T., Schuler, B., Seidel, H., Streit, L., Thurn, J., Tinnefeld, P., Tyagi, S., Vandenberk, N., Vera, A., Weninger, K. R., Wunsch, B., Yanez-Orozco, I. S., Michaelis, J., Seidel, C. M., Craggs, T. D., Hugel, T. 2018; 15 (9): 669-+

    Abstract

    Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between ±0.02 and ±0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and discuss potential uncertainties in the experiment and the modeling. Our quantitative assessment of the reproducibility of intensity-based smFRET measurements and a unified correction procedure represents an important step toward the validation of distance networks, with the ultimate aim of achieving reliable structural models of biomolecular systems by smFRET-based hybrid methods.

    View details for DOI 10.1038/s41592-018-0085-0

    View details for Web of Science ID 000443439700020

    View details for PubMedID 30171252

    View details for PubMedCentralID PMC6121742

  • Single-Molecule FRET to Measure Conformational Dynamics of DNA Mismatch Repair Proteins. Methods in enzymology Gauer, J. W., LeBlanc, S., Hao, P., Qiu, R., Case, B. C., Sakato, M., Hingorani, M. M., Erie, D. A., Weninger, K. R. 2016; 581: 285-315

    Abstract

    Single-molecule FRET measurements have a unique sensitivity to protein conformational dynamics. The FRET signals can either be interpreted quantitatively to provide estimates of absolute distance in a molecule configuration or can be qualitatively interpreted as distinct states, from which quantitative kinetic schemes for conformational transitions can be deduced. Here we describe methods utilizing single-molecule FRET to reveal the conformational dynamics of the proteins responsible for DNA mismatch repair. Experimental details about the proteins, DNA substrates, fluorescent labeling, and data analysis are included. The complementarity of single molecule and ensemble kinetic methods is discussed as well.

    View details for DOI 10.1016/bs.mie.2016.08.012

    View details for PubMedID 27793283

  • Dynamics of MutS-Mismatched DNA Complexes Are Predictive of Their Repair Phenotypes BIOCHEMISTRY DeRocco, V. C., Sass, L. E., Qiu, R., Weninger, K. R., Erie, D. A. 2014; 53 (12): 2043-2052

    Abstract

    MutS recognizes base-base mismatches and base insertions/deletions (IDLs) in newly replicated DNA. Specific interactions between MutS and these errors trigger a cascade of protein-protein interactions that ultimately lead to their repair. The inability to explain why different DNA errors are repaired with widely varying efficiencies in vivo remains an outstanding example of our limited knowledge of this process. Here, we present single-molecule Förster resonance energy transfer measurements of the DNA bending dynamics induced by Thermus aquaticus MutS and the E41A mutant of MutS, which is known to have error specific deficiencies in signaling repair. We compared three DNA mismatches/IDLs (T-bulge, GT, and CC) with repair efficiencies ranging from high to low. We identify three dominant DNA bending states [slightly bent/unbent (U), intermediately bent (I), and significantly bent (B)] and find that the kinetics of interconverting among states varies widely for different complexes. The increased stability of MutS-mismatch/IDL complexes is associated with stabilization of U and lowering of the B to U transition barrier. Destabilization of U is always accompanied by a destabilization of B, supporting the suggestion that B is a "required" precursor to U. Comparison of MutS and MutS-E41A dynamics on GT and the T-bulge suggests that hydrogen bonding to MutS facilitates the changes in base-base hydrogen bonding that are required to achieve the U state, which has been implicated in repair signaling. Taken together with repair propensities, our data suggest that the bending kinetics of MutS-mismatched DNA complexes may control the entry into functional pathways for downstream signaling of repair.

    View details for DOI 10.1021/bi401429b

    View details for Web of Science ID 000333776300016

    View details for PubMedID 24588663

  • Cancer/Testis Antigen PAGE4, a Regulator of c-Jun Transactivation, Is Phosphorylated by Homeodomain-Interacting Protein Kinase 1, a Component of the Stress-Response Pathway BIOCHEMISTRY Mooney, S. M., Qiu, R., Kim, J. J., Sacho, E. J., Rajagopalan, K., Johng, D., Shiraishi, T., Kulkarni, P., Weninger, K. R. 2014; 53 (10): 1670-1679

    Abstract

    Prostate-associated gene 4 (PAGE4) is a cancer/testis antigen that is typically restricted to the testicular germ cells but is aberrantly expressed in cancer. Furthermore, PAGE4 is developmentally regulated with dynamic expression patterns in the developing prostate and is also a stress-response protein that is upregulated in response to cellular stress. PAGE4 interacts with c-Jun, which is activated by the stress-response kinase JNK1, and plays an important role in the development and pathology of the prostate gland. Here, we have identified homeodomain-interacting protein kinase 1 (HIPK1), also a component of the stress-response pathway, as a kinase that phosphorylates PAGE4 at T51. We show that phosphorylation of PAGE4 is critical for its transcriptional activity since mutating this T residue abolishes its ability to potentiate c-Jun transactivation. In vitro single molecule FRET indicates phosphorylation results in compaction of (still) intrinsically disordered PAGE4. Interestingly, however, while our previous observations indicated that the wild-type nonphosphorylated PAGE4 protein interacted with c-Jun [Rajagopalan , K. et al. ( 2014 ) Biochim, Biophys. Acta 1842 , 154 -163], here we show that phosphorylation of PAGE4 weakens its interaction with c-Jun in vitro. These data suggest that phosphorylation induces conformational changes in natively disordered PAGE4 resulting in its decreased affinity for c-Jun to promote interaction of c-Jun with another, unidentified, partner. Alternatively, phosphorylated PAGE4 may induce transcription of a novel partner, which then potentiates c-Jun transactivation. Regardless, the present results clearly implicate PAGE4 as a component of the stress-response pathway and uncover a novel link between components of this pathway and prostatic development and disease.

    View details for DOI 10.1021/bi500013w

    View details for Web of Science ID 000333235600015

    View details for PubMedID 24559171

  • The Stress-response protein prostate-associated gene 4, interacts with c-Jun and potentiates its transactivation BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE Rajagopalan, K., Qiu, R., Mooney, S. M., Rao, S., Shiraishi, T., Sacho, E., Huang, H., Shapiro, E., Weninger, K. R., Kulkarni, P. 2014; 1842 (2): 154-163

    Abstract

    The Cancer/Testis Antigen (CTA), Prostate-associated Gene 4 (PAGE4), is a stress-response protein that is upregulated in prostate cancer (PCa) especially in precursor lesions that result from inflammatory stress. In cells under stress, translocation of PAGE4 to mitochondria increases while production of reactive oxygen species decreases. Furthermore, PAGE4 is also upregulated in human fetal prostate, underscoring its potential role in development. However, the proteins that interact with PAGE4 and the mechanisms underlying its pleiotropic functions in prostatic development and disease remain unknown. Here, we identified c-Jun as a PAGE4 interacting partner. We show that both PAGE4 and c-Jun are overexpressed in the human fetal prostate; and in cell-based assays, PAGE4 robustly potentiates c-Jun transactivation. Single-molecule Förster resonance energy transfer experiments indicate that upon binding to c-Jun, PAGE4 undergoes conformational changes. However, no interaction is observed in presence of BSA or unilamellar vesicles containing the mitochondrial inner membrane diphosphatidylglycerol lipid marker cardiolipin. Together, our data indicate that PAGE4 specifically interacts with c-Jun and that, conformational dynamics may account for its observed pleiotropic functions. To our knowledge, this is the first report demonstrating crosstalk between a CTA and a proto-oncogene. Disrupting PAGE4/c-Jun interactions using small molecules may represent a novel therapeutic strategy for PCa.

    View details for DOI 10.1016/j.bbadis.2013.11.014

    View details for Web of Science ID 000331414900004

    View details for PubMedID 24263171