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Biological Sciences Staff information

Yijia Xiong

Biochemistry & Structural Biology
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-02
Richland, WA 99352


Built a confocal far-field single molecule fluorescence microscope with capabilities of fluorescence correlation spectroscopy (FCS), fluorescence imaging, and single molecule fluorescence burst analysis. It was used for the protein-protein or protein-metal oxide binding kinetics and the photonic properties of fluorescent probes.

Participated in the discovery of the Cy3-based biarsenical fluorescent probe AsCy3 that targets to a complementary binding peptide. AsCy3 provides an important next step in developing a whole toolkit of colored probes directed to different small binding motifs. This work was highlighted by Nature (Game of tag, Vol 448, Page 4, 2007).

Measured the extinction coefficients, triplet state lifetime and other photochemical parameters of given dyes. Demonstrated that fluorescence correlation spectroscopy was a general method for the rapid determination of photo physical properties.

Studied high-affinity binding and direct electron transfer to hematite (mineral form of Iron Oxide, Fe2O3) by the bacteria Shewanella oneidensis MR-1 outer membrane protein OmcA using FCS. For the first time the directly binding between protein OmcA and solid surface of hematite was observed.

Studied the cooperative binding of oxidized calmodulin by methionine sulfoxide reductase (MsrA) using multiplying biochemical methods. MsrA reduces the oxidized proteins whose amount increase during the process of aging. High-affinity and cooperative binding of two MsrA to each oxidized calmodulin was observed.

Research Interests

  • Protein Protein Interaction
  • Advance Fluorescence Method Development
  • Super Resolution Imaging
  • Single Molecular Spectroscopy
  • Fluorescence Correlation Spectroscopy

Education and Credentials

  • 1989-1994,B.S. Chemical Physics,University of Science and Technology of China (USTC), Hefei, China
  • 1994-2000,Ph.D. Physical Chemistry,Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing, China

Affiliations and Professional Service

  • Biophysical Society, 2002
  • Protein Society, 2005

PNNL Publications


  • Fu N, Y Xiong, and TC Squier. 2013. "Optimized Design and Synthesis of Cell Permeable Biarsenical Cyanine Probe for Imaging Tagged Cytosolic Bacterial Proteins ." Bioconjugate Chemistry 24(2):251-259.  doi:10.1021/bc300619m
  • Fu N, D Su, JR Cort, B Chen, Y Xiong, W Qian, A Konopka, DJ Bigelow, and TC Squier. 2013. "Synthesis and Application of an Environmentally Insensitive Cy3-Based Arsenical Fluorescent Probe to Identify Adaptive Microbial Responses Involving Proximal Dithiol Oxidation." Journal of the American Chemical Society 135(9):3567-3575.  doi:10.1021/ja3117284
  • Minard KR, MH Littke, W Wang, Y Xiong, JG Teeguarden, and BD Thrall. 2013. "Magnetic Particle Detection (MPD) for In-Vitro Dosimetry." Biosensors and Bioelectronics 43:88-93.  doi:10.1016/j.bios.2012.12.011


  • Fu N, Y Xiong, and TC Squier. 2012. "Synthesis of a Targeted Biarsenical Cy3-Cy5 Affinity Probe for Superresolution Fluorescence Imaging." Journal of the American Chemical Society 134(45):18530-18533.  doi:10.1021/JA308503x
  • Jin H, Y Yu, WB Chrisler, Y Xiong, D Hu, and C Lei. 2012. "Delivery of MicroR A-10b with Polylysine Nanoparticles for Inhibition of Breast Cancer Cell Wound Healing." Breast Cancer: Basic and Clinical Research 6:9-19.  doi:10.4137/BCBCR.S8513
  • Smith DMA, Y Xiong, TP Straatsma, KM Rosso, and TC Squier. 2012. "Force Field Development and Molecular Dynamics of [NiFe] Hydrogenase." Journal of Chemical Theory and Computation 8(6):2103-2114.  doi:10.1021/ct300185u


  • Xiong Y, B Chen, L Shi, JK Fredrickson, DJ Bigelow, and TC Squier. 2011. "Targeted Protein Degradation of Outer Membrane Decaheme Cytochrome MtrC Metal Reductase in Shewanella oneidensis MR-1 Measured Using Biarsenical Probe CrAsH-EDT2." Biochemistry 50(45):9738-9751.  doi:10.1021/bi200602f
  • Cao B, L Shi, RN Brown, Y Xiong, JK Fredrickson, MF Romine, MJ Marshall, MS Lipton, and H Beyenal. 2011. "Extracellular Polymeric Substances from Shewanella sp. HRCR-1 Biofilms: Characterization by Infrared Spectroscopy and Proteomics." Environmental Microbiology 13(4):1018-1031.  doi:10.1111/j.1462-2920.2010.02407.x
  • Hou C, Y Xiong, N Fu, CC Jacquot, TC Squier, and H Cao. 2011. "Turn-on Ratiometric Fluorescent Sensor for Pb+2 Detection." Tetrahedron Letters 52(21):2692-2696.  doi:10.1016/j.tetlet.2011.03.075


  • Yan P, T Wang, GJ Newton, TV Knyushko, Y Xiong, DJ Bigelow, TC Squier, and MU Mayer. 2009. "A Targeted Releasable Affinity Probe (TRAP) for In Vivo Photo-Crosslinking." Chembiochem 10(9):1507-1518.  doi:10.1002/cbic.200900029


  • Cao H, Y Xiong, T Wang, B Chen, TC Squier, and MU Mayer. 2007. "A Red Cy3-Based Biarsenical Fluorescent Probe Targeted to a Complementary Binding Peptide." Journal of the American Chemical Society 129(28):8672-8673.  doi:10.1021/ja070003c
  • Cao H, Y Xiong, T Wang, B Chen, TC Squier, and MU Mayer. 2007. "A Red Cy3-Based Biarsenical Fluorescent Probe Targeted to a Complementary Binding Peptide." Journal of the American Chemical Society 129:8672-73.  doi:10.1021/ja070003c
  • Chen B, LM Markillie, Y Xiong, MU Mayer, and TC Squier. 2007. "Increased Catalytic Efficiency Following Gene Fusion of Bifunctional Methionine Sulfoxide Reductase Enzymes from Shewanella oneidensis." Biochemistry 46(49):14153-14161.  doi:10.1021/bi701151t
  • Verma S, Y Xiong, MU Mayer, and TC Squier. 2007. " Remodeling of Bacterial RNA Polymerase Supramolecular Complex in Response to Environmental Conditions." Biochemistry 46(11):3023-3035.  doi:10.1021/bi0621157


  • Xiong Y, B Chen, HS Smallwood, RJ Urbauer, LM Markillie, NA Galeva, TD Williams, and TC Squier. 2006. " High-Affinity and Cooperative Binding of Oxidized Calmodulin by Methionine Sulfoxide Reductase." Biochemistry 45(49):14642-14654.  doi:10.1021/bi0612465
  • Sacksteder CA, JE Whittier, Y Xiong, J Li, NA Galeva, ME Jacoby, SO Purvine, TD Williams, MC Rechsteiner, DJ Bigelow, and TC Squier. 2006. "Tertiary Structural Rearrangements upon Oxidation of Methionine145 in Calmodulin Promotes Targeted Proteasomal Degradation." Biophysical Journal 91(4):1480-1493. 
  • Xiong Y, L Shi, B Chen, MU Mayer, BH Lower, londer, S Bose, MF Hochella, JM Zachara, JK Fredrickson, and TC Squier. 2006. "High-Affinity Binding and Direct Electron Transfer to Solid Metals by the Shewanella oneidensis MR-1 Outer Membrane c-type Cytochrome OmcA." Journal of the American Chemical Society 128(43):13978-13979.  doi:10.1021/ja063526d
  • Yan P, Y Xiong, B Chen, S Negash, TC Squier, and MU Mayer. 2006. "Fluorophore-Assisted Light Inactivation of Calmodulin Involves Singlet-Oxygen Mediated Cross-Linking and Methionine Oxidation." Biochemistry 45(15):4736-4748.  doi:10.1021/bi052395a


  • Li J, CB Boschek, Y Xiong, CA Sacksteder, TC Squier, and DJ Bigelow. 2005. "Essential Role for Pro(21) in Phospholamban for Optimal Inhibition of the Ca-ATPase ." Biochemistry 44(49):16181-16191. 


  • Li J, Y Xiong, DJ Bigelow, and TC Squier. 2004. "Phospholamban Binds in a Compact and Ordered Conformation to the Ca-ATPase." Biochemistry 43(2):455-463. 
  • Whittier JE, Y Xiong, MC Rechsteiner, and TC Squier. 2004. "Hsp90 Enhances Degradation of Oxidized Calmodulin by the 20S Proteasome ." Journal of Biological Chemistry 279(44):46135-46142. 

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