Publications

  1. Yuan X, Su Y, Johnson B, Kirchner M, Zhang X, Xu S, Jiang S, Wu J, Shi S, Russo JJ, Chen Q, Zhang S*. Mass Spectrometry-Based Direct Sequencing of tRNAs De Novo and Quantitative Mapping of Multiple RNA Modifications. J Am Chem Soc., 2024, DOI: 10.1021/jacs.4c07280.
  2. Zhang N, Shi S, Yuan X, Ni W, Wang X, Yoo B, Jia TZ, Li W, Zhang S*. A general LC-MS-based method for direct and de novo sequencing of RNA mixtures containing both canonical and modified nucleotides. Methods Mol. Biol., 2021, 2298: 261-277.
  3. Zhang N, Shi S, Wang X, Ni W, Yuan X, Duan J, Jia TZ, Yoo B, Ziegler A, Russo JJ, Li W, Zhang S*. Direct sequencing of tRNA by 2D-HELS-AA MS Seq reveals its different isoforms and multiple dynamic base modifications. ACS Chemical Biology, 2020, 15(6):1464-1472.
  4. Zhang N, Shi S., Yoo B, Yuan X, Li W, Zhang S*. 2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications. J. Vis. Exp. 2020. 161: e61281, doi:10.3791/61281.
  5. Zhang N, Shi S, Jia TZ, Ziegler A, Yoo B, Yuan X, Li W, Zhang S*. A General LC-MS-based RNA Sequencing Method for Direct Analysis of Multiple-base Modifications in RNA Mixture. Nucleic Acids Research, 2019, 47 (20): e125, https://doi.org/10.1093/nar/gkz731.
  6. Wang R, Luo Z, Shen F, Liu H, Zhang S, Gan J, Sheng J. Crystal Structures of RNA Duplexes Containing Multiple Non-Canonical 2′-5′-Linkages. Nucleic Acids Research, 2017, 45 (6): 3537-3546.
  7. Björkbom A#, Lelyveld VS#, Zhang S#, Zhang W, Tam CP, Blain JC, Szostak JW. Bidirectional Direct Sequencing of Non-Canonical RNA by Two-dimensional Analysis of Mass Chromatograms. J Am Chem Soc., 2015, 137 (45): 14430-14438.

Early Career Publications

  1. Zhang S, Blain JC, Zielinska D, Gryaznov SM, Szostak JW. Fast and Accurate Non-Enzymatic Copying of an RNA-like Synthetic Genetic Polymer. Proc Natl Acad Sci USA., 2013, 110 (44): 17732-17737. This work was highlighted in Proc Natl Acad Sci USA., 2013, 110 (44): 17601-17602; and was featured as a research highlight in Nature Chemistry, 2013, 5: 984-985
  2. Zhang S, Zhang N, Blain JC, Szostak JW. Synthesis of N3´-P5´-linked Phosphoramidate DNA by Non-Enzymatic Template-directed Primer Extension. J Am Chem Soc., 2013, 135 (2): 924-932.
  3. Zhang N, Zhang S, Szostak JW. Activated Ribonucleotides Undergo a Sugar Pucker Switch upon Binding to a Single-Stranded RNA Template. J Am Chem Soc., 2012, 134 (8): 3691–3694.
  4. Guo J, Xu N, Li Z, Zhang S, Wu J, Kim DH, Marma MS, Meng Q, Cao H, Li X, Shi S, Yu L, Kalachikov S, Russo JJ, Turro NJ, Ju J. Four-color DNA Sequencing with 3´-O-modified Nucleotide Reversible Terminators and Cleavable Fluorophore-modified Dideoxynucleotides. Proc Natl Acad Sci USA., 2008, 105 (27): 9145-9150.
  5. Wu J, Zhang S, Meng Q, Cao H, Li Z, Li X, Shi S, Kim DH, Bi L, Turro NJ, Ju J. 3´-O-labeled Reversible Terminators for Pyrosequencing. Proc Natl Acad Sci USA., 2007, 104 (42): 16462-16467.
  6. Matsuda H, Zhang S, Holmes AE, Krane S, Itagaki Y, Nakanishi K, Nesnas N. Synthesis of an 11-cis-Locked Biotinylated Retinoid for Sequestering 11-cis-Retinoid Binding Proteins. Can J Chem., 2006, 84 (10): 1363-1370.
  7. Cheng Q, Peng TZ, Zhang S, Yang CF. Enhanced Electrogravimetric Detection of DNA Hybridization on an Electrochemical Quartz Crystal Microbalance. Indian J Chem., Sec A., 2003, 42 (4): 797-800.
  8. Zhang S, Peng TZ, Yang CF. A Piezoelectric Gene-Sensor Using Actinomycin D-Functionalized Nano-Microspheres as Amplifying Probes. J Electroanal Chem., 2002, 522 (2): 152-157.
  9. Zhang S, Peng TZ. Microgravimetric Amplification and the Detection of Short DNA Sequences on a Quartz Crystal Microbalance by Modified Nano-microspheres. Chemical Journal of Chinese Universities, 2002, 23 (6): 1022-1025 (Chinese National Science Foundation Journal).
  10. Zhang S, Peng TZ. Real-time Characterization and Determination of Short DNA Sequences with Electrochemical Quartz Crystal Microbalance. Acta Chimica Sinica, 2001, 59 (11): 1989-1993 (Chinese Academy of Sciences Journal).

Patents

  1. USA patent application 62/853,269 (2019). Zhang S, Zhang N. Direct 2-D LC-MS sequencing of tRNA.
  2. USA patent application 62/676,754 (2018). Zhang S, Wang TZ, Jia TZ, Li W. Method and system for use in direct sequencing of RNA.
  3. USA patent application 62/676,703 (2018). Zhang S, Zhang N. Direct nucleic acid sequencing method.
  4. WO 2009051807 2009: Design and synthesis of labile azido linkers for conjugation of fluorescent dyes to nucleotides for use as reversible terminators in DNA sequencing by synthesis.
  5. CN 1375696 2002: Ultrasentive DNA bioassay with nanobead amplification and piezoelectric DNA biosensor.
  6. CN 1376917 2002: Method for detecting ultratrace DNA by using dual amplification technique and electrochemical quartz crystal microbalance.