5e08 › Citations

Specific Recognition of a Single-Stranded RNA Sequence by a Synthetic Antibody Fragment.

Shao Y, Huang H, Qin D, Li NS, Koide A, Staley JP, Koide S, Kossiakoff AA, Piccirilli JA
J Mol Biol 428 4100-4114 (2016)
Cited: 10 times
EuropePMC logo PMID: 27593161

Abstract

Antibodies that bind RNA represent an unrealized source of reagents for synthetic biology and for characterizing cellular transcriptomes. However, facile access to RNA-binding antibodies requires the engineering of effective Fab libraries guided by the knowledge of the principles that govern RNA recognition. Here, we describe a Fab identified from a minimalist synthetic library during phage display against a branched RNA target. The Fab (BRG) binds with 20nM dissociation constant to a single-stranded RNA (ssRNA) sequence adjacent to the branch site and can block the action of debranchase enzyme. We report the crystal structure in complex with RNA target at 2.38Å. The Fab traps the RNA in a hairpin conformation that contains a 2-bp duplex capped by a tetraloop. The paratope surface consists of residues located in four complementarity-determining regions including a major contribution from H3, which adopts a helical structure that projects into a deep, wide groove formed by the RNA. The amino acid composition of the paratope reflects the library diversity, consisting mostly of tyrosine and serine residues and a small but significant contribution from a single arginine residue. This structure, involving the recognition of ssRNA via a stem-loop conformation, together with our two previous structures involving the recognition of an RNA hairpin loop and an RNA tertiary structure, reveals the capacity of minimalist libraries biased with tyrosine, serine, glycine, and arginine to form binding surfaces for specific RNA conformations and distinct levels of RNA structural hierarchy.

Articles - 5e08 mentioned but not cited (3)

  1. Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins. Pal A, Levy Y. PLoS Comput Biol 15 e1006768 (2019)
  2. Structural basis for inhibition of the drug efflux pump NorA from Staphylococcus aureus. Brawley DN, Sauer DB, Li J, Zheng X, Koide A, Jedhe GS, Suwatthee T, Song J, Liu Z, Arora PS, Koide S, Torres VJ, Wang DN, Traaseth NJ. Nat Chem Biol 18 706-712 (2022)
  3. Specific Recognition of a Single-Stranded RNA Sequence by a Synthetic Antibody Fragment. Shao Y, Huang H, Qin D, Li NS, Koide A, Staley JP, Koide S, Kossiakoff AA, Piccirilli JA. J Mol Biol 428 4100-4114 (2016)


Reviews citing this publication (1)

  1. Protein Engineering: Advances in Phage Display for Basic Science and Medical Research. Davydova EK. Biochemistry (Mosc) 87 S146-S110 (2022)

Articles citing this publication (6)

  1. Affinity maturation of a portable Fab-RNA module for chaperone-assisted RNA crystallography. Koirala D, Shelke SA, Dupont M, Ruiz S, DasGupta S, Bailey LJ, Benner SA, Piccirilli JA. Nucleic Acids Res 46 2624-2635 (2018)
  2. A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites. Koirala D, Shao Y, Koldobskaya Y, Fuller JR, Watkins AM, Shelke SA, Pilipenko EV, Das R, Rice PA, Piccirilli JA. Nat Commun 10 3629 (2019)
  3. Synthetic Antibody Binding to a Preorganized RNA Domain of Hepatitis C Virus Internal Ribosome Entry Site Inhibits Translation. Koirala D, Lewicka A, Koldobskaya Y, Huang H, Piccirilli JA. ACS Chem Biol 15 205-216 (2020)
  4. Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing. Srivastava Y, Bonn-Breach R, Chavali SS, Lippa GM, Jenkins JL, Wedekind JE. Crystals (Basel) 11 273 (2021)
  5. Isolation and Characterization of scFv Antibody against Internal Ribosomal Entry Site of Enterovirus A71. Hlaing ST, Srimanote P, Tongtawe P, Khantisitthiporn O, Glab-Ampai K, Chulanetra M, Thanongsaksrikul J. Int J Mol Sci 24 9865 (2023)
  6. Structural Basis for Fluorescence Activation by Pepper RNA. Rees HC, Gogacz W, Li NS, Koirala D, Piccirilli JA. ACS Chem Biol 17 1866-1875 (2022)


Quick links