title: Evoking picomolar binding in RNA by a single phosphorodithioate linkage.
abstract: RNA aptamers are synthetic oligonucleotide-based affinity molecules that utilize unique three-dimensional structures for their affinity and specificity to a target such as a protein. They hold the promise of numerous advantages over biologically produced antibodies; however, the binding affinity and specificity of RNA aptamers are often insufficient for successful implementation in diagnostic assays or as therapeutic agents. Strong binding affinity is important to improve the downstream applications. We report here the use of the phosphorodithioate (PS2) substitution on a single nucleotide of RNA aptamers to dramatically improve target binding affinity by ∼1000-fold (from nanomolar to picomolar). An X-ray co-crystal structure of the α-thrombin:PS2-aptamer complex reveals a localized induced-fit rearrangement of the PS2-containing nucleotide which leads to enhanced target interaction. High-level quantum mechanical calculations for model systems that mimic the PS2 moiety and phenylalanine demonstrate that an edge-on interaction between sulfur and the aromatic ring is quite favorable, and also confirm that the sulfur analogs are much more polarizable than the corresponding phosphates. This favorable interaction involving the sulfur atom is likely even more significant in the full aptamer-protein complexes than in the model systems.
authors: AM Biotechnologies, LLC, 12521 Gulf Freeway, Houston, TX 77034, USA.
authors: N Dinuka
authors: ND
authors: Abeydeera
authors: Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA martin.egli@vanderbilt.edu.
authors: Martin
authors: M
authors: Egli
authors: Department of Biology, Texas A&M University, College Station, TX 77843, USA.
authors: Nehemiah
authors: N
authors: Cox
authors: Biointeractions Division, Horiba Scientific, Avenue de la Vauve - Passage JobinYvon CS 45002 Palaiseau, France.
authors: Karen
authors: K
authors: Mercier
authors: Instituto de Biofísica Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941, Brazil.
authors: Jonas Nascimento
authors: JN
authors: Conde
authors: Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA.
authors: Pradeep S
authors: PS
authors: Pallan
authors: Instituto de Bioquimica Médica Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941, Brazil.
authors: Daniella M
authors: DM
authors: Mizurini
authors: Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90-363 Lodz, Sienkiewicza 112, Poland.
authors: Malgorzata
authors: M
authors: Sierant
authors: Biointeractions Division, Horiba Scientific, Avenue de la Vauve - Passage JobinYvon CS 45002 Palaiseau, France.
authors: Fatima-Ezzahra
authors: FE
authors: Hibti
authors: MilliporeSigma, 9186 Six Pines, The Woodlands, TX 77380, USA.
authors: Tom
authors: T
authors: Hassell
authors: The Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
authors: Tianzhi
authors: T
authors: Wang
authors: School of Pharmaceutical Sciences, Zhengzhou University, Science Avenue 100, Zhengzhou 450001, Henan, China.
authors: Feng-Wu
authors: FW
authors: Liu
authors: School of Pharmaceutical Sciences, Zhengzhou University, Science Avenue 100, Zhengzhou 450001, Henan, China.
authors: Hong-Min
authors: HM
authors: Liu
authors: MilliporeSigma, 9186 Six Pines, The Woodlands, TX 77380, USA.
authors: Carlos
authors: C
authors: Martinez
authors: Departments of Gynecologic Oncology and Cancer Biology, and Center for RNAi and Non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
authors: Anil K
authors: AK
authors: Sood
authors: Departments of Chemistry and Pharmacology, and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.
authors: Terry P
authors: TP
authors: Lybrand
authors: Biointeractions Division, Horiba Scientific, Avenue de la Vauve - Passage JobinYvon CS 45002 Palaiseau, France.
authors: Chiraz
authors: C
authors: Frydman
authors: Instituto de Bioquimica Médica Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941, Brazil.
authors: Robson Q
authors: RQ
authors: Monteiro
authors: Department of Biology, Texas A&M University, College Station, TX 77843, USA.
authors: Richard H
authors: RH
authors: Gomer
authors: Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90-363 Lodz, Sienkiewicza 112, Poland.
authors: Barbara
authors: B
authors: Nawrot
authors: AM Biotechnologies, LLC, 12521 Gulf Freeway, Houston, TX 77034, USA Xianbin.yang@thioaptamer.com xianbin@hotmail.com.
authors: Xianbin
authors: X
authors: Yang
mesh_terms: D052157:Aptamers, Nucleotide; D002460:Cell Line; D006801:Humans; D007700:Kinetics; D057230:Limit of Detection; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010710:Phosphates / Q000378:metabolism*; D011485:Protein Binding; D011506:Proteins / Q000378:metabolism; D012313:RNA / Q000378:metabolism*; D020871:RNA Stability; D012015:Reference Standards; D044967:Serum / Q000378:metabolism; D013816:Thermodynamics; D042461:Vascular Endothelial Growth Factor A / Q000378:metabolism
chemical_list: D052157:Aptamers, Nucleotide; D010710:Phosphates; D011506:Proteins; D042461:Vascular Endothelial Growth Factor A; D012313:RNA; C083120:phosphorodithioic acid