Open Access

Nucleic Acids Research, volume 44, issue 17, pages 8052-8064

Evoking picomolar binding in RNA by a single phosphorodithioate linkage

N Dinuka Abeydeera ¹

Martin Egli ²

Nehemiah Cox ³

Karen Mercier ⁴

Jonas N Conde ⁵

Pradeep S. Pallan ²

Daniella M. Mizurini ⁶

Malgorzata Sierant ⁷

Fatima Ezzahra Hibti ⁴

Tom Hassell ⁸

Tianzhi Wang ⁹

Feng Wu Liu ¹⁰

Hong-Min Liu ¹⁰

Carlos Martínez ⁸

Anil K. Sood ¹¹

Terry P. Lybrand ¹²

Chiraz Frydman ⁴

Robson Q. Monteiro ⁶

R. Gomer ³

Barbara Nawrot ⁷

Xianbin Yang ¹

Hide authors affiliations Show authors affiliations: 12 affiliations

AM Biotechnologies, LLC, 12521 Gulf Freeway, Houston, TX 77034, USA |

Department of Biochemistry, Vanderbilt University, School of Medicine Nashville, TN 37232 (USA) |

Department of Biology, Texas A&M University, College Station, TX 77843, USA. |

⁴

Biointeractions Division, Horiba Scientific, Avenue de la Vauve - Passage JobinYvon CS 45002 Palaiseau, France |

⁵

Instituto de Biofísica Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941, Brazil |

⁶

Instituto de Bioquimica Médica Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941, Brazil |

⁷

Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90–363 Lodz, Sienkiewicza 112, Poland |

⁸

MilliporeSigma, 9186 Six Pines, The Woodlands, TX 77380, USA |

⁹

The Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA. |

¹⁰

School of Pharmaceutical Sciences, Zhengzhou University, Science Avenue 100, Zhengzhou 450001, Henan, China. |

¹¹

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. |

¹²

Departments of Chemistry and Pharmacology, and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA. |

Publication type: Journal Article

Publication date: 2016-08-26

Oxford University Press

Journal: Nucleic Acids Research

Quartile SCImago

Quartile WOS

Impact factor: 14.9

ISSN: 03051048, 13624962

DOI: 10.1093/nar/gkw725

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Genetics

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.

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Abeydeera N. D. et al. Evoking picomolar binding in RNA by a single phosphorodithioate linkage // Nucleic Acids Research. 2016. Vol. 44. No. 17. pp. 8052-8064.

GOST all authors (up to 50) Copy

Abeydeera N. D., Egli M., Cox N., Mercier K., Conde J. N., Pallan P. S., Mizurini D. M., Sierant M., Hibti F. E., Hassell T., Wang T., Liu F. W., Liu H., Martínez C., Sood A. K., Lybrand T. P., Frydman C., Monteiro R. Q., Gomer R., Nawrot B., Yang X. Evoking picomolar binding in RNA by a single phosphorodithioate linkage // Nucleic Acids Research. 2016. Vol. 44. No. 17. pp. 8052-8064.

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TY - JOUR

DO - 10.1093/nar/gkw725

UR - https://doi.org/10.1093/nar/gkw725

TI - Evoking picomolar binding in RNA by a single phosphorodithioate linkage

T2 - Nucleic Acids Research

AU - Abeydeera, N Dinuka

AU - Egli, Martin

AU - Cox, Nehemiah

AU - Mercier, Karen

AU - Conde, Jonas N

AU - Pallan, Pradeep S.

AU - Mizurini, Daniella M.

AU - Sierant, Malgorzata

AU - Hibti, Fatima Ezzahra

AU - Hassell, Tom

AU - Wang, Tianzhi

AU - Liu, Feng Wu

AU - Liu, Hong-Min

AU - Martínez, Carlos

AU - Sood, Anil K.

AU - Lybrand, Terry P.

AU - Frydman, Chiraz

AU - Monteiro, Robson Q.

AU - Gomer, R.

AU - Nawrot, Barbara

AU - Yang, Xianbin

PY - 2016

DA - 2016/08/26 00:00:00

PB - Oxford University Press

SP - 8052-8064

IS - 17

VL - 44

SN - 0305-1048

SN - 1362-4962

ER -

BibTex |

Cite this

BibTex Copy

@article{2016_Abeydeera,

author = {N Dinuka Abeydeera and Martin Egli and Nehemiah Cox and Karen Mercier and Jonas N Conde and Pradeep S. Pallan and Daniella M. Mizurini and Malgorzata Sierant and Fatima Ezzahra Hibti and Tom Hassell and Tianzhi Wang and Feng Wu Liu and Hong-Min Liu and Carlos Martínez and Anil K. Sood and Terry P. Lybrand and Chiraz Frydman and Robson Q. Monteiro and R. Gomer and Barbara Nawrot and Xianbin Yang},

title = {Evoking picomolar binding in RNA by a single phosphorodithioate linkage},

journal = {Nucleic Acids Research},

year = {2016},

volume = {44},

publisher = {Oxford University Press},

month = {aug},

url = {https://doi.org/10.1093/nar/gkw725},

number = {17},

pages = {8052--8064},

doi = {10.1093/nar/gkw725}

}

MLA

Cite this

MLA Copy

Abeydeera, N. Dinuka, et al. “Evoking picomolar binding in RNA by a single phosphorodithioate linkage.” Nucleic Acids Research, vol. 44, no. 17, Aug. 2016, pp. 8052-8064. https://doi.org/10.1093/nar/gkw725.

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Publisher

Oxford University Press

Journal

Nucleic Acids Research

Quartile SCImago

Quartile WOS

Impact factor

14.9

ISSN

03051048 (Print)
13624962 (Electronic)