An Amphipathic trans‐Acting Phosphorothioate DNA Element Delivers Uncharged PNA and PMO Nucleic Acid Sequences in Mammalian Cells

Harsh V. Jain1, Serge L. Beaucage1

1 Laboratory of Biological Chemistry, Food and Drug Administration, Silver Spring, Maryland
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 4.69
DOI:  10.1002/0471142700.nc0469s64
Online Posting Date:  March, 2016
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An innovative approach to the delivery of uncharged peptide nucleic acids (PNAs) and phosphorodiamidate morpholino (PMO) oligomers in mammalian cells is described and consists of extending the sequence of those oligomers with a short PNA‐polyA or PMO‐polyA tail. Recognition of the polyA‐tailed PNA or PMO oligomers by an amphipathic trans‐acting polythymidylic thiophosphate triester element (dTtaPS) results in efficient internalization of those oligomers in several cell lines. The authors’ findings indicate that cellular uptake of the oligomers occurs through an energy‐dependent mechanism and macropinocytosis appears to be the predominant endocytic pathway used for internalization. The functionality of the internalized oligomers is demonstrated by alternate splicing of the pre‐mRNA encoding luciferase in HeLa pLuc 705 cells. Amphipathic phosphorothioate DNA elements may represent a unique class of cellular transporters for robust delivery of uncharged nucleic acid sequences in live mammalian cells. © 2016 by John Wiley & Sons, Inc.

Keywords: PNA oligomers; PMO oligomers; nucleic acid–based drug delivery; cellular internalization; alternate splicing of luciferase pre‐mRNA

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Table of Contents

  • Introduction
  • Basic Protocol 1: Preparation of Deoxyribonucleoside Phosphoramidites (4 and 5)
  • Support Protocol 1: Preparation of N,N,N′,N′‐Tetraisopropylphosphordiamidites (2 and 3)
  • Basic Protocol 2: Solid‐Phase Synthesis of trans‐Acting Polythymidylic Thiophosphate Triester Element dTtaPS (6)
  • Support Protocol 2: Formation of Complexes Between dTtaPS and PNA or PMO Oligomers
  • Basic Protocol 3: dTtaPS‐Mediated Cellular Internalization of PNA or PMO Oligomers in Live Mammalian Cells
  • Basic Protocol 4: Luciferase Assay for Determining the Bioactivity of PNA and PMO Oligomers in HeLa pLUC 705 Cells
  • Alternate Protocol 1: Luciferase PRE‐mRNA Splice Correction Assay for Determining the Bioactivity of PNA and PMO Oligomers in HeLa pLUC 705 Cells
  • Reagents and Solutions
  • Commentary
  • Literature Cited
  • Figures
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Basic Protocol 1: Preparation of Deoxyribonucleoside Phosphoramidites (4 and 5)

  • N,N,N′,N′‐Tetraisopropyl‐O‐[3‐(N,N‐dimethylamino)prop‐1‐yl]phosphordiamidite (2; see protocol 2) or N,N,N′,N′‐tetraisopropyl‐O‐(octan‐1‐yl)phosphordiamidite (3; see protocol 2)
  • Argon or nitrogen source
  • Anhydrous acetonitrile (MeCN, Glen Research)
  • 5′‐O‐(4,4′‐Dimethoxytrityl)‐2′‐deoxythymidine (1; ChemGenes Corporation)
  • 0.45 M 1H‐tetrazole in MeCN (Glen Research)
  • Triethylamine (Aldrich)
  • Hexane (Fisher)
  • Dichloromethane (CH 2Cl 2; Fisher)
  • Silica gel (60‐Å, 230 to 400 mesh; EMD)
  • Anhydrous benzene (Aldrich)
  • Dry ice/acetone bath
  • 50‐, 100‐, and 250‐mL round‐bottom flasks
  • Magnetic stirrer and stir bars
  • Rubber septa for 14/20‐ and 24/40‐glass joints
  • 1‐, 3‐ and 10‐mL Luer‐tipped glass syringes
  • 5‐mm NMR tubes
  • NMR spectrometer (Bruker)
  • Rotary evaporator equipped with dry ice condenser and connected to oil pump
  • 2.5 × 20–cm disposable Flex chromatography columns (Kontes)
  • 2.5 × 7.5–cm EMD TLC plates pre‐coated with a 250‐μm layer of silica gel 60 F 254
  • Hand‐held UV 254 lamp (UVP)
  • Lyophilizer

Support Protocol 1: Preparation of N,N,N′,N′‐Tetraisopropylphosphordiamidites (2 and 3)

  Additional Materials (also see protocol 1)
  • bis(N,N‐Diisopropylamino)chlorophosphine (Aldrich)
  • 3‐(N,N‐Dimethylamino)propan‐1‐ol (Aldrich) or 1‐octanol (Aldrich)
  • 1‐mL syringes
  • Pasteur pipets
  • Vacuum desiccator
  • High‐vacuum oil pump
  • Büchner funnel setup with vacuum source

Basic Protocol 2: Solid‐Phase Synthesis of trans‐Acting Polythymidylic Thiophosphate Triester Element dTtaPS (6)

  • Reagents for automated solid‐phase oligonucleotide synthesis (Glen Research):
    • 5′‐O‐(4,4′‐Dimethoxytrityl)‐3′‐O‐[(N,N‐diisopropylamino)(3‐[N,N‐dimethylamino]prop‐1‐yl)oxy]phosphinyl‐2′‐deoxythymidine (4, see protocol 2)
    • 5′‐O‐(4,4′‐Dimethoxytrityl)‐3′‐O‐[(N,N‐diisopropylamino)(octan‐1‐yl)oxy]phosphinyl‐2′‐deoxythymidine (5, see protocol 2)
    • Succinylated long chain alkylamine controlled‐pore glass support loaded with 0.2 μmol 5′‐O‐(4,4′‐dimethoxytrityl)‐2′‐deoxythymidine
    • Deblocking solution: trichloroacetic acid (TCA) in dichloromethane (CH 2Cl 2)
    • Activator solution: 1H‐tetrazole in acetonitrile
    • Cap A solution: acetic anhydride in THF/pyridine
    • Cap B solution: 1‐methylimidazole in THF
    • Sulfuration solution: 0.05 M 3‐(dimethylaminomethylidene)amino‐3H‐1,2,4‐dithiazole‐3‐thione in (2:3 v/v) pyridine/MeCN
  • Methylamine gas cylinder (Aldrich)
  • Triethylamine (Aldrich)
  • Anhydrous acetonitrile (Glen Research)
  • DNA/RNA synthesizer (e.g., 394 DNA/RNA synthesizer, Applied Biosystems)
  • Stainless‐steel pressure vessel equipped with a valve system (Parr Instrument)
  • High‐vacuum oil pump
  • 1‐mL glass syringe
  • 1.5‐mL microcentrifuge tubes
  • UV/vis spectrophotometer (Agilent Technologies)
  • 25‐cm × 4.6‐mm, 300‐Å Jupiter C‐4 HPLC column (5 μm; Phenomenex)
  • HPLC instrument (Agilent Technologies)

Support Protocol 2: Formation of Complexes Between dTtaPS and PNA or PMO Oligomers

  Additional Materials (also see protocol 3)
  • OptiMEM (Life Technologies)
  • PNA oligomers 7 to 15 (PNA Bio, Inc.) and PMO oligomers 16 to 21 (GeneTools, LLC)
  • dTtaPS (6, see protocol 3)
  • 1.5‐mL microcentrifuge tubes
  • Pipettor (Corning)
  • 37°C water bath (Thermo Scientific)

Basic Protocol 3: dTtaPS‐Mediated Cellular Internalization of PNA or PMO Oligomers in Live Mammalian Cells

  • Live mammalian cells:
    • HEK293 cells (ATCC CRL‐1573)
    • HeLa cells (ATCC CCL‐2)
    • HeLa pLuc 705 cells (donated by Professor Rudolph Juliano, University of North Carolina‐Chapel Hill School of Medicine, )
    • MCF7 cells (ATCC HTB‐22)
    • SK‐N‐SH cells (ATCC HTB‐11)
  • Fetal bovine serum (FBS, Life Technologies)
  • Dulbecco's minimum essential medium (DMEM) supplemented with 10% (and 20%) heat‐inactivated fetal bovine serum (10% FBS‐DMEM and 20% FBS‐DMEM) (see recipe)
  • 0.25% Trypsin (MediaTech)
  • Dulbecco's phosphate‐buffered saline, pH 7.4, supplemented with 2% fetal bovine serum (Life Technologies), ice cold
  • 0.4% Trypan blue (MediaTech)
  • Monensin (Sigma)
  • 100× L‐glutamine (Life Technologies)
  • 100× penicillin‐streptomycin (Life Technologies)
  • 100 mM sodium pyruvate (Life Technologies)
  • 50 mg/mL hygromycin B (Life Technologies)
  • 75‐cm2 flask (Corning)
  • 37°C, 5% CO 2 humidified incubator (Thermo Scientific)
  • Cellometer Auto T4 Cell Viability Counter (Nexcelom)
  • Flat‐bottom, 96‐well tissue‐culture plates (BD‐Falcon)
  • Vacuum aspirator
  • FACS tubes (Falcon)
  • 1.5‐mL microcentrifuge tubes
  • FACScan flow cytometer (Becton Dickinson)

Basic Protocol 4: Luciferase Assay for Determining the Bioactivity of PNA and PMO Oligomers in HeLa pLUC 705 Cells

  • HeLa pLuc 705 cells (donated by Professor Rudolph Juliano, Uiversity of North Carolina, Chapel Hill)
  • Fetal bovine serum (FBS, Life Technologies)
  • DMEM (Life Technologies)
  • Serum‐free medium (OptiMEM, Life Technologies)
  • 2× stock solution of each of the dTtaPS/PNA oligomer 10, 11, or 12 complexes and each of the dTtaPS/PMO oligomer 19, 20, or 21 complexes (see protocol 4)
  • 2× Pierce luciferase cell lysis buffer (ThermoFisher)
  • Bright‐Glow reagent (Promega)
  • Pierce Coomassie (Bradford) protein assay kit (ThermoFisher)
  • Black 96‐well plate (Corning)
  • Vacuum aspirator
  • 1.5‐mL microcentrifuge tubes
  • 37°C, 5% CO 2 humidified incubator (Thermo Scientific)
  • Mechanical shaker
  • White 96‐well plate (Corning)
  • Luminescence microplate reader (FilterMax F3 Multi‐Mode microplate reader, Molecular Devices)

Alternate Protocol 1: Luciferase PRE‐mRNA Splice Correction Assay for Determining the Bioactivity of PNA and PMO Oligomers in HeLa pLUC 705 Cells

  Additional Materials (also see protocol 6)
  • HeLa pLuc 705 cell lysates (see protocol 6)
  • 2× stock solutions of dTtaPS/PNA oligomer 10 complexes and dTtaPS/PMO oligomer 19 complexes (see protocol 4)
  • TRIzol (Life Technologies)
  • High‐capacity cDNA reverse transcription kit (Applied Biosystems, cat. no. 4368813)
  • Power SYBR Green PCR Master Mix (Thermo Fisher)
  • Forward and reverse primers 5′‐TTGATATGTGGATTTCGAGTCGTC and 5′‐TGTCAATCAGAGTGCTTTTGGCG, respectively (Integrated DNA Technologies)
  • 1× phosphate buffered saline, pH 7.4 (PBS, MediaTech)
  • DEPC‐treated water (Invitrogen)
  • 5× nucleic acid sample buffer (Bio‐Rad)
  • 3% agarose gels stained with ethidium bromide (Bio‐Rad)
  • 10× TBE buffer, pH 8.3 (Bio‐Rad)
  • 20‐bp molecular ladder (Bio‐Rad)
  • 0.2‐mL 8‐strip PCR tubes (Eppendorf)
  • 1.5‐mL microcentrifuge tubes
  • PCR thermal cycler (e.g., GeneAmp PCR System 9700, Applied Biosystems)
  • DNA Sub Cell electrophoresis horizontal gel chamber (Bio‐Rad)
  • Power supply (Pharmacia)
  • GE ImageQuant LAS 4000 scanner (GE Healthcare)
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