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Abi 3400 synthesizer

Manufactured by Thermo Fisher Scientific

The ABI 3400 synthesizer is a DNA/RNA synthesis instrument designed for automated, high-throughput oligonucleotide production. The instrument utilizes phosphoramidite chemistry to synthesize and purify oligonucleotides, including DNA, RNA, and modified nucleic acids. The ABI 3400 can handle multiple synthesis columns simultaneously, providing efficient and reliable oligonucleotide synthesis.

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2 protocols using abi 3400 synthesizer

1

Synthesis and Purification of Fluorescent Nucleic Acid Probes

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All DNA synthesis reagents were purchased from Glen Research. FNA F6, F4, FM6 and M6 were synthesized and purified by Sangon Biotech (Shanghai). FNA Ft6, Ft8 and other oligonucleotides were synthesized on an ABI 3400 synthesizer (Applied Biosystems). Dabcyl CPG was used for all FAM-labeled FNA. The completed sequences were then deprotected in AMA (ammonium hydroxide/40% aqueous methylamine, 1:1) at 65 °C for 30 min and further purified by reversed-phase HPLC (ProStar; Varian) on a C-18 column using 0.1 M triethylamine acetate(TEAA) buffer (Glen Research) and acetonitrile (SigmaAldrich) as the eluents. The collected DNA products were dried and detritylated by dissolving and incubating DNA products in 200 μL of 80% acetic acid for 20 min. The detritylated DNA product was precipitated with NaCl (3 M, 25 μL) and ethanol (600 μL).
Unless otherwise noted below, all commercially available reagents and solvents were purchased from Sigma Aldrich and used without further purification. 1H NMR (TMS as the internal standard) and 19F NMR spectra (CFCl3 as the outside standard and low field positive) were recorded on a Bruker AM300 or Bruker AM400 spectrometer. 13C NMR was recorded on a Bruker AM400 spectrometer. Chemical shifts (δ) are reported in ppm, and coupling constants (J) are in Hertz (Hz).
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2

Aptamer-Mediated Delivery of Doxorubicin

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All chemicals including DxR were purchased from Sigma-Aldrich unless otherwise specified and were used as received. cMet-Fc, which represents the ectodomain of cMet fused to the Fc domain of human IgG1, was purchased from R&D Systems. Wheat Germ Agglutinin, Alexa Fluor® 488 Conjugate, and Hoechst 33342 were purchased from Life Technologies (Grand Island, NY, USA). γ-32P-labeled ATP (250 μCi) was purchased from PerkinElmer Health Science B. V., The Netherlands. T4 Polynucleotide kinase and 1 × polynucleotide buffer were obtained from New England Biolabs, Frankfurt a. M., Germany. Binding buffer used for the aptamer competition-binding assay was prepared by adding E. coli tRNA (Roche AG, Mannheim, Germany), BSA (Thermo Fischer Scientific) into Dulbeccos PBS (Gibco, Life Technologies).
All solvents, reagents, and building blocks for oligonucleotide synthesis were obtained from Proligo, Hamburg, Germany. The anti-cMet aptamer motif (trCLN3) and its lipid derivatives (trCLN3-L4 and trCLN3.mut-L4) were synthesized according to the phosphoramidite protocol using an ABI 3400 synthesizer (Applied Biosystems). DxR-carrying DxR-L4 modified with DMAB and C12-lipid tails as well as the fluorescent-labeled (Atto647N-, Atto550-, and 6FAM) trCLN3-L4 and DxR-L4 motifs were purchased in HPLC purified form from Ella Biotech GmbH, Munich, Germany.
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