WO2017115655A1 - Procédé de séparation et analyse - Google Patents

Procédé de séparation et analyse Download PDF

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Publication number
WO2017115655A1
WO2017115655A1 PCT/JP2016/087219 JP2016087219W WO2017115655A1 WO 2017115655 A1 WO2017115655 A1 WO 2017115655A1 JP 2016087219 W JP2016087219 W JP 2016087219W WO 2017115655 A1 WO2017115655 A1 WO 2017115655A1
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WIPO (PCT)
Prior art keywords
column
eluent
water
synthetic oligonucleotide
separation
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PCT/JP2016/087219
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English (en)
Japanese (ja)
Inventor
謙 小木戸
青木　裕史
米田　正
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昭和電工株式会社
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Priority to JP2017558925A priority Critical patent/JPWO2017115655A1/ja
Publication of WO2017115655A1 publication Critical patent/WO2017115655A1/fr

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    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01D—SEPARATION
    • B01D15/00—Separating processes involving the treatment of liquids with solid sorbents; Apparatus therefor
    • B01D15/08—Selective adsorption, e.g. chromatography
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J20/00—Solid sorbent compositions or filter aid compositions; Sorbents for chromatography; Processes for preparing, regenerating or reactivating thereof
    • B01J20/281—Sorbents specially adapted for preparative, analytical or investigative chromatography
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12M—APPARATUS FOR ENZYMOLOGY OR MICROBIOLOGY; APPARATUS FOR CULTURING MICROORGANISMS FOR PRODUCING BIOMASS, FOR GROWING CELLS OR FOR OBTAINING FERMENTATION OR METABOLIC PRODUCTS, i.e. BIOREACTORS OR FERMENTERS
    • C12M1/00—Apparatus for enzymology or microbiology
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N30/00—Investigating or analysing materials by separation into components using adsorption, absorption or similar phenomena or using ion-exchange, e.g. chromatography or field flow fractionation
    • G01N30/02—Column chromatography
    • G01N30/26—Conditioning of the fluid carrier; Flow patterns
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N30/00—Investigating or analysing materials by separation into components using adsorption, absorption or similar phenomena or using ion-exchange, e.g. chromatography or field flow fractionation
    • G01N30/02—Column chromatography
    • G01N30/88—Integrated analysis systems specially adapted therefor, not covered by a single one of the groups G01N30/04 - G01N30/86

Definitions

  • the present invention relates to a method for separating and analyzing synthetic oligonucleotides.
  • Synthetic oligonucleotides are used in various molecular biological experiments such as polymerase chain reaction primers, diagnostic probes, single nucleotide polymorphism (SNP) detection, and DNA sequencing. Synthetic oligonucleotides are synthesized primarily by a continuous reaction using phosphoramidite nucleic acid monomers on a solid support.
  • RNAi RNA interference
  • Various factors such as binding strength, target specificity, serum stability, nuclease resistance, and cell permeability need to be considered for stable transport of synthetic oligonucleotides in the body.
  • techniques for improving these include skeletal modifications such as modification of phosphorothioate and methylphosphonate, use of locked nucleic acid (LNA), and the like. While these skeletal modifications impart nuclease resistance, they can exhibit non-sequence-specific effects, reduced permeation performance, and even cytotoxicity.
  • Oligonucleotide synthesis methods are optimized to the level that does not require purification when used for PCR primers, but more sophisticated purification and analysis are required for application to pharmaceuticals.
  • long-chain DNA and modified / backbone variants are prone to unreacted coupling and side reactions during synthesis.
  • a synthetic oligonucleotide reaction mixture contains mainly incomplete oligonucleotides or incomplete oligonucleotides.
  • nx fragment a fragment in which a nucleic acid is deleted from a target oligonucleotide
  • n is the number of target nucleotides (nucleic acids)
  • x is a number deleted
  • n, x are positive integers
  • n> x For example, n-1, n-2, etc.
  • n + 1 fragments incorporated in duplicate are included as impurities.
  • incomplete or inaccurately deprotected fragments and isomers having partial chirality are also included (Patent Document 1).
  • gel electrophoresis, gel filtration chromatography, reverse phase chromatography, and ion exchange chromatography are selected as methods for separating highly synthetic oligonucleotides. Chromatography is excellent in operability, and in particular, reverse phase chromatography that does not require desalting is widely used.
  • reverse-phase chromatography of synthetic oligonucleotides an ion-pairing reagent having a positive dissociation group and a hydrophobic functional group in the molecule is generally used (Patent Document 1).
  • Non-Patent Document 1 describes a method by anion exchange chromatography using Thermo DNAPac PA200.
  • DNAPac PA200 is a nonporous substrate having a diameter of 8 ⁇ m bonded with 130 nm microbeads having a quaternary ammonium functional group.
  • a substrate designed to allow rapid mass transfer allows a high degree of separation of 12-mer to 60-mer synthetic oligonucleotides.
  • Non-Patent Document 2 describes a method by reverse phase chromatography using Imstakt Presto FF-C18.
  • Presto FF-C18 is a silica column with a non-porous octadecyl group having a particle size of 2 ⁇ m.
  • a non-porous column having a characteristic that a decrease in column efficiency is small can highly separate 12-mer to 18-mer synthetic oligonucleotides.
  • An object of the present invention is to provide a technique for highly separating and analyzing impurities such as incomplete length oligonucleotides contained in an oligonucleotide reaction mixture in order to apply synthetic oligonucleotides to pharmaceuticals.
  • the present inventors are able to highly analyze and analyze 19-mer or more synthetic oligonucleotides using a non-porous column having a hydrophobic functional group immobilized thereon. And found the present invention.
  • the present invention is as follows.
  • a method for separating and analyzing 19-mer or more synthetic oligonucleotides by column chromatography using an eluent containing a water-soluble organic solvent and water, which is nonporous with a hydrophobic functional group immobilized A separation analysis method characterized by using a column containing a particle packing material.
  • the separation and analysis method comprises equilibrating the column with water or a first eluent containing the water-soluble organic solvent and water; dissolving the synthetic oligonucleotide in the first eluent and analyzing Preparing a sample for use; injecting the analytical sample into the column equilibrated with the sample in the equilibration step and fixing the sample to the column; and at least the water-soluble organic from the first eluent And the step of selectively eluting the synthetic oligonucleotide using a second eluent having a high solvent content.
  • a method for separating and analyzing synthetic oligonucleotides that can be separated and analyzed to a high degree by reverse phase chromatography even for long-chain synthetic oligonucleotides of 19-mers or more.
  • FIG. 2 is a UV detection method (wavelength 254 nm) chromatogram measured using the chromatographic filler and eluent of Example 1.
  • FIG. It is the ultraviolet detection method (wavelength 254nm) chromatogram measured using the packing material for chromatography of Example 2, and an eluent.
  • It is an ultraviolet detection method (wavelength 254 nm) chromatogram measured using the chromatography filler and the eluent of Comparative Example 1.
  • the method for separating and analyzing a synthetic oligonucleotide according to the present invention uses a eluent containing a water-soluble organic solvent, an alkylammonium salt and water, and a column containing a non-porous particle packing to which a hydrophobic functional group is fixed. This is a technique for highly separating and analyzing impurities contained in the process of synthesizing 19-mer or higher synthetic oligonucleotides by the column chromatography used.
  • the separation analysis method of one embodiment of the present invention includes a step of equilibrating with a first eluent containing a water-soluble organic solvent and water in a column; and dissolving a synthetic oligonucleotide in the first eluent to prepare a sample for analysis And a step of injecting the analytical sample into the column equilibrated in the equilibration step in the equilibration step and fixing the analytical sample to the column; and at least a second content of the water-soluble organic solvent higher than that of the first eluent. Selectively eluting synthetic oligonucleotides using an eluent.
  • the “synthetic oligonucleotide” is generally synthesized by continuously reacting a nucleic acid monomer on a solid phase carrier, and a nucleic acid oligomer synthesized by a phosphoramidite method is preferable.
  • the target chain length of a synthetic oligonucleotide is 10 to 110 mer, preferably 10 to 70 mer, more preferably 19 to 62 mer.
  • Reverse Phase Chromatography uses the difference in hydrophobicity of the target object to determine the movement speed due to the difference in partitioning between the hydrophobic stationary phase (filler) and the non-hydrophobic mobile phase (eluent). Reverse phase partition chromatography based on the difference. Depending on the form of the stationary phase (packing agent) and the mobile phase (eluent), for example, there is column reverse phase chromatography.
  • Nonporous particle filler with fixed hydrophobic functional groups means that hydrophobic functional groups are fixed to particle fillers composed of silica or polymers that do not have pores that allow substances to enter the medium. It has been done. “Non-porous particles” refers to particles that contain substantially no pores that contain and hold oligonucleic acids having a base number of 110 or less to be separated in the present invention. That is, the peak elution volume obtained by filling the particles into a column and injecting the oligonucleic acid under a mobile phase of 100% acetonitrile, that is, under the condition that the hydrophobic interaction between the target and the carrier does not substantially work.
  • the exclusion limit molecular weight is 700 or less.
  • the method for obtaining the exclusion limit from the calibration curve is described in detail in Japanese Patent Publication No. 08-7197 ((4) right line 37 to (5) left line 8).
  • Japanese Patent No. 4662967 describes an analysis method using a separation column packed with particles exhibiting a specific exclusion limit.
  • the particle filler of one embodiment of the present invention is preferably silica.
  • the particle size is preferably 3 ⁇ m or less, more preferably 2 ⁇ m or less.
  • the hydrophobic functional group to be fixed is preferably a butyl group, a phenyl group, an octyl group or an octadecyl group, and particularly preferably an octadecyl group.
  • “Impurity contained in the synthesis process” means an impurity having a molecular weight different from that of the target synthetic oligonucleotide, for example, an incomplete length oligonucleotide often referred to as an nx fragment (n is the number of target nucleotides (nucleic acids), x Is a missing number, n, x is a positive integer, n> x, for example, n-1, n-2, etc.), n + 1 fragment incorporated in duplicate, acetyl group, isobutyryl group, cyanoethyl group, methyl group Oligonucleotides with insufficient deprotection of functional groups protecting nucleic acid monomers such as incomplete oligonucleotides such as depurinated and depyrimidines, insufficient backbone modified oligonucleotides such as phosphodiester impurities in phosphorothioates, and It is an isomer having partial chirality.
  • the typical synthetic oligonucleotide separation and analysis method of the present invention is as follows. That is, equilibrate a column containing a non-porous particle packing with a hydrophobic functional group immobilized in advance by passing an appropriate eluent, for example, an eluent containing a water-soluble organic solvent, an alkylammonium salt, and water. Then, a solution in which the synthetic oligonucleotide is dissolved is passed through the same eluent to bind the synthetic oligonucleotide into the column.
  • an appropriate eluent for example, an eluent containing a water-soluble organic solvent, an alkylammonium salt, and water.
  • the impurities contained in the synthetic oligonucleotide synthesis process and the target synthetic oligonucleotide are separated and eluted by a gradient that gradually increases the concentration of the water-soluble organic solvent in the eluent to be passed, that is, a so-called gradient. Pass the eluent that was passed again during equilibration to regenerate the column.
  • the eluent is not particularly limited, but it is preferable to combine an aqueous eluent containing an ammonium salt, preferably a salt of C1 to 4 alkylamine and an acid, with a C1 to 3 alcohol or nitrile water-soluble organic solvent.
  • Triethylamine and dibutylamine are preferable for the alkylamine, and carbonic acid, acetic acid, formic acid, trifluoroacetic acid, and propionic acid are preferable for the acid.
  • a combination of an aqueous eluent containing dibutylamine and acetic acid and acetonitrile is most preferred.
  • the salt concentration of the aqueous eluent is not particularly limited, but is preferably 1 to 100 mM, more preferably 5 to 50 mM, and particularly preferably 10 to 20 mM. Further, the pH of the aqueous eluent is not limited as long as it can be bound to and eluted from the column, preferably 6 to 8, and more preferably 6.5 to 7.5.
  • the column temperature during the measurement is preferably 25 to 80 ° C, more preferably 30 to 60 ° C, and most preferably 40 to 50 ° C.
  • a commercially available reverse phase chromatography apparatus can be used, and examples thereof include an analysis / separation apparatus such as Shimadzu Corporation Prominence or Waters Acquity. .
  • a commercially available analytical or separation column can be used.
  • MICRA registered trademark
  • NPS ODS-1 manufactured by EPROGEN particle size: 1.5 ⁇ m, 33 x 4.6 mm ID
  • Imtakt Prest Examples include a preparative column such as FF-C18 (particle diameter 2.0 ⁇ m, 75 ⁇ 4.6 mm ID).
  • Examples of the detection method used in the separation analysis method of one embodiment of the present invention include a detector using ultraviolet / visible absorption such as a synthetic oligonucleotide, a detector using a mass spectrum of a synthetic oligonucleotide, and the like.
  • the detection wavelength is, for example, 254 nm.
  • Acetonitrile was added to a 10 mM dibutylammonium acetate aqueous solution (pH 7.0), and an aqueous dibutylamine acetate solution (pH 7.0) containing acetonitrile having a final concentration of 4.5 v / v% was prepared as the first eluent.
  • the column was equilibrated by passing 10 mL or more of the first eluent.
  • the mobile phase flow rate was 1 mL / min.
  • NPS ODS-1 is a column containing a non-porous silica particle filler to which octadecyl groups are bonded.
  • the mobile phase flow rate was 1 mL / min.
  • the mobile phase was the first stage from the first eluent, with a linear gradient that increased the final concentration of acetonitrile to 18 v / v% in the first 7.5 minutes.
  • a two-stage gradient including a second-stage gradient with a gradient that increased the final acetonitrile concentration to 31.5 v / v% in the next 32.5 minutes.
  • Synthetic oligonucleotides and impurities bound to the column were separated and eluted by a linear gradient gradient that gradually increased the acetonitrile concentration.
  • the detector is an ultraviolet / visible (uv / vis) detector, and the detection wavelength is 254 nm.
  • Synthetic oligonucleotide 62-mer purchased from Eurofin Genomics (trade name: Standard Oligo 50 nmol scale product salt-free grade; SEQ ID NO: 1 (5′-CATGAGAAGTATGACAACAGCCCCACACCGGCTGTTTGTCATACTTCCTCATGGTTCTTCGGAA-3 ′) 40-mer (trade name: standard oligo 50 nmol scale product salt-free grade; SEQ ID NO: 2 (base sequence represented by 5′-CCACACCCGCGTTGTCATACTTCTCCATGGTTCTTCGGAA-3 ′)), 80-mer (trade name: Standard oligo 50 nmol scale salt-free grade; SEQ ID NO: 3 (5′-GTTT CATGTTGTTGGGATTGAGTTTTGAACTCGGCAACAAGAAACTGCCTGAGTTACATCAGTCGGTTTTCGTCGAGGGC-3 ') nucleotide sequence represented by), 100-mer (trade name: Standard oligo 50nmol-scale product salt-free grade; SEQ ID NO: 1 (5′-CAT
  • the detector was implemented in the same manner as in Example 1.
  • the peak of the synthetic oligonucleotide 40-mer at the retention time of 24 minutes the peak of the synthetic oligonucleotide 62-mer at the retention time of 29 minutes, and the synthetic oligonucleotide 80-mer at the retention time of 32 minutes.
  • a peak of the synthetic oligonucleotide 100-mer was observed at a retention time of 35 minutes, and a peak of the synthetic oligonucleotide 110-mer was observed at a retention time of 37 minutes.
  • the first eluent used in the equilibration step (1) of Example 1 was a 10 mM dibutylamine acetate aqueous solution (pH 7.0) containing acetonitrile having a final concentration of 9 v / v%, and the linear gradient of the separation elution step (3). This was carried out in the same manner as in Example 1 except that the concentration of acetonitrile collected was 54 v / v%.

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Abstract

L'invention fournit une technique destinée à séparer et analyser à un niveau élevé des impuretés telles qu'un oligonucléotide de longueur incomplète, ou similaire, contenu dans un mélange réactif d'oligonucléotide, dans le but d'une application d'un oligonucléotide synthétique à un médicament. Plus précisément, l'invention concerne un procédé selon lequel un oligonucléotide synthétique d'un 19 mère ou plus est soumis à une séparation et à une analyse par chromatographie sur colonne mettant en œuvre un éluant contenant un solvant organique hydrosoluble et de l'eau. Cet éluant contient une charge de particules non poreuse à laquelle est fixé un groupe fonctionnel hydrophobe.
PCT/JP2016/087219 2015-12-28 2016-12-14 Procédé de séparation et analyse WO2017115655A1 (fr)

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Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN113976187A (zh) * 2021-11-08 2022-01-28 天津中科博蕴生物技术有限公司 一种采用硅胶键合基质分离核酸的方法
WO2023282120A1 (fr) * 2021-07-06 2023-01-12 住友化学株式会社 Composition contenant un oligomère d'acide nucléique

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JPH08505700A (ja) * 1992-11-18 1996-06-18 サラセプ インコーポレイテッド 核酸断片の分離法
JP2002506425A (ja) * 1997-04-25 2002-02-26 トランスジエノミツク・インコーポレーテツド ポリヌクレオチド分離のための改良された液体クロマトグラフィー媒体

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JPH08505700A (ja) * 1992-11-18 1996-06-18 サラセプ インコーポレイテッド 核酸断片の分離法
JP2002506425A (ja) * 1997-04-25 2002-02-26 トランスジエノミツク・インコーポレーテツド ポリヌクレオチド分離のための改良された液体クロマトグラフィー媒体

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2023282120A1 (fr) * 2021-07-06 2023-01-12 住友化学株式会社 Composition contenant un oligomère d'acide nucléique
CN113976187A (zh) * 2021-11-08 2022-01-28 天津中科博蕴生物技术有限公司 一种采用硅胶键合基质分离核酸的方法

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TW201726917A (zh) 2017-08-01
JPWO2017115655A1 (ja) 2018-10-18

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