Patent Application
20050027116
The present invention relates to a support system for solid phase synthesis of oligomers, such as oligonucleotides. Furthermore, the invention relates to a method for synthesis of oligonucleotides on a solid support.
Oligonucleotides are polymers built up by polycondensation of ribonucleoside (RNA) or deoxyribonucleoside (DNA) phosphates.
Oligonucleotides can be assembled by repetitive addition of nucleotide monomers using solid-phase methods. Since the introduction of solid-phase synthesis [R. B. Merrifield, J. Am. Chem. Soc. 85 (1963) 2149], the following requirements have been worked out: (1) The solid support must be insoluble and preferably unswellable in the solvent used. (2) Functional groups on the solid support must allow covalent binding of the first nucleoside in a reproducible manner. (3) The solid support must be chemically inert to all reagents used during synthesis and deprotection. The most commonly used supports are controlled pore glass beads (CPG), silica, or polystyrene beads.
Below the synthesis cycle of the commonly used phosphoramidite method is described:
The process is repeated until the desired oligonucleotide sequence has been synthesized. After synthesis, all protecting groups are removed and the oligonucleotide is cleaved from the solid support.
In the synthesis, defective oligonucleotides are produced as a consequence of several effects, prominently premature termination of synthesis, followed by capping, which results in 5′ truncated molecules, and depurination during the synthetic cycles that is followed by strand scission during deprotection. Recently, attention has also been directed at the appearance of shorter, internally deleted products—so called n-1 and n-2 fragments [Temsamani et al, (1995), Nucleic Acids Research 23(11), 1841-1844]; [Fearon et al, (1995) Nucleic acids Res., 23(14), 2754-2761].
The need for pure oligonucleotides is exemplified by the requirement for high quality products in antisense therapy [Gelfi et al, (1996), Antisense and Nucleic Acid Drug Development, 6, 47-53], in routine diagnostics applications, or for physicochemical and structural studies [Agback et al, (1994) Nucleic Acids Res, 22(8), 1404-12]. Also in molecular cloning impure oligonucleotides frequently reduce efficiency an complicate interpretation of results [McClain et al, (1986) Nucleic Acids Res. 14(16), 6770]; [Nassal, (1988) Gene, 66(2), 279-94].
Preparative gel electrophoresis provides the best resolution for purification of oligonucleotides. The method is however laborious, often leading to considerable loss of material, and it is poorly suited for automation and scale-up.
Chromatographic separation can solve some of these problems, offering a potential for scale-up with minimal losses and using fully automatized instruments. These positive aspects are off-set by the rather poor resolving power of most chromatographic systems. As a partial solution to this problem chromatographic separation of oligonucleotides labeled with affinity tags has been used. The commonly used trityl-on oligonucleotide separation on reversed-phase columns, or capture of 5′-thiol labelled or biotinylated oligonucleotides on respective thiol-affinity [Bannwarth et al, (1990), Helv. Chim. Acta, 73, 1139-1147] or avidin columns [Olejnik et al, (1996), 24(2), 361-366] offer the possibility to isolate fragments with intact 5′-ends. However, the 5′ part of depurinated molecules notoriously contaminate oligonucleotides purified by this method.
A mild basic system has been proposed for partial deprotection and cleavage of apurinic-sites with the oligonucleotides still bound to the solid support. In this manner the 5′ ends of depurinated molecules can be discarded before the oligonucleotides are released from the support, followed by isolation of molecules with intact 5′ ends [Horn et al, (1988), Nucleic Acids Res, 16(24), 11559-71]. In practice, this strategy was accompanied by a substantial loss of products, due to inadvertent release of oligonucleotides during cleavage of depurinated sites.
In WO92/09615 there is described the use of an alkoxysilyl group as a linker of the oligonucleotide to the support. This linker is inert during the synthetic cycles and it resists conditions that cleave apurinic sites. The linker is finally cleaved from the solid support with tetra butyl ammonium fluoride (TBAF) to obtain, after reversed-phase separation of DMTr-containing material, an oligonucleotide with both 3′- and 5′-ends intact. However, synthesis of this support was laborious and inconvenient. Due to low reactivity of the functional group of the linker the degree of substitution of the support becomes low which leads to insufficient nucleoside loadings of the support. Thus, this method is not suitable for preparation of support useful for large scale synthesis.
According to a first aspect, the invention provides a support system for solid phase synthesis of oligomers. The support system comprises a support, a linker and a starting compound of the oligomer. The starting compound is bound to the support via a disiloxyl linkage. The disiloxyl function is linked to a hydroxyl group on the support. The functional groups connected to the disiloxyl group are very reactive allowing for reproducible and controlled loading of the starting compounds.
The support system of the invention is easier to produce compared to prior art systems and provides for high loadings to the support. According to the invention high loading values are obtained for the starting nucleoside. These loadings, often higher than 200 μmol/g, are required for cost-effective large scale synthesis.
The linkage is inert during the synthesis cycles and resists conditions that cleave apurinic sites.
In a preferred embodiment, the starting compound is a nucleoside and the solid phase synthesis is used for the synthesis of oligonucleotides.
Supports with immobilized oligonucleotides can be used as hybridization affinity matrices. Some possible applications of such supports are: purification of DNA-binding proteins, affinity purification of plasmids, as a support for gene assembly (from oligonucleotides) and for diagnostic purposes, etc.
In the new support system of the present invention the first nucleoside is bound to the support via a disiloxyl linkage and the system is preferably represented by the following formula (I).
wherein
The protecting groups R1 and R7 are protecting groups usually used for protection of 5′ and 2′ position of ribo- and deoxiribonucleosides. R1 may bee selected from a trityl, monomethoxy trityl, dimethoxytrityl, pixyl or other higher alkoxy-substituted trityl-protecting groups.
R7 may bee selected from tertbutyldimehylsilyl (TBDMS), methoxytetrahydropyranoyl (MTHP), tetrahydropyranoyl, methyl or allyl.
In a preferred embodiment of the invention R3, R4, R5, R6 are isopropyl. The choice of R3, R4, R5, R6 is dictated by stability vs. lability requirements of the disiloxyl linker. It is known that these properties can easily be controlled by modifying electron donating parameters of the substituents.
X can be any anchoring group, preferably O, S or an amide function, provided it is stable to the conditions used under synthesis and the reagent to cleave apurinic sites. The same proviso applies also to the (p-Y)n linker and (p-Z)m. Thus, there are no other restrictions on Y and Z.
Z is exemplified by a tetraethylene glycol residue.
A wide range of porous as well as non-porous solid supports can be used as supports in methods according to the present invention. The group of preferred supports includes cross linked polystyrenes, silica, polysaccharides, crosslinked polysaccharides and various glasses.
When the oligophosphotriester linker (-Y)n is present the above formula a support is provided resulting in even greater oligonucleotide purity than without said linker. By preparing the supports through a series of synthetic cycles before addition of the cleavable disiloxyl linker and synthesis of the desired oligonucleotide, any nonspecific sites of synthesis will be neutralized. This linker gives improved contact between the starting nucleoside and an incoming reagent and ensures that also oligonucleotides starting from sites not intended for synthesis on the support none the less contribute to the production of the desired oligonucleotide.
According to a second aspect the invention provides a method for oligonucleotide synthesis on a solid support Supp. The method comprises the steps:
In step (i) an oligophosphotriester linker (-Y)n is synthesized on the solid support and a starting nucleoside is bound to the linker via a (
-z)m linker and a disiloxyl group.
According to one embodiment of the method, the disiloxyl linkage is cleaved selectively according to known methods (Markiewicz W. T., 1979, Journal of Chemical Reserche (M) 0181-0197) with a compound containing fluoride ions, before step (v). A preferred fluoride containing compound is tetra alkyl ammonium fluoride. Trityl ammonium hydrogene fluoride is also suitable. The purification is performed by reversed phase chromatography, using the 5′-protecting group as an affinity handle.
According to an alternative embodiment of the method according to the invention, step (v) is performed by exonuclease treatment whereby non-protected oligonucleotides will be digested. This embodiment is especially suitable for in situ synthesis where chromatography is not possible.
The invention will be described more closely below in association with an Experimental part and the accompanying drawings, in which
The preparation of the support system according to the invention can be performed according to scheme 1 illustrated below:
This procedure comprises the following steps:
According to the invention the homobifunctional, readily available reagent 1,3-dichloro-1,1,3,3-tetraisopropyl disiloxane (2) (scheme 1) was used. In other words, the reagent used in the present invention has two reactive functions which enables high and controllable substitution.
A disiloxyl residue was applied as a stable linker function between a nucleoside and a solid support. The reactive intermediates (3) or (5) were synthesized in one or three steps, respectively according to Scheme 1 above.
No attempts were made to isolate intermediate (3), therefore silylation of appropriately protected nucleosides (1) were performed using only a slight excess of (2). The addition of an excess of an 13-atoms long chain diol (tetraethyleneglycol) resulted in the formation of an unsymmetrical disiloxyl derivative (4), used subsequently for the synthesis of phosphoroamidite (5).
The invention requires a support functionalized with hydroxyl groups linked to the support through nonhydrolyzable bonds. Mono R, hydroxyalkyl-derivatized polystyrene particles (from Pharmacia) was used without modifications. Derivatization of CPG proceeded according to Scheme 2, below.
This scheme includes the following reactions:
The CPG was activated by conventional aminopropylsilanizing [Pon, (1993) In Agraval, S. (ed.), Methods in Molecular Biology. Protocols for Oligonucleotides and Analogs. Humana Press Inc.]. Prior to further derivatization, the amino CPG support was treated with trichloracetic acid in dichlormethane according to Pon [Pon, (1993), supra]. Compound (10) was prepared in high yield starting from an inexpensive 6-aminohexanoic acid and γ-butyrolacton. It was conveniently converted to the mixed anhydride (11) in a reaction with isobutylchloroformate, and immediately used for coupling to CPG, see Scheme 2. Using different ratios of (11) and a solid support, loadings ranging from 15 to 60 μmol/g were obtained. The derivatized support was exhaustively capped with acetic anhydride and silanized with trimethylsilylchloride, TMSCl.
Controlled-pore glass (CPG) (1000 Å) was obtained from CPG Inc. (Fairfield, USA) and was aminopropylsilanized according to Pon et al. [Pon, 1993, supra]. Crosslinked polystyrene particles (10 μm diameter) derivatized with hydroxylalkyl functions (Mono R) (from Pharmacia, Uppsala, Sweden).
Oligonucleotide syntheses were performed either on an ABI 394 DNA Synthesizer (Perkin Elmer) or on a Gene Assembler Plus (Pharmacia Biotech AB) instrument. Analytical liquid chromatography of the synthesized oligonucleotides was performed on a Hitachi-Merck La Chrom HPLC system equipped with a LiChrospher RP 18 (5 mm) column (Merck) and using a linear gradient of solvent A: acetonitrile 5% v/v in triethylammonium acetate 0.1 M, pH 7.0 and solvent B: acetonitrile 40% v/v in triethylammonium acetate 0.1 M, pH 7.0. Preparative separations were made on an FPLC system (Pharmacia Biotech AB) using a reversed-phase Pep RPC 10/10 column (Pharmacia) and the above solvent gradient.
5′-Dimethoxytrityl-3′-O-1,1,3,3-tetraisopropyl-3-tetraethylen-glycoloxy-disiloxyl thymidine (4)(B=T).
5′-DMTr-thymidine (1) (1.30 g, 2.3 mmol) and imidazol (0.32 g, 4.8 mmol) were dried by coevaporation with dry pyridine and dissolved in 20 ml of dry pyridine. 1,3-Dichloro-1,1,3,3-tetraisopropyl disiloxane (2) (0.75 g, 2.4 mmol) was added and the mixture was stirred at 20° C. for 3 hrs to achieve complete consumption of starting material. Tetraethylene glycol (3.9 g, 23 mmol) was added to the 9 formed compound (3) (see Scheme 1) and the mixture was stirred for 6 hr. Pure compound (4) was isolated as an oil (1.62 g, 72%), following standard bicarbonate work-up, extraction with dichloromethane, evaporation of the organic phase, and flash column chromatography. 1H-NMR (CDCl3): 0.85-1.05 (m, 28H), 1.43 (s, 3H), 2.25-2.42 (m, 2H), 2.85 (s, broad, 1H), 3.27-3.52 (dd, 2H), 3.54-3.76 (m, 12H), 3.79 (s, 3H), 3.80-3.85 (m, 2H), 4.09 (m, 1H), 4.68 (m, 1H), 6.40 (t, 1H), 6.83 (d, 4H), 7.23-7.40 (m, 9H), 7.63 (d, 1H), 9.19 (s, broad, 1H).
The other three nucleoside derivatives were obtained in a similar manner.
Synthesis of a (2-cyanoethyl) N,N-diisopropylphosphoramidite (5) (B=T). The thymidine derivative (4) (1.50 g, 1.53 mmol) was dried by coevaporation with toluene (20 ml) and dissolved in anhydrous dichlormethane (15 ml). To this magnetically stirred solution dry triethylamine (0.85 ml, 6.0 mmol) was added followed by 2-cyanoethyl-N,N-diisopropylaminophosphochloridate (710 mg, 3.0 mmol). After 15 min stirring at 20° C., TLC showed consumption of all starting material and formation of a single product. The reaction mixture was quickly partitioned between saturated aqueous sodium bicarbonate and dichloromethane and extracted with dichlormethane (2×50 ml). The residue obtained after evaporation of the organic phase was dried by coevaporation with toluene and purified on a short silica gel column, prepared and eluted with CH2Cl2/Et3N 9/1 v/v. Fractions containing the desired product were combined, evaporated in vacuo, coevaporated with dry
triethylamine, and dried in high vacuum to yield 1.57 g (87%) of an oil; 31P-NMR (CDCl3+2 drops of triethylamine) 148.61 ppm.
The remaining amidites were prepared as above.
Asymmetrical anhydride (11) (see Scheme 2) was used for derivatization of aminopropylated CPG. The substitution level was analyzed based on DMTr cation release as described in [Gait, (ed) (1984) Oligonucleotide synthesis; a practical approach. IRL Press]. CPG derivatized to the extent of 28 μmol/g was selected for further experiments. Several DNA synthesis columns were loaded with this support (ca 10 mg each), and they were subjected to 10 coupling cycles with a standard thymidine amidite, followed by coupling of one of the nucleoside amidites (5) to obtain support (14). These supports were used for oligonucleotide synthesis.
Method A: Construction of Support (13),
Several portions of a cross-linked polystyrene support (Mono R) (from Pharmacia) (0.50 g) were dried by coevaporation with pyridine and suspended in pyridine (2 ml). Different volumes of compound (3) (Scheme 1), prepared at a 1 mmol scale in pyridine (10 ml), see Example 1 above, were added to the above suspensions and the mixtures were shaken at 20° C. for 2 hr. All activated sites that could theoretically form in the reaction of unreacted (2) with the solid support were quenched by the addition of methanol (5 ml). After 1 hr shaking, the mixture was filtered, dried by washing with dry pyridine, and transferred back to the stoppered flask, where unreacted hydroxyl groups were capped with Ac2O/DMAP (4-dimethylaminopyridine)/pyridine for 2 hrs. The amounts of DMTr thymidine bound directly to the support via the disiloxyl bond (13) were checked spectrophotometrically as above.
Method B: Construction of Support (14),
A polystyrene support (10 mg), derivatized with hydroxyalkyl groups, was packed into cassettes for synthesis of oligonucleotides on a Gene Assembler Plus instrument (Pharmacia). These packed supports were subjected to one coupling cycle using a standard thymidine amidite that was 5 times more diluted than recommended in standard coupling procedures. The support was extensively capped (10 min) on the machine operating in a manual mode. Under the above conditions the DMTr release experiments gave values comparable to those from the orginal 0.2 μmol supports. All supports were further derivatized by coupling 9 consecutive thymidine nucleotides, followed by coupling of the appropriate amidite (5) from Example 2 above. These couplings were performed using standard amidite concentrations and synthesis protocols.
Using the ABI 394 DNA Synthesizer and CPG Supports
The CPG support (14) described above was used for oligonucleotide synthesis. All couplings were performed using amidites protected by a benzoyl group at the exocyclic amine functions, under conditions recommended by the manufacturer for 0.2 μmol scale synthesis, except that nucleoside amidites were used at half the recommended concentrations. The final DMTr groups were left on the synthesized oligonucleotide.
Synthesis on a Gene Assembler (Pharmacia) using the Polystyrene Support
All syntheses were done at the 0.2 μmol scale using PAC amidites (Pharmacia Biotech AB), according to the manufacturer's instructions and without any changes in the recommended amidite concentrations. Supports constructed according to methods A (13) or B (14) in Example 4 above were used, see also
Normal scale reaction of standard nucleoside amidites or the modified amidite (5) with hydroxyalkyl-polystyrene support resulted in a very high loading. Quantitative analysis of the released DMTr-group revealed loadings of as much as 250 to 290 μmol/g. Also functionalizations involving an excess of reagent (3) gave a relatively high degree of substitution. Reaction of 0.5 mmol of (3) per 1 g of solid support at 20° C. for 2 hrs resulted in a support loaded at 180 μmol/g. These comparatively large numbers were a consequence of the high density of hydroxyl groups on the support and of the high reactivity of the reagents used. Such highly derivatized supports are valuble for large-scale synthesis of short therapeutic oligonucleotides. For the synthesis of relatively long oligonucleotides measures had to be taken to limit this high degree of substitution. A satisfactory loading (38 μmol/g) could be obtained by using only 0.1 mmol of (3) per 1 g of support. Several-fold dilution of (5) under the recommended 0.1 M concentration was the best method for direct incorporation of (5) on the polystyrene support. The same dilution method was applied to the first standard amidite used for synthesis of the polystyrene version of the support (14). All coupling reactions described above were followed by an extensive capping procedure to block any unreacted hydroxyl groups.
Different deprotection procedures were used, depending on the type of support that was applied in the synthesis.
CPG-anchored oligonucleotides. A syringe filled with a mixture of Et3N/EtOH 1:1 v/v was connected to a cassette containing support for oligonucleotide synthesis. Treatment of the support with base proceeded for 3 hrs at 20° C., with the occasional addition of a new aliquot of the solvent to the cassette. The support was washed with ethanol (2 ml), water (2×2 ml), dried with acetonitrile (3×2 ml), and after opening the cassette the solid support was transfered to a Sarstedt screw-lock tube. Tetrabutyl ammonium fluoride (TBAF) 0.5 M in dry tetrahydrofuran (THF) (200 μl) was added and the mixture was incubated for 4 hr at 20° C. The cleavage of the disiloxyl linker could alternatively be done using 200 ml of 0.5 M TBAF in dry DMF at 65° C. for 30 min. Concentrated aq. NH3 (2 ml) was introduced and the mixture was placed in a 65° C. oven for 12 hrs. After partial concentration the oligonucleotide was desalted on a NAP 10 Sephadex column (Pharmacia Biotech AB) and analyzed by HPLC on a RP 18 column. Preparative runs were done on an FPLC using a reversed-phase Pep RPC column. Care was taken not to fractionate the hydrophobic trityl-containing product but rather to collect the whole peak, which closely resembles separations on disposable RP cartridges (Sep-Pak, C18, Waters, USA). After evaporation, the final removal of the DMTr groups was done using 80% aq. acetic acid for 20 min at 20° C., with subsequent evaporation of the acid. Alternatively, oligonucleotides phosphorylated at their 5′-position by the Tr-S phosphorylating reagent were finally deprotected according to the published procedure [Connolly, (1987) Tetrahedron Lett., 28(4), 463-466].
Polystyrene support-anchored oligonucleotides. After completed synthesis, the support was transfered from the cassette into a Sarstedt tube and subjected to treatment with concentrated aq. NH3 for 90 min at 65° C. After cooling, the particles were briefly centrifuged and the upper liquid phase was removed. The solid-support was washed 3 times with 2 ml of water and dried by washing with acetonitrile. Two hundred μl of 0.5 M TBAF in THF was added and the mixture was incubated for 4 hr. Finally, the mixture was diluted with 0.8 ml water and the oligonucleotide was desalted on a NAP 10 Sephadex column. The further deprotection and purification steps follow exactly those described for CPG-bound oligonucleotides.
Oligonucleotides to be analyzed electrophoretically were labelled with 32P at their 5′-end using polynucleotide kinase in a 50 μl reaction volume of 50 mM KAc, 10 mM MgCl2, 10 mM Tris-HAc (pH 7.5), 10 μCi (g-32P)ATP (3000 Ci/mmol), and 10 U polynucleotide kinase (Amersham) at 37° C. for 30 min. The labelling reaction was stopped by desalting on a Sephadex G-50 spin column, followed by incubation at 65° C. for 5 min. All oligonucleotides analyzed electrophoretically in this study were synthesized with a 5′-phosphate to ensure that cleaved apurinic oligonucleotides would label with the same efficiency as the full-length molecules. After separation on a denaturing 6% polyacrylamide gel the radioactivity was recorded by autoradiography (Amersham Hyperfilm) or, for quantitative measurements of band intensities, scanned on a Phosphorimager instrument (Molecular Dynamics).
The risk of depurination of an oligonucleotide increases with the number of purines and the total length of the oligonucleotide. An increased amount of purines in an oligodeoxynucleotide gives a high probability of its depurination and the following brake-down. To show the capability of the new method to eliminate these short sequences, two 81-mer (AG)40T sequences were synthesized in parallel using standard and novel CPG-based supports (14), respectively. Partially deprotected 5′-DMTr-substituted oligonucleotides were analyzed and isolated by HPLC. Both products were detritylated, 5′-32P kinased and electrophoretically separated on a denaturing polyacrylamide gel. The results, presented in
A 91-mer oligonucleotide (M13C91: 5′-P-GCCTGCAGGTCGACTCTAGA(T)50CGGCCAGTGCCAAGCTTGCA-3′) were synthesized according to the invention in order to test how it would work as a padlock probe [Nilsson et al (1994), supra] that is able to circularize in presence of an oligonucleotide template (M1350comp: 5′-TTTTTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTTTTT-3′) and a DNA-ligase. The ligation reaction was performed using 0.3 pmol of 5′-labelled probe and 5.5 pmol of template in a volume of 10 μl 20 mM Tris-HCl (pH 8.3), 25 mM KCl, 10 mM MgCl2, 1 mM NAD, 0.01% Triton X-100 and 10 U of Tth DNA ligase. The sample were subjected to one, two or three cycles of 94° C. for 15 seconds and 55° C. for 10 min. The reactions were cooled on ice and stopped by adding 10 μl of loading buffer containing 50% formamide and 10 mM EDTA followed by a incubation at 65° C. for 10 min. The reactions were analyzed on a denaturing polyacrylamide gel as above.
The result of the ligation is shown in
The present invention delivers products free of truncated and post-depurination cleaved fragments, morover, the isolated products contain much less n-1 fragments. The amount of this n-1 material was estimated, in a study performed on a short 5-mer sequence and using a standard synthesis protocol ([Iyer et al, (1995), 14(6) 1349-1357]), to be roughly 3, to 5%. By applying pre-cap procedure according to Iyer et al and short contact time of ammonia with the CPG support it was possible to lower this figure to 1.5 to 2%. In contrast, in an experiment according to the present invention for synthesis of a 20-mer using CPG support (14), the amount of contaminating n-1 sequences was found to be 1.9%.
The support system of the present invention is not limited to the solid-phase synthesis of oligonucleotides described above. Another contemplated possibility is to use it as a linker between support and hydroxyl containing components in the combinatorial
chemistry ([Plunkett et al, (1995), J. Org. Chem., 60(19), 6006-6007]).
| Number | Date | Country | Kind |
|---|---|---|---|
| 9603171-1 | Aug 1996 | SE | national |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 09254048 | Jul 1999 | US |
| Child | 09921203 | Aug 2001 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 10106832 | Mar 2002 | US |
| Child | 10685331 | Oct 2003 | US |
| Parent | 09921203 | Aug 2001 | US |
| Child | 10106832 | Mar 2002 | US |
