Oligonucleotide synthesis
Oligonucleotide synthesis is the chemical synthesis of relatively short fragments of
To obtain the desired oligonucleotide, the building blocks are sequentially coupled to the growing oligonucleotide chain in the order required by the sequence of the product (see
Oligonucleotides find a variety of applications in molecular biology and medicine. They are most commonly used as
History
The evolution of oligonucleotide synthesis saw four major methods of the formation of internucleosidic linkages and has been reviewed in the literature in great detail.[2][3][4]
Early work and contemporary H-phosphonate synthesis
In the early 1950s,
Thirty years later, this work inspired, independently, two research groups to adopt the H-phosphonate chemistry to the solid-phase synthesis using nucleoside H-phosphonate monoesters 7 as building blocks and pivaloyl chloride, 2,4,6-triisopropylbenzenesulfonyl chloride (TPS-Cl), and other compounds as activators.
Most often, H-phosphonate building blocks are protected at the 5'-hydroxy group and at the amino group of nucleic bases A, C, and G in the same manner as phosphoramidite building blocks (see below). However, protection at the amino group is not mandatory.[9][20]
Phosphodiester synthesis
In the 1950s,
Phosphotriester synthesis
In the 1960s, groups led by R. Letsinger[22] and C. Reese[23] developed a phosphotriester approach. The defining difference from the phosphodiester approach was the protection of the phosphate moiety in the building block 1 (Scheme 4) and in the product 3 with 2-cyanoethyl group. This precluded the formation of oligonucleotides branched at the internucleosidic phosphate. The higher selectivity of the method allowed the use of more efficient coupling agents and catalysts,[24][25] which dramatically reduced the length of the synthesis. The method, initially developed for the solution-phase synthesis, was also implemented on low-cross-linked "popcorn" polystyrene,[26] and later on controlled pore glass (CPG, see "Solid support material" below), which initiated a massive research effort in solid-phase synthesis of oligonucleotides and eventually led to the automation of the oligonucleotide chain assembly.
Phosphite triester synthesis
In the 1970s, substantially more reactive P(III) derivatives of nucleosides, 3'-O-chlorophosphites, were successfully used for the formation of internucleosidic linkages.
Synthesis by the phosphoramidite method
Building blocks
Nucleoside phosphoramidites
As mentioned above, the naturally occurring nucleotides (nucleoside-3'- or 5'-phosphates) and their phosphodiester analogs are insufficiently reactive to afford an expeditious synthetic preparation of oligonucleotides in high yields. The selectivity and the rate of the formation of internucleosidic linkages is dramatically improved by using 3'-O-(N,N-diisopropyl phosphoramidite) derivatives of nucleosides (nucleoside phosphoramidites) that serve as building blocks in phosphite triester methodology. To prevent undesired side reactions, all other functional groups present in nucleosides have to be rendered unreactive (protected) by attaching
- The 5'-hydroxyl group is protected by an acid-labile DMT (4,4'-dimethoxytrityl) group.
- Thymine and uracil, nucleic bases of thymidine and uridine, respectively, do not have exocyclic amino groups and hence do not require any protection.
- Although the nucleic base of guanosine and 2'-deoxyguanosine does have an exocyclic amino group, its basicity is low to an extent that it does not react with phosphoramidites under the conditions of the coupling reaction. However, a phosphoramidite derived from the N2-unprotected 5'-O-DMT-2'-deoxyguanosine is poorly soluble in acetonitrile, the solvent commonly used in oligonucleotide synthesis.[37] In contrast, the N2-protected versions of the same compound dissolve in acetonitrile well and hence are widely used. Nucleic bases adenine and cytosine bear the exocyclic amino groups reactive with the activated phosphoramidites under the conditions of the coupling reaction. By the use of additional steps in the synthetic cycle[38][39] or alternative coupling agents and solvent systems,[37]the oligonucleotide chain assembly may be carried out using dA and dC phosphoramidites with unprotected amino groups. However, these approaches currently remain in the research stage. In routine oligonucleotide synthesis, exocyclic amino groups in nucleosides are kept permanently protected over the entire length of the oligonucleotide chain assembly.
The protection of the exocyclic amino groups has to be orthogonal to that of the 5'-hydroxy group because the latter is removed at the end of each synthetic cycle. The simplest to implement, and hence the most widely used, strategy is to install a base-labile protection group on the exocyclic amino groups. Most often, two protection schemes are used.
- In the first, the standard and more robust scheme (Figure), Bz (benzoyl) protection is used for A, dA, C, and dC, while G and dG are protected with isobutyryl group. More recently, Ac (acetyl) group is used to protect C and dC as shown in Figure.[40]
- In the second, mild protection scheme, A and dA are protected with isobutyryl[41] or phenoxyacetyl groups (PAC).[42] C and dC bear acetyl protection,[40] and G and dG are protected with 4-isopropylphenoxyacetyl (iPr-PAC)[43] or dimethylformamidino (dmf)[44] groups. Mild protecting groups are removed more readily than the standard protecting groups. However, the phosphoramidites bearing these groups are less stable when stored in solution.
- The phosphite group is protected by a base-labile 2-cyanoethyl protecting group.[30] Once a phosphoramidite has been coupled to the solid support-bound oligonucleotide and the phosphite moieties have been converted to the P(V) species, the presence of the phosphate protection is not mandatory for the successful conducting of further coupling reactions.[45]
- In RNA synthesis, the 2'-hydroxy group is protected with TBDMS (t-butyldimethylsilyl) group.[46][47][48][49] or with TOM (tri-iso-propylsilyloxymethyl) group,[50][51] both being removable by treatment with fluoride ion.
- The phosphite moiety also bears a diisopropylamino (iPr2N) group reactive under acidic conditions. Upon activation, the diisopropylamino group leaves to be substituted by the 5'-hydroxy group of the support-bound oligonucleotide (see "Step 2: Coupling" below).
Non-nucleoside phosphoramidites
Non-nucleoside phosphoramidites are the phosphoramidite reagents designed to introduce various functionalities at the termini of synthetic oligonucleotides or between nucleotide residues in the middle of the sequence. In order to be introduced inside the sequence, a non-nucleosidic modifier has to possess at least two hydroxy groups, one of which is often protected with the DMT group while the other bears the reactive phosphoramidite moiety.[citation needed]
Non-nucleosidic phosphoramidites are used to introduce desired groups that are not available in natural nucleosides or that can be introduced more readily using simpler chemical designs. A very short selection of commercial phosphoramidite reagents is shown in Scheme for the demonstration of the available structural and functional diversity. These reagents serve for the attachment of 5'-terminal phosphate (1),
Synthesis cycle
Oligonucleotide synthesis is carried out by a stepwise addition of nucleotide residues to the 5'-terminus of the growing chain until the desired sequence is assembled. Each addition is referred to as a synthesis cycle (Scheme 5) and consists of four chemical reactions:
Step 1: De-blocking (detritylation)
The DMT group is removed with a solution of an acid, such as 2% trichloroacetic acid (TCA) or 3% dichloroacetic acid (DCA), in an inert solvent (dichloromethane or toluene). The orange-colored DMT cation formed is washed out; the step results in the solid support-bound oligonucleotide precursor bearing a free 5'-terminal hydroxyl group. It is worth remembering that conducting detritylation for an extended time or with stronger than recommended solutions of acids leads to depurination of solid support-bound oligonucleotide and thus reduces the yield of the desired full-length product.[citation needed]
Step 2: Coupling
A 0.02–0.2 M solution of nucleoside phosphoramidite (or a mixture of several phosphoramidites) in acetonitrile is activated by a 0.2–0.7 M solution of an acidic azole catalyst, 1H-tetrazole, 5-ethylthio-1H-tetrazole,[64] 2-benzylthiotetrazole,[65][66] 4,5-dicyanoimidazole,[67] or a number of similar compounds. A more extensive information on the use of various coupling agents in oligonucleotide synthesis can be found in a recent review.[68] The mixing is usually very brief and occurs in fluid lines of oligonucleotide synthesizers (see below) while the components are being delivered to the reactors containing solid support. The activated phosphoramidite in 1.5 – 20-fold excess over the support-bound material is then brought in contact with the starting solid support (first coupling) or a support-bound oligonucleotide precursor (following couplings) whose 5'-hydroxy group reacts with the activated phosphoramidite moiety of the incoming nucleoside phosphoramidite to form a phosphite triester linkage. The coupling of 2'-deoxynucleoside phosphoramidites is very rapid and requires, on small scale, about 20 s for its completion. In contrast, sterically hindered 2'-O-protected ribonucleoside phosphoramidites require 5-15 min to be coupled in high yields.[47][69][70][71] The reaction is also highly sensitive to the presence of water, particularly when dilute solutions of phosphoramidites are used, and is commonly carried out in anhydrous acetonitrile. Generally, the larger the scale of the synthesis, the lower the excess and the higher the concentration of the phosphoramidites is used. In contrast, the concentration of the activator is primarily determined by its solubility in acetonitrile and is irrespective of the scale of the synthesis. Upon the completion of the coupling, any unbound reagents and by-products are removed by washing.
Step 3: Capping
The capping step is performed by treating the solid support-bound material with a mixture of acetic anhydride and
- After the completion of the coupling reaction, a small percentage of the solid support-bound 5'-OH groups (0.1 to 1%) remains unreacted and needs to be permanently blocked from further chain elongation to prevent the formation of oligonucleotides with an internal base deletion commonly referred to as (n-1) shortmers. The unreacted 5'-hydroxy groups are, to a large extent, acetylated by the capping mixture.
- It has also been reported that phosphoramidites activated with 1H-tetrazole react, to a small extent, with the O6 position of guanosine.apurinic sitesthus formed are readily cleaved in the course of the final deprotection of the oligonucleotide under the basic conditions (see below) to give two shorter oligonucleotides thus reducing the yield of the full-length product. The O6 modifications are rapidly removed by treatment with the capping reagent as long as the capping step is performed prior to oxidation with I2/water.
- The synthesis of oligonucleotide phosphorothioates (OPS, see below) does not involve the oxidation with I2/water, and, respectively, does not suffer from the side reaction described above. On the other hand, if the capping step is performed prior to sulfurization, the solid support may contain the residual acetic anhydride and N-methylimidazole left after the capping step. The capping mixture interferes with the sulfur transfer reaction, which results in the extensive formation of the phosphate triester internucleosidic linkages in place of the desired PS triesters. Therefore, for the synthesis of OPS, it is advisable to conduct the sulfurization step prior to the capping step.[73]
Step 4: Oxidation
The newly formed tricoordinated phosphite triester linkage is not natural and is of limited stability under the conditions of oligonucleotide synthesis. The treatment of the support-bound material with iodine and water in the presence of a weak base (pyridine,
Solid supports
In solid-phase synthesis, an oligonucleotide being assembled is
Solid support material
In contrast to organic solid-phase synthesis and peptide synthesis, the synthesis of oligonucleotides proceeds best on non-swellable or low-swellable solid supports. The two most often used solid-phase materials are controlled pore glass (CPG) and macroporous polystyrene (MPPS).[79]
- CPG is commonly defined by its pore size. In oligonucleotide chemistry, pore sizes of 500, 1000, 1500, 2000, and 3000 Å are used to allow the preparation of about 50, 80, 100, 150, and 200-mer oligonucleotides, respectively. To make native CPG suitable for further processing, the surface of the material is treated with (3-aminopropyl)triethoxysilane to give aminopropyl CPG. The aminopropyl arm may be further extended to result in long chain aminoalkyl (LCAA) CPG. The amino group is then used as an anchoring point for linkers suitable for oligonucleotide synthesis (see below).
- MPPS suitable for oligonucleotide synthesis is a low-swellable, highly chloromethylstyrenein the presence of a porogeneous agent. The macroporous chloromethyl MPPS obtained is converted to aminomethyl MPPS.
Linker chemistry
To make the solid support material suitable for oligonucleotide synthesis, non-nucleosidic linkers or nucleoside succinates are covalently attached to the reactive amino groups in aminopropyl CPG, LCAA CPG, or aminomethyl MPPS. The remaining unreacted amino groups are capped with acetic anhydride. Typically, three conceptually different groups of solid supports are used.
- Universal supports. In a more recent, more convenient, and more widely used method, the synthesis starts with the universal support where a non-nucleosidic linker is attached to the solid support material (compounds 1 and 2). A phosphoramidite respective to the 3'-terminal nucleoside residue is coupled to the universal solid support in the first synthetic cycle of oligonucleotide chain assembly using the standard protocols. The chain assembly is then continued until the completion, after which the solid support-bound oligonucleotide is deprotected. The characteristic feature of the universal solid supports is that the release of the oligonucleotides occurs by the hydrolytic cleavage of a P-O bond that attaches the 3'-O of the 3'-terminal nucleotide residue to the universal linker as shown in Scheme 6. The critical advantage of this approach is that the same solid support is used irrespectively of the sequence of the oligonucleotide to be synthesized. For the complete removal of the linker and the 3'-terminal phosphate from the assembled oligonucleotide, the solid support 1 and several similar solid supports[80] require gaseous ammonia,[81] aqueous ammonium hydroxide, aqueous methylamine,[82] or their mixture[83] and are commercially available.[84][85] The solid support 2[86] requires a solution of ammonia in anhydrous methanol and is also commercially available.[87][88]
- Nucleosidic solid supports. In a historically first and still popular approach, the 3'-hydroxy group of the 3'-terminal nucleoside residue is attached to the solid support via, most often, 3'-O-succinyl arm as in compound 3. The oligonucleotide chain assembly starts with the coupling of a phosphoramidite building block respective to the nucleotide residue second from the 3'-terminus. The 3'-terminal hydroxy group in oligonucleotides synthesized on nucleosidic solid supports is deprotected under the conditions somewhat milder than those applicable for universal solid supports. However, the fact that a nucleosidic solid support has to be selected in a sequence-specific manner reduces the throughput of the entire synthetic process and increases the likelihood of human error.
- Special solid supports are used for the attachment of desired functional or reporter groups at the 3'-terminus of synthetic oligonucleotides. For example, the commercial[89] solid support 4[90] allows the preparation of oligonucleotides bearing 3'-terminal 3-aminopropyl linker. Similarly to non-nucleosidic phosphoramidites, many other special solid supports designed for the attachment of reactive functional groups, non-radioactive reporter groups, and terminal modifiers (e.c. cholesterol or other hydrophobic tethers) and suited for various applications are commercially available. A more detailed information on various solid supports for oligonucleotide synthesis can be found in a recent review.[78]
Oligonucleotide phosphorothioates and their synthesis
Oligonucleotide phosphorothioates (OPS) are modified oligonucleotides where one of the oxygen atoms in the phosphate moiety is replaced by sulfur. Only the phosphorothioates having sulfur at a non-bridging position as shown in figure are widely used and are available commercially. The replacement of the non-bridging oxygen with sulfur creates a new center of
Synthesis of OPS is very similar to that of natural oligonucleotides. The difference is that the oxidation step is replaced by sulfur transfer reaction (sulfurization) and that the capping step is performed after the sulfurization. Of many reported reagents capable of the efficient sulfur transfer, only three are commercially available:
- 3-(Dimethylaminomethylidene)amino-3H-1,2,4-dithiazole-3-thione, DDTT (3) provides rapid kinetics of sulfurization and high stability in solution.[73][93][94] The reagent is available from several sources.[95][96]
- 3H-1,2-benzodithiol-3-one 1,1-dioxide (4)[97][98] also known as Beaucage reagent displays a better solubility in acetonitrile and short reaction times. However, the reagent is of limited stability in solution and is less efficient in sulfurizing RNA linkages.[93][94]
- N,N,N'N'-Tetraethylthiuram disulfide (TETD) is soluble in acetonitrile and is commercially available.[99] However, the sulfurization reaction of an internucleosidic DNA linkage with TETD requires 15 min,[100] which is more than 10 times as slow as that with compounds 3 and 4.
Automation
In the past, oligonucleotide synthesis was carried out manually in solution or on solid phase. The solid phase synthesis was implemented using, as containers for the solid phase, miniature glass columns similar in their shape to low-pressure chromatography columns or syringes equipped with porous filters.[101] Currently, solid-phase oligonucleotide synthesis is carried out automatically using computer-controlled instruments (oligonucleotide synthesizers) and is technically implemented in column, multi-well plate, and array formats. The column format is best suited for research and large scale applications where a high-throughput is not required.[102] Multi-well plate format is designed specifically for high-throughput synthesis on small scale to satisfy the growing demand of industry and academia for synthetic oligonucleotides.[103]
History of mid to large scale oligonucleotide synthesis
Large scale oligonucleotide synthesizers were often developed by augmenting the capabilities of a preexisting instrument platform. One of the first mid scale synthesizers appeared in the late 1980s, manufactured by the Biosearch company in Novato, CA (The 8800). This platform was originally designed as a peptide synthesizer and made use of a fluidized bed reactor essential for accommodating the swelling characteristics of polystyrene supports used in the Merrifield methodology. Oligonucleotide synthesis involved the use of CPG (controlled pore glass) which is a rigid support and is more suited for column reactors as described above. The scale of the 8800 was limited to the flow rate required to fluidize the support. Some novel reactor designs as well as higher than normal pressures enabled the 8800 to achieve scales that would prepare 1 mmol of oligonucleotide. In the mid 1990s several companies developed platforms that were based on semi-preparative and preparative liquid chromatographs. These systems were well suited for a column reactor approach. In most cases all that was required was to augment the number of fluids that could be delivered to the column. Oligo synthesis requires a minimum of 10 and liquid chromatographs usually accommodate 4. This was an easy design task and some semi-automatic strategies worked without any modifications to the preexisting LC equipment. PerSeptive Biosystems as well as Pharmacia (GE) were two of several companies that developed synthesizers out of liquid chromatographs. Genomic Technologies, Inc.[104] was one of the few companies to develop a large scale oligonucleotide synthesizer that was, from the ground up, an oligonucleotide synthesizer. The initial platform called the VLSS for very large scale synthesizer utilized large Pharmacia liquid chromatograph columns as reactors and could synthesize up to 75 mmol of material. Many oligonucleotide synthesis factories designed and manufactured their own custom platforms and little is known due to the designs being proprietary. The VLSS design continued to be refined and is continued in the QMaster synthesizer[105] which is a scaled down platform providing milligram to gram amounts of synthetic oligonucleotide.
The current practices of synthesis of chemically modified oligonucleotides on large scale have been recently reviewed.[106]
Synthesis of oligonucleotide microarrays
One may visualize an oligonucleotide microarray as a miniature multi-well plate where physical dividers between the wells (plastic walls) are intentionally removed. With respect to the chemistry, synthesis of oligonucleotide microarrays is different from the conventional oligonucleotide synthesis in two respects:
- Oligonucleotides remain permanently attached to the solid phase, which requires the use of linkers that are stable under the conditions of the final deprotection procedure.
- The absence of physical dividers between the sites occupied by individual oligonucleotides, a very limited space on the surface of the microarray (one oligonucleotide sequence occupies a square 25×25 μm)[107] and the requirement of high fidelity of oligonucleotide synthesis dictate the use of site-selective 5'-deprotection techniques. In one approach, the removal of the 5'-O-DMT group is effected by electrochemical generation of the acid at the required site(s).[108] Another approach uses 5'-O-(α-methyl-6-nitropiperonyloxycarbonyl) (MeNPOC) protecting group, which can be removed by irradiation with UV light of 365 nm wavelength.[107]
Post-synthetic processing
After the completion of the chain assembly, the solid support-bound oligonucleotide is fully protected:
- The 5'-terminal 5'-hydroxy group is protected with DMT group;
- The internucleosidic phosphate or phosphorothioate moieties are protected with 2-cyanoethyl groups;
- The exocyclic amino groups in all nucleic bases except for T and U are protected with acyl protecting groups.
To furnish a functional oligonucleotide, all the protecting groups have to be removed. The N-acyl base protection and the 2-cyanoethyl phosphate protection may be, and is often removed simultaneously by treatment with inorganic bases or amines. However, the applicability of this method is limited by the fact that the cleavage of 2-cyanoethyl phosphate protection gives rise to
Regardless of whether the phosphate protecting groups were removed first, the solid support-bound oligonucleotides are deprotected using one of the two general approaches.
- (1) Most often, 5'-DMT group is removed at the end of the oligonucleotide chain assembly. The oligonucleotides are then released from the solid phase and deprotected (base and phosphate) by treatment with aqueous anion-exchangeHPLC followed by desalting.
- (2) The second approach is only used when the intended method of purification is reverse-phase HPLC. In this case, the 5'-terminal DMT group that serves as a hydrophobic handle for purification is kept on at the end of the synthesis. The oligonucleotide is deprotected under basic conditions as described above and, upon evaporation, is purified by reverse-phase HPLC. The collected material is then detritylated under aqueous acidic conditions. On small scale (less than 0.01–0.02 mmol), the treatment with 80% aqueous acetic acid for 15–30 min at room temperature is often used followed by evaporation of the reaction mixture to dryness in vacuo. Finally, the product is desalted as described above.
- For some applications, additional reporter groups may be attached to an oligonucleotide using a variety of post-synthetic procedures.
Characterization
As with any other organic compound, it is prudent to characterize synthetic oligonucleotides upon their preparation. In more complex cases (research and large scale syntheses) oligonucleotides are characterized after their deprotection and after purification. Although the ultimate approach to the characterization is
- In ESI MS spectra, a given oligonucleotide generates a set of ions that correspond to different ionization states of the compound. Thus, the oligonucleotide with Da). Most useful for characterization are the ions with n ranging from 2 to 5. Software supplied with the more recently manufactured instruments is capable of performing a deconvolution procedure that is, it finds peaks of ions that belong to the same set and derives the molecular massof the oligonucleotide.
- To obtain more detailed information on the impurity profile of oligonucleotides, capillary electrophoresis mass spectrometry (CEMS)[114]are used.
See also
- Nucleic acids
- Nucleic acid analogues
- Peptide nucleic acid
- Bridged Nucleic Acids
References
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Further reading
- Comprehensive Natural Products Chemistry, Volume 7: DNA and Aspects of Molecular Biology. Kool, Eric T., Editor. Neth. (1999), 733 pp. Publisher: (Elsevier, Amsterdam, Neth.)
- Beaucage, S. L.; Iyer, R. P. (1992). "Advances in the synthesis of oligonucleotides by the phosphoramidite approach". Tetrahedron. 48 (12): 2223–2311. .
- Beaucage, S. L.; Iyer, R. P. (1993). "The functionalization of oligonucleotides via phosphoramidite derivatives". Tetrahedron. 49 (10): 1925–1963. .
- Beaucage, S. L.; Iyer, R. P. (1993). "The synthesis of modified oligonucleotides by the phosphoramidite approach and their applications". Tetrahedron. 49 (28): 6123–6194. .
- Beaucage, S L. "Oligodeoxyribonucleotides synthesis. Phosphoramidite approach. Methods in Molecular Biology (Totowa, NJ, United States) (1993), 20 (Protocols for Oligonucleotides and Analogs), 33–61.
- Reese, C. B. (2002). "The chemical synthesis of oligo- and poly-nucleotides: a personal commentary". Tetrahedron. 58 (44): 8893–8920. .
- Glaser, Vicki (1 May 2009). Oligo Market Benefits from RNAi Focus. Bioprocessing. Vol. 29. Mary Ann Liebert. pp. 46–49. OCLC 77706455. Archived from the original on 16 April 2010. Retrieved 25 July 2009.)
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