ORDERING INFO
(2004) Oligo Synthesis Ch 13 (2003) NNNA 22, 1439-1441 (2003) NNNA 22, 1407-1409 (2001) NNNA 20, 973-976 (2004) BACs 1, Ch 16, 21 (2004) Oligo Synthesis Ch 18 (2002) PNAS. 99, 4644-4649 (2001) NNNA 20, 507-514 (2000) NAR 28, 3125-3133 (1999) US Pat 5,902,879 (1997) NAR 25, 1155-1161 |
Amino Linkers are primarily used to functionalize an oligonucleotide at the 5'-end. The resulting amino modified oligonucleotides are used in DNA microarray production and as intermediates to functionally labeled oligonucleotides. Our non-nucleosidic amino linkers are made from a common secondary aminoalcohol, trans-4-aminocyclohexanol, which is subsequently derivatized utilizing our proprietary methoxyoxalamido (MOX) chemistry. This strategy allows us to easily tailor or customize the synthesis of any amino-linker amidite based on any commercially-available primary aliphatic diamine. These phosphoramidites exhibit increased stability in solution in comparison to other commercially available amino linkers made from primary aliphatic aminoalcohols. Our amino linkers have very long synthesizer lifetimes - typically 3-4 weeks. This translates to an overall cost savings to the end-user who sporadically incorporates these linkers into oligonucleotides, since a fresh amino-linker amidite preparation per use is no longer needed. In addition, most of our amino linkers are solids, which makes handling much easier. Our amino-linker phosphoramidites are available in different lengths and variable hydrophobicity and can only be added at the terminal 5'-end of an oligonucleotide on the synthesizer. All of our amino linkers have the MMT protecting group allowing the end-user to purify using a "trityl-on" protocol. Biotin phosphoramidites with increased stability in solution are convenient for the introduction of a biotin internally or at the 5'-end of an oligonucleotide. DMT-Biotin-Arm34-Ach, DMT-Biotin-Arm17-Ach, and DMT-Biotin-Arm17-T can be added singly at the 5'-end of the oligonucleotide. Biotin-Amino-propanediol- DMT and 5'-DMT-2'-Biotin-Arm19- 2'-dU can be added internally and sequentially to make highly biotinylated oligonucleotides for applications demanding fast binding kinetics and increased stability of the biotin-streptavidin complex. Furthermore, 5'-DMT-2'-Biotin-Arm19- 2'-dU (a biotin-modified uridine analog) can be used internally for oligoribonucleotides or, in place of thymidine, for oligodeoxyribonucleotides without altering the hybridization properties of the oligonucleotide. A special investigation conducted by Southern lab has shown that optimal spacer for immobilized oligos should have a low charge density and a length exceeding 40 atoms in length, giving up to 150-fold increase in the yield of hybridisation. At that time it was impossible to make an optimal 40 atoms spacer without any charged atoms. The spacer arms of our new super-long biotin amidites are designed to meet these criteria. They are non-charged and have up to 40 atoms between biotin and the closest negative charge on phosphate. They also have optimal rigidity and flexibility. Our longest arm amidite, DMT-Biotin-Arm34-Ach, is ideal for making large biotinylated DNA fragments where steric hindrance may otherwise reduce its streptavidin binding capacity. In addition, the long arm maximizes the density of the biotinylated oligonucleotides on the streptavidin coated matrices and allows nucleic acid processing enzymes to function efficiently at the surface. Applications where long arm spacers for biotin-modified oligos may be important include: All of our biotin amidites have the DMT protecting group, and thus, trityl monitoring and "trityl-on" oligonucleotide purification is possible. Spacers are normally used to position tags/labels at a desired length from the oligonucleotide and to form non-nucleoside hairpin loops within the oligonucleotide. Our non-nucleosidic spacers are made from a common secondary aminoalcohol, trans-4-aminocyclohexanol, which is subsequently derivatized utilizing our proprietary MOX chemistry. This strategy allows us to easily tailor or customize the synthesis of any spacer amidite based on any commercially-available primary aliphatic aminoalcohol. These phosphoramidites exhibit increased stability in solution in comparison to other commercially available spacers made from primary aliphatic alcohols. Our spacers have very long synthesizer lifetimes - typically 3-4 weeks. This translates to an overall cost savings to the end-user who sporadically incorporates spacers into oligonucleotides, since a fresh spacer amidite preparation per use is no longer needed. In addition, the majority of our spacers are solids, which makes handling much easier. Our spacer phosphoramidites are available in different lengths and variable hydrophobicity and can be added singly or sequentially to the 5'-end or in the middle of an oligonucleotide during synthesis. All of our spacers have the DMT protecting group, and thus, trityl monitoring and "trityl-on" oligonucleotide purification is still possible. Cleavable spacers extend the capabilities of normal spacers to allow for the chemical transformation produced by scission. They are used to introduce an internal linker which can subsequently be functionalized (cleaved) to form a new 5'-end of the oligonucleotide for the tethering of the oligo to a diagnostic probe. Alternatively, the oligo can be attached via the 5'-end to a solid support and subsequently be cleaved off. These phosphoramidites exhibit increased stability in solution in comparison to other commercially available spacers made from primary aliphatic alcohols. Our spacers have very long synthesizer lifetimes - typically 3-4 weeks. This translates to an overall cost savings to the end-user who sporadically incorporates spacers into oligonucleotides, since a fresh spacer amidite preparation per use is no longer needed. In addition, the majority of our spacers are solids, which makes handling much easier. Our cleavable spacers come in two flavors - disulfides and diols. Our diol spacers can be selectively cleaved using saturated aqueous NaIO4 for 30-40 min. The disulfide spacers can be cleaved with dithiothreitol or any other appropriate reducing reagent. All of our spacers have the DMT protecting group, and thus, trityl monitoring and "trityl-on" oligonucleotide purification is still possible. Our branching unit phosphoramidites are convenient for the introduction of a junction point internally or at the 5'-end of an oligonucleotide. They can be added singly or sequentially to make highly branched oligonucleotides. These phosphoramidites exhibit increased stability in solution in comparison to other commercially available branching amidites made from primary aliphatic alcohols. Our branching units have very long synthesizer lifetimes - typically 3-4 weeks. This translates to an overall cost savings to the end-user who sporadically incorporates branching units into oligonucleotides, since a fresh amidite preparation per use is no longer necessary. Our branching unit amidites have the DMT protecting group, and thus, trityl monitoring and "trityl-on" oligonucleotide purification is possible. For a single incorporation of a branching unit a 5 min coupling is necessary to ensure high yield. For a second and third incorporation of branching units a 20 min coupling time and adequately increased total amounts of amidites are needed to ensure optimum yield. |
These MOX precursor phosphoramidites are introduced at the 5'-end or internally in an oligonucleotide, and as in the case of the terminus MOX modifiers, the oligo can be post-synthetically derivatized with either primary aliphatic amines, amino alcohols, hydroxide, or ammonia. Since there are many commercially available primary aliphatic amines, this strategy not only enables the formation of adducts containing user-desired functionalities, but also allows the same parent oligonucleotide to be used to construct a vast number of differently modified products. One key advantage of the 2'-MOX precursors lies in being able not only to incorporate the monomer multiple times within the oligo, but also placing the precursor at any position other than at the 3'-end. Our 2'-MOX precursors have successfully been used to produce modified oligonucleotides exhibiting certain aberrations in physico-chemical properties to produce a desired effect. One example lies in the use of these precursor amidites to make modified oligonucleotides, which when annealed to their complementary unmodified strands, altered Tms while increasing annealing specificity compared to unmodified counterparts. Another example lies in the use of these modified oligonucleotides as primers (Fimers) for sequencing reactions. Fimers are routinely used to inhibit primer-dimer extension and non-specific PCR, which are two events that interfere in sequencing reactions. Finally, 2'-MOX precursors have been used in the preparation of highly functionalized oligonucleotides bearing multiple imidazole residues in the use as artificial ribonucleases. The MOX precursor amidites contain the DMT protecting group. An increased coupling time is necessary requiring the use of 5-ethylthio-1H-tetrazole as the catalyst. The 2'-SUC (2'-succinimido) precursor phosphoramidites are introduced at the 5'-end or internally in an oligonucleotide, and as in the case of our MOX modifiers, the oligo can be post-synthetically derivatized with either primary aliphatic amines, amino alcohols, hydroxide, or ammonia. Since there are many commercially available primary aliphatic amines, this strategy not only enables the formation of adducts containing user-desired functionalities, but also allows the same parent oligonucleotide to be used to construct a vast number of differently modified products. As with 2'-MOX precursors, 2'-SUC precursors can be incorporated multiple times within the oligo at any position other than at the 3'-end. Our 2'-SUC precursors have successfully been used to produce modified oligonucleotides exhibiting certain aberrations in physico-chemical properties to produce a desired effect. One example lies in the use of these precursor amidites to make modified oligonucleotides, which when annealed to their complementary unmodified strands, altered Tms while increasing annealing specificity compared to unmodified counterparts. Another example lies in the use of these modified oligonucleotides as primers (Fimers) for sequencing reactions. Fimers are routinely used to inhibit primer-dimer extension and non-specific PCR, which are two events that interfere in sequencing reactions. The SUC precursor amidites contain the DMT protecting group. An increased coupling time is necessary requiring the use of 5-ethylthio-1H-tetrazole as the catalyst. Terminus MOX modifiers are introduced at the 5'-end of oligonucleotides and can be post-synthetically derivatized with either primary aliphatic amines, amino alcohols, hydroxide, or ammonia. Since there are many commercially available primary aliphatic amines, this strategy not only enables the formation of adducts containing user-desired functionalities, but also allows the same parent oligonucleotide to be used to construct a vast number of differently modified products. We have successfully used these modifiers to make highly functionalized oligonucleotides bearing multiple imidazole residues in the use as artificial ribonucleases. Our terminus MOX modifiers come in two flavors - non-nucleosidic and thymidine based. The non-nucleosidic MOX modifiers, as in the case of our spacers and amino linkers, have trans-4-aminocyclohexanol as its core skeleton. Both types of these MOX modifiers, each having a rigid cyclic carbon scaffold at its core, are solids and exhibit the same high stability as our spacers and amino linkers in solution. These terminus MOX modifiers are available at different degrees of multiplicity with regard to the number of MOX groups incorporated onto the amidite. They do not contain any trityl protecting group. Therefore, neither trityl monitoring nor "trityl-on" purification of the modified oligonucleotide is possible. Covered by U.S. Patents 5,902,879, 6,548,251. Patents pending. Fimer, HyperStable and PluriPotent are trademark of Fidelity Systems. CONTACT INFO 301-527-0804 (tel) 301-527-8250 (fax) fsi1@fidelitysystems.com |