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  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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Definitions

• the present invention relates to a polynucleotide diagnostic system and method.
• polynucleotide diagnostic systems both based on hybridization between complementary segments of a polynucleotide probe and a single-strand polynucleotide analyte.
• the polynucleotide analyte is made single stranded and fixed to a solid support, such as a nitrocellulose filter.
• the support is then reacted, under complementary-strand annealing conditions, with a reporter-labeled probe which is complementary to a target base-sequence region of the analyte. After washing several times to remove unbound probe, the solid support is analyzed for the presence of reporter.
• a second type of polynucleotide diagnostic system involves two analyte-specific probes which are each complementary to a distinct region of the analyte polynucleotide. The first probe is linked to a solid support, and the second probe is free in solution and carries multiple reporter molecules.
• the analyte is mixed with the two probes under conditions which allow annealing of complementary polynucleotide strands, including annealing of both the immobilized and reporter-carrying probes to the polynucleotide analyte, to attach the reporter to the solid support by means of the analyte.
• the dual-probe system avoids the problem of having to fix the test nucleic acid material to a solid support, nevertheless, the method has a number of limitations.
• the test nucleic acid is derived from duplex nucleic acid, as is often the case, hybridization between the analyte polynucleotide and its complementary strand competes with the hybridization between the analyte and the two probes.
• the two-probe system relies on higher order kinetics than is the case for single-probe systems, it is inherently slower than a single-probe system.
• the need for two different probes increases the cost of the system.
• the dual-probe system suffers the same limitation as the single-probe system mentioned above--each analyte polynucleotide binds only one "reporter" probe.
• the analyte binding can therefore be performed under conditions in which sequence-specific pairing between the reagent polymer and analyte occurs without competition from analyte-complementary strand annealing in the assay reaction mixture.
• the system therefore has the capacity for very high signal levels by virtue of the relatively large number of reporter molecules which can combine with each polynucleotide analyte molecule.
• the invention includes a diagnostic reagent for use in detecting an analyte polynucleotide having a defined target base sequence.
• the reagent comprises a solid support, and linked to the support, multiple polynucleotide-binding polymers.
• Each polymer is composed of a sequence of base-complementary recognition moieties, each of which is adapted to hydrogen bond to corresponding, in-sequence base of the target region of the analyte, under selected binding conditions, and an unbranched, substantially stereoregular backbone (1) supporting the recognition moieties at positions which allow hydrogen bonding between the recognition moieties and the corresponding in-sequence bases of the target, and (2) having a backbone charge density which is substantially less than that of the analyte under the selected binding conditions.
• the recognition moieties include purine and pyrimidine bases and the backbone is composed of a series of backbone moeities joined by achiral, predominantly uncharged linkages.
• the same recognition moieties are carried on a backbone whose linkages include uncharged, stereoisomerically defined or achiral linkages alternating with negatively charged, achiral linkages.
• a diagnostic system for detecting a polynucleotide analyte having a defined target sequence includes the diagnostic reagent and a reporter having a polycationic tail adapted to bind by electrostatic attraction to the charged backbone of the polynucleotide analyte, but not to the substantially less charged, or uncharged, backbone of the reagent polymers under preselected binding conditions.
• One or more reporter groups attached to the polycationic tail are adapted to produce a signal by which the presence of the reporter can be detected.
• the polynucleotide analyte is added to the diagnostic reagent under conditions in which the analyte is in a single-strand form and which allow sequence-specific pairing between the analyte and the reagent polymers.
• the reagent is washed to remove unbound test material.
• the reagent and bound analyte are then reacted with the reporter, under preselected conditions in which the polycationic tail in the reporter binds electrostatically to the charged backbone of the polynucleotide but not to the substantially less charged or uncharged backbone of the reagent polymers.
• the reagent is again washed to remove unbound reporter.
• the presence and/or amount of analyte bound to the reagent is determined in situ by measuring the reporter signal associated with the reagent-bound analyte, or the reporter is eluted from the reagent/analyte and the reporter signal in the eluate is measured.
• Figure 1 shows preferred purine and pyrimidine structures used in forming polymer molecules of the invention
• Figure 2 shows preferred purine-like and pyrimidine-like recognition moieties used in forming the polymer molecules
• Figure 3 shows preferred cyclic backbone moities used in forming the polymer molecules
• Figure 4 shows preferred acyclic backbone moieties used in forming the polymer molecules
• Figures 5A and 5B illustrate two preferred subunit assembly schemes for coupling N 1 ---N 2 type subunit backbones
• Figure 6 shows the backbone structures of subunit dimers A-A through D-D formed in accordance with the methods illustrated in Figures 5A and 5B, and two cyclic backbone structures formed in accordance with the methods illustrated in Figures 7A and 7B;
• Figures 7A-7C illustrate three preferred subunit assembly schemes for coupling N 1 ---E type subunit backbones; and Figure 8 shows preferred acyclic backbone structures of subunit dimers formed in accordance with the methods illustrated in Figures 7A-7C; and
• Figure 9 shows the sythesis of a tetranucleotide analog having methylphosponate backbone linkages alternating with a phosphotriester linkage
• Figure 10 illustrates reactions for attaching spacer-arm molecules to a solid support
• Figure 11 shows a general method for synthesis of polyamines from N-methyl amino acids
• Figure 12 shows a method for synthesis of polyamines having a terminal primary amino group
• Figure 13 shows the preparation of the quaternary arnmoniuim cationic tail having a terminal primary amino group
• Figure 14 illustrates a reaction for preparing a multi-charge enzymatic reporter according to an embodiment of the invention
• Figure 15 illustrates a reaction for preparing a two-charge fluorescent reporter according to an embodiment of the invention.
• Figure 16 illustrates various components involved in the diagnostic system and method of the invention.
• the diagnostic system of the invention includes a solid support reagent composed of a solid support carrying a plurality of nucleotide-binding polymer molecules.
• the polymeric composition of the invention is designed to bind, with a selected binding affinity, to a polynucleotide containing a target sequence of bases.
• the composition is composed of non-homopolymeric, substantially stereoregular molecules or species of the form:
• B-R i are a series of base-specific subunits containing a backbone moiety B and a recognition moiety R i which is selected to bind specifically by Watson/Crick base pairing to a corresponding, in-sequence base in the target sequence, and the subunits are joined through their backbone moieties predominantly achiral, substantially uncharged bonds.
• the design and selection of suitable subunits for use in constructing the polymer species will be described in Section I below. Methods for coupling subunits through achiral linkages are described in Section III, with subunit-protective group strategies involved in subunit synthesis being discussed in Section II.
• the polymer species are synthesized by sequential subunit coupling, to form polymer molecules of a selected length and sequence.
• the length of the target sequence and polymer sequence is selected to achieve a desired binding specificity.
• the binding affinity of the polymer for the target can be selectively varied by several strategies discussed in Section IV, including the choice of recognition moieties which are capable of forming either three (for greater binding affinity) or two (for lesser affinity) base-paired hydrogen bonds with the corresponding target base.
• the resulting composition contains polymer species or molecules, all having substantially the same sequence of subunits and substantially the same sequence of intersubunit linkage types. In functional terms, all of the polymer species have substantially the same binding affinity for the target polynucleotide. Methods for assembling the polymer, once a desired subunit sequence is selected, are given in Section V.
• the polymer composition is useful in a novel solid-phase diagnostic system which is described in Section VI-VII. This system is based on the binding of analyte polynucleotide molecules to support-bound polymer molecules and subsequent elctrostatic attac hme nt of multiple polycationic reporter molecules to the polynucleotide, to give an amplified reporter signal for each bound analyte molecule.
• the design of the subunits B-R i which are suitable for use in forming the polymer species of the inventicon involves a number of structural and/or s tereochemical criteria which must be met both by the backbone and recognition moieties and by the linkage between the two. The design requirement of the recognition moiety will be considered first.
• the recognition moiety of each subunit must provide two or three hydrogen-bonding groups held in an unambiguous configuration adapted for hydrogen bonding to two or three of the Watson/Crick hydrogen bonding sites on a specified in-sequence base of the target genetic sequence.
• the tautomeric state of the recognition moiety should be relatively stable, and (2) the recognition moiety should have a structure which provides a relatively rigid arrangement of the hydrogen-bonding groups. Such rigidity is best afforded by a ring structure having the polar hydrogen-bonding groups either forming part of the ring or directly attached to the ring.
• the preferred recognition moiety structures include purine, purine-like, pyrimidine, and pyrimidine-like structures which are designed to form Watson/Crick base pairing, through either two or three hydrogen bonds, with selected polynucleotide bases.
• the group of subunits used in polymer synthesis includes at least two recognition moieties which are base-specific for different polynucleotide bases, and preferably one or more recognition moieties for each of the four bases in a natural DNA or RNA polynucleotide.
• FIG. 1 shows exemplary purine and pyrimidine type recognition moieties.
• the purine structures 1 and 2 are designed to bind to thyrnine or uracil bases, structures 3-6, to guanine bases; structures 7-9, to cytosine bases, and structures 10-12, to adenine bases.
• Structures 1, 4, 5, 6, 8, and 10-12 are R i type moieties adapted to bind to corresponding in-sequence bases through two hydrogen bonds, and the remaining structures are R j type moieties which form three hydrogen bonds on base pairing.
• purine and pyrimidine nucleosides are useful in synthesizing a variety of other subunits which are suitable for use in polymer synthesis. These subuni,ts, modified if necessary with amine protective groups, can be obtained from commercial sources, or prepared according to known methods, such as those described or referenced in Example 1.
• a number of purine-like or pyrimidine-like structures in which the recognition moiety is joined to the backbone through an annular carbon are shown in Figure 2. These structures have base pairing specificities and hydrogen bonding properties like those of the analogous structures shown in Figure 1.
• the binding properties of a polymer containing a carbon-linked recognition moiety may not be significantly different from that of a polymer whose recognition moities are nitrogen-linked, as in Figure 1, subunits incorporating the carbon-linked moieties generally require a greater synthetic effort than do subunits containing preformed purine and pyrimidines However, for some subunit syntheses, such as the synthesis of the achiral acyclic backbone subunits described in Example 10, the carbon-linked recognition moieties provide a useful starting material.
• each subunit has the general form N 1 ---E, or N 1 ---N 2 , where N 1 and
• N 2 are nucleophilic groups and E is an electrophilic group.
• the preferred nucleophilic groups are amino, hydroxyl and hydrazino; and the preferred electrophilic groups, and/or electrophilic linking agents, are derivatives of carbonic, thiocarbonic, carboxylic, and sulfonic acid.s.
• Backbone moieties can have either a cyclic or an acyclic structure. While the total number of possible backbone moiety structures is very large, nevertheless, only a rather limited number of structures are of actual practical value due to a number of factors. The initial procedure by which promising backbone moieties were selected was as follows.
• Each resulting polynucleotide/polymer duplex was then examined for coplanarity of the Watson/Crick base-pairs, torsional and angle strain in the prospective polymer backbone, degree of distortion imposed on the nucleic acid strand, and interstrand and intrastrand nonbonded interactions. Special attention was paid to whether or not each amide-containing backbone could readily adopt a conformation wherein its amide moieties were planar.
• the required unit backbone length i.e., the N 1 ---E spacing in an N 1 ---E or activated N 1 ---N 2 -E subunit
• the required unit backbone length is 5-7 atoms for backbone moieties constituting or derived from deoxyribose or ribose (cyclic backbone structures), with a 6-atom length being optimal.
• Subunit structure judged acceptable in the above modeling studies were then assessed for feasibility of synthesis (on the basis of key synthetic reactions reported in the literature, or reactions carried out on model compounds, and/or via actual synthesis of the subunits) and stability of the assembled polymer backbone (preliminary stability studies were generally carried out with suitably linked model compounds or subunit dimers). These types of studies were used to further restrict the number of candidate backbone structures. From this restricted candidate pool the cyclic backbone structures A-G shown in Figure 3 were ultimately selected as preferred structures.
• subunits A-D containing N 1 ----N 2 type cyclic backbone moieties include: 2'-deoxyribonucleosides (structure A);
• acylic backbone moiety structures I-N shown in Figure 4 all of which contain a one-atom methylene spacer between the backbone and recognition moieties, gave a good modeling prediction for favorable base-pairing to a complementray polynucleotide.
• Analogous structures containing a two-carbon spacer showed acceptable, but less favorable, binding conformation.
• the structures shown in the figure, and the analogous two-carbon spacer structures, are preferred acylcic backbone moieties because of their general ease of synthesis. It should be mentioned, however, that a number of other backbone moieties are also entirely feasible and suitable -- although generally not as easy and/or inexpensive, to synthesize.
• the moiety is attached at normal point of attachment and with the normal stereoisomeric configuration of purine or pyrimidine bases to the ribose or deoxyribose groups of nucleosides.
• one-and two-carbon atom spacers are required for placing the recognition moieties at favorable binding positions, with one-atom spacers being preferred, as discussed above.
• all of the backbone/recognition moiety linkages be either of define chirality or achiral.
• the linkages are considered to be of defined chirality, for purposes of definition herein, if each of the linkages in any given subunit position in all of the polymer molecules has the same stereoisomeric configuration, or chirality. That is, although the subunits in different sequence positions may have different internal stereoisomer configurations (including achirality at specific sequence positions), all of the linkages at a given sequence position among the polymer molecules have the same stereoisomeric configuration. Usually defined chirality is most easily achieved by using the same stereoisomeric configuration in all of the subunits.
• Subunits of this type are also readily synthesized, as will be discussed below, using natural D-nucleoside starting material. With reference to Figure 4, it is seen that only structures I and L have chiral linkages between the backbone and recognition moieties. These subunits are readily synthesized in homochiral form by using homochiral starting material , as will be described.
• the one-atom linkages are attached to backbone nitrogen atoms, are are therfore achiral. Also, of course, the rnethylene spacers are themselves achiral.
• nucleophile-insensitive intersubunit linkages include carbamate, amide, and sulfonamide linkages.
• the corresponding nucleophile-sensitive protective groups for the recognition moieties include: benzoyl for the N4 of C; benzoyl or p-nitrobenzoyl for the N6 of A; acetyl or isobutyryl for the N2 of G; and N2,N6-bisisobutyryl for 2,6-diaminopurine residues. Removal of these groups after completion of polymer assembly is effected by treatment with ammonium hydroxide.
• intersubunit linkage to be used is sensitive to nucleophiles, such as ammonium hydroxide
• suitable protective groups are those which can be removed by strong non-nucleophilic bases -- via a ⁇ elimination mechanism.
• nucleophile-sensitive intersubunit linkages include: carbonate; ester; and, to a lesser extent, triocarbamate linkages.
• Suitable protective groups for the recognition moieties removable via ⁇ elimination include: 2-(4-nitrophenyl)ethoxy carbonyl or 2-(phenyl sulfonyl) ethoxycarbonyl for both the N4 of C and the N6 of A; and the 9-fluorenyl inethoxycarbonyl for the N2 of G and the N2 and N6 of 2,6-diaminopurine residues. Removal of these groups after completion of polymer assembly is effected by treatment with the strong nonucleophilic base 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU), under stringently anhydrous conditions.
• DBU strong nonucleophilic base 1,8-diazabicyclo[5.4.0]undec-7-ene
• nucleophile of the backbone moiety generally N1 in the above structures
• polymer assembly strategy employs selected backbone-protective groups which are readily cleared by mild acid.
• One primary criterion for selection of protective groups is that they be adequately stable, but not so stable that conditions required for their removal would damage the growing polymer.
• a principal problem in the case of polymers assembled from cyclic backbone moieties is the particular acid sensitivity of the glycosidic bond linking protected purine residues to the C1 of their backbone moieties.
• a secondary criterion for selection of the backbone protective group is that it be easily introduced.
• the following backbone-protecting groups are preferred: for primary hydroxyls, the di(p-methoxy) trityl group; for primary amines, p-methoxytrityl; and for a secondary amine (as in morphilino-type backbone moieties), the phenylisopropoxycarbonyl group.
• These protective groups can be readily removed by treatment with 0.2 M dichloroacetic acid in dichloromethane.
• Subunits having a deoxydeoxynucleoside subunit structure can be obtained from commercial sources or prepared via literature methods, as described in Example I.
• the subunits include the following ribosides and deoxyribosides, which are identified according to the struture numbers of the recognition moieties given in Figure 1: adenosine and deoxyadenosine (structure 1); 2,6-diaminopurine riboside and deoxyriboside (structure 2); cytodine and deoxycytodine (structure 3); 4-methoxy-2- ⁇ yrimidinone deoxyriboside (structure 4); 2-hydroxy-5-methyl pyrimidine deoxiriboside (structure 5);
• 2-hydroxypyrimidine riboside structure 6
• guanosine and deoxyguanosine structure 7
• inosine and deoxyinosine structure 8
• thioguanosine and deoxythioguanosine structure 9
• uradine and deoxyuridine structure 10
• thymidine 2-hydroxypyrimidine riboside
• guanosine and deoxyguanosine structure 7
• inosine and deoxyinosine structure 8
• thioguanosine and deoxythioguanosine structure 9
• uradine and deoxyuridine structure 10
• thymidine 2-hydroxypyrimidine riboside
• guanosine and deoxyguanosine structure 7
• inosine and deoxyinosine structure 8
• thioguanosine and deoxythioguanosine structure 9
• uradine and deoxyuridine structure 10
• the 5'-arnino-2',5'-dideoxyribonucleosides (structure B in Figure 3) are prepared according to methods detailed in Example 3. Briefly, the selected deoxyribonucleosides, base-protected if necessary, are reacted with triphenyl phosphine, carbon tetrabromide, and lithium azide to form the corresponding 5'-azidonucleoside, which is then reduced by hydrogenation in the presence of a palladium on carbon catylyst.
• the nucleosides may be obtained as in Example 1, and base-protected as in Example 2. The stereochemistry of the reactant nucleosides is preserved in forming the 5' amino nucleoside analogs.
• An alternative reduction method is used in reducing the azide group of 5'-azido-5-bromo uridine, as described in Example 3.2.
• non-catalytic hydrogenation is needed to prevent removal of the ring bromine atom.
• the azide is placed on the 5' position by first tosylating the 5' hydroxyl group, then displacing with azide, as detailed in Example 3.2.
• the 3'-amino-2',3'-dideoxyribosnucleosides are prepared according to methods detailed in Example 4. Briefly, thymidine which is protected at its 5' hydroxyl is tosylated at its 3' hydroxyl, and this is followed by an intramolecular displacement involving the 2 oxy base substituent. The resulting ring is now opened by treatment with azide, yielding a 3' azido analog of the correct stereoisomeric form. This analog can be be converted to a selected-base analog by reacting the azide compound with a selected purine or pyrimidine base. The latter may be base protected, if necessary, for subsequent subunit coupling reactions, as described below. The thymidine or other azide analog is then reduced to produce the desired 3' amine nucleoside. The stereochemistry is of the thymidine starting material is preserved in the synthesis.
• morpholino-type subunit derivatives represented by structure D in Figure 3 are detailed in Example 5 for a variety of different recognition moieties. Briefly, a selected nucleoside, base-protected if necessary, is dissolved in an ammonium salt, such as ammonium biborate, and then reacted with sodium periodate to form transient 2', 3' dialdehydes, which then close upon an ammonium ion to form morpholino ring having 2' and 4' hydroxyls. The compound is then treated with sodium cyanoborohydride to remove the ring hydroxyls. The ring nitrogen is preferably protected as a 2-phe ⁇ ylisopropylcarbamate for subsequent subunit coupling. The sterochemistry of the nucleoside starting material is retained.
• an ammonium salt such as ammonium biborate
• Deoxyribose subunit structures having a 5' acetic acid group can be prepared according the general synthetic scheme described in Example 6, which details the synthesis of the 5' acetic acid compounds represented by structureF.
• a selected deoxyribonucleoside which is protected at the 3' hydroxyl is converted to the 5' aldehyde, and subsequently treated with a 2-carbon Wittig reagent to give the unsaturated acetic acid derivative.
• Reduction of the side-chain olefin gives the desired 5' acetic acid compound.
• the reaction preserves the sterochemistry of the starting nucleoside material
• the analogous 5' formate compound (structure E in Figure 3) is formed by treating the above 5' nucleoside aldehyde with a one-carbon Wittig reagent, and hydrosly sing the resulting enol to form form the corresponding formaldehyde derivative, which is oxidized to the desired acid.
• the reaction preserves the stereochemistry of the starting nucleoside material.
• the 5-atom chain amino acid, subunit represented by Structure I in Figure 4 is prepared according to the general procedures outlined in Examples 7-9. Briefly, an (S)-5 carboxy pyrrolidone was converted to the corresponding stereochemically pure
• the purine used in subunit synthesis is preferably contains an electron-withdrawing group at the 6 position, to reduce the reactivity of the 1 and 3 ring nitrogens, i.e., to minimize pyrrolidone coupling at a ring nitrogen.
• the pyrrolidone-derivized purine or pyrimidine may then be converted to the amine derivative, and base protected, if necessary, prior to the ring opening step which will be described below.
• Example 7.1 and 7.2 detail methods for forming the cytosine pyrrolidone and its base-protected derivative.
• the adenosine pyrrolidone formed in Examples 7.3-7.5 employs 6-chloropurine as the starting material, and the corresponding pyrrolidone is converted to the adenosine derivative through azide formation as described.
• the adenosine is base-protected, as in
• Example 7.6 prior to ring opening.
• a similar approach is used to generate base protected guanine pyrrolidone, starting from 2-amino-6 chloropurine, as described in Examples 7.7-7.9.
• Similar methods are used in synthesizing 2,6-diaminopurine pyrrolidone, inosine pyrrolidone, and 2-hydroxypyrimidine pyrrolidone, also as detailed in Example 7.
• the pyrrolidone is then treated via a series of reactions which cleave the pyrrolidone ring to form an amino acid with a t-BOC protected amine.
• Examples 8.1-8.4 describe the synthesis of such t-BOC amino acids having one of a number of selected recognition moieties.
• the t-BOC protective group may be removed to form the corresponding amino acid represented by structure I in Figure 4.
• the amino acid may be used directly for subunit coupling, according to reactions given below.
• the t-BOC protected compound may be activated at its acid group for use in subunit coupling reactions.
• a 6-member heterocycle such as a pyrimidine or nicotinate
• a reactive methylene on the carbon ring position at which attachment to the backbone is desired.
• the cytosine analog is formed by reacting 5-amino-5-bromopyrimidine to form the corresponding 5-position carboxaldehyde.
• the uridine analog is formed by converting 6-hydroxynicotinic esters to the corresponding benzylic alcohols. This compound is converted to the aldehyde by reaction in the presence of manganese dioxide.
• the aldehyde compound is then reacted with the desired amino acids, such as 4-aminobutyric acid, with reaction at the amine group producing an unstable imine which is reduced to form the stable amine subunit.
• the secondary amine can be protected, for subunit coupling involving activation of the acid group, by a tBOC group as described in Example 10.1.
• the C-carbon backbone analog of the above compound is prepared, using 3-aminopro ⁇ rionic acid, and this compound is further treated with nitrous oxide to form the corresponding N-nitroso compound, which is subsequently reduced with H 2 IPd in the presence of iron salts to give the hydrazino acid subunit.
• the coupling reactions used in forming the polymer molecules of the invention are stepwise reactions which join one selected subunit or subunit sequence to another selected subunit or subunit sequence.
• the coupling reactions will be described generally with respect to coupling a single subunit B-R 1 having a selected recognition moiety R 1 to another single subunit B-R 2 having the same or a different selected recognition moiety R 2 , to form a dimer of the form
• R 1 and R 2 have the specific sequence shown.
• N 1 and N 2 are nucleophilic backbone groups, such as hydroxyl and amine groups, which can be activated with an electrophile E, to form an activated
• N 1 -E or N 2 -E backbone group which can then react with a second N 1 ----N 2 type backbone moiety to form an N 1 ----N 2 -E-N 1 ----N 2 backbone-linked dimer.
• the subunit backbones of this types which have been described specifically above are the cyclic backbone structures A-D in Figure 3.
• the activated N 2 nucleophile is the 3' hydroxyl group in structure C is the 5' hydroxyl and in structure D, the 6' position hydroxyl corresponding to the 5' position hydroxyl in structure C.
• a subunit having a selected recognition moiety R 1 is activated with an electrophile E.
• the star at the recognition moiety indicates any required base protection.
• the selected subunit is protected at its N 1 nucleophile, to ensure that (a) only the N 2 nucleophile is activated and (b) the activated subunit cannot self-polymerize.
• the protective group is preferably an acid-labile group, such as dirnethoxytrityl (DMTO).
• the activating reagent shown in Figure 5A has the general form:
• X is oxygen or sulfur
• C is an active electrophile capable of reacting with a nucleophile, such as a hydroxyl oxygen or amine nitrogen, with displacement of Y, to form the activated subunit:
• Subunit activation reactions involving carbonyl activated subunits are detailed in Example 11 for the 5'-protected, 2' deoxynucleosides represented at A in Figure 4; in Example 12 for the 5'-protected amino nucleosides represented at B in Figure 4; and in Example 13 for the N-protected morpholino-type subunits shown at D in Figure 4.
• the general reaction conditions used to activate the hydroxyl groups in these structures are generally applicable; subunit activation reactions involving thiocarbonyl-activated subunits are detailed in Example 14 for the 5'-amino nucleosides represented at B; and in Example 15, for the morpholino-type subunits shown at D in Figure 3.
• the activated complex is purified by conventional methods, such as silica gel chromoatography, and then reacted with a second subunit whose selected recognition moiety R 2 will form the next in-sequence recognition moiety in the completed polymer.
• the coupling reaction is preferably carried out under mild conditions in which the activated group can react with backbone N 2 amine groups, but not N 1 hydroxyl groups. Therefore, the method is suitable for coupling subunits of the type represented by structures B-D in Figure 4, but not subunit structure A.
• the oligomer can be extended by repeating the above steps of (a) activating the free N 2 nucleophile in the second subunit, separating the activated species from the activating agent, and coupling the activated compound with the next-in-sequence subunit, whose backbone is unprotected.
• This method is used particularly in forming short oligomer blocks by solution methods which will be described below and which are suitable for solid-phase block assembly.
• the second coupling method outlined in Figure 58 is much preferred.
• the second method differs from the first method in that polymer growth occurs by addition of an excess of activated subunit to an existing subunit or polymer chain, rather than, as in the first method, by addition of an unactivated subunit to an activated chain.
• the existing subunit or subunit chain is shown by a subunit whose recognition moiety is R 1 (second line in Figure 5B).
• This subunit has a free N 1 backbone nucleophile and an N 2 nucleophile which is protected by a preferably acid-stable linkage to a solid support or by virtue of being linked to a chain of subunits which are linked to a solid support.
• the coupling reaction adds the N 2 -activated second subunit to the N 1 -protected first subunit to couple the two through an N 2 -E-N 1 bond, and form a compound which is protected at both free backbone nucleophile sites.
• This compound is now treated, for example by reaction with acid, to deprotect the acid-labile N 1 protective group on last-added subunit, and the procedure is repeated to build up a desired sequence polymer.
• the N 2 -activated subunit which will form the last-in-sequence subunit must be protected at its N 1 backbone site, to allow selective activation at the N 2 site and to prevent self-polymerization of the activated compound.
• the N 1 -deprotected subunit which is to couple to the activated subunit should be protected at its N 2 site to allow selective reaction of its N 1 moiety with the N 2 -activated subunit.
• the method is suitable for oupling nucleosides (structure A in Figure 4) as well as subunits whose cyclic backbones contain both amine and hydroxyl backbone nucleophiles, such as structures B-D in this figure.
• the reaction methods used in coupling structure A subunits through a carbonate bond are detailed in Example 12, Briefly, a subunit containing a 5' protected backbone moiety is activated at its 3' hydroxyl, and reacted with another subunit (or growing chain) which is protected at its 3' hydroxyl.
• the coupling reaction is carried out in the presence of a catalyst, such as N-methylimidazole or N,N-dirnethylaminopyridine, which is necessary for forming the carbonate bond.
• a catalyst such as N-methylimidazole or N,N-dirnethylaminopyridine
• For coupling subunits containing structure 8-D cyclic backbones, where intersubunit carbamate or thiocarbamate bonds are formed much milder uncatalyzed coupling conditions, such as those described with reference to the first method above, are suitable.
• this second coupling method for forming a polymer by solid-phase subunit addition, is that a substantial molar exess of the activated subunit can be added to the growing support-bound polymer at each polymer-addition step, to achieve subunit coupling to a very high percentage of the support-bound polymers. This insures that a large percentage of the support-bound polymers will contain the complete sequence of subunits desired.
• the efficiency of subunit addition is limited by the efficiency of the activations steps.
• Figure 6 shows the dimeric structures produced by coupling the cyclic backbone subunits indicated at
• the structures, when joined to form polymers show acceptible Watson/Crick base pairing with complementary polynucleotides.
• polymers formed from the subunits are stereoregular. This is achieved in the structures shown by (a) using natural nucleosides or nucleoside derivatives or synthetic nucleosides having the natural stereoisomeric configuration as subunits, and (b) joining the subunits by achiral intersubunit linkages.
• N 1 is a nucleophilic backbone group, such as a hydroxyl or amine group
• E is an electrophile, such as a carboxyl or sulfonyl group, which, when activated, can react with a second N 1 -----E type backbone to form an N 1 -----E-N 1 -----E backbone-linked dimer.
• the subunit backbones of this types which have been described specifically above are the cyclic backbone structures E-H in Figure 3, and the acyclic backbone structures I-N in Figure 4.
• the N 1 nucleophile is the 3' hydroxyl group, and in structures G and H, the amine attached to the 3' nitrogen on the morpholino ring.
• the E group in all of the cyclic structures is the carboxyl or corresponding sulfonyl group attached to the 5' position of the ribose ring, or to the 6' position of the morpholino ring.
• the N 1 and E groups are respectively, the backbone amine or hydrazine and carboxylic or sulfonic acid groups on the backbone moiety ends
• the first coupling method which is illustrated in Figure 7A, is analogous to the method described above with reference to Figure 5A, where a first N 1 -protected subunit is activated, then coupled directly to a backbone-unprotected subunit which forms the next-in-sequence subunit in the growing polymer.
• the P 1 protective group on the subunit N 1 is preferably an acid-labile protective group, such as t-butoxycarbonyl or a clevable linker bound to a solid support.
• Methods for N 1 -protecting cyclic backbone structures are analogous to procedures described above for cyclic structures A-D. Similar methods are effective to protect the amine nitrogens in the acyclic bonebone structures.
• the backbone N 1 site may be protected by its attachment to a solid support, with subunit addition to the growing polymer occuring via the activated E electrophile of the last-added subunit.
• the activation reaction is designed to yield an activated or chain-terminal moiety of the form N 1 -----E-X, where X is as described above with reference to Figure 6, and the activated subunit has much the same reactivity toward backbone nucleophilic groups as does the activated subunit in the previously described method. That is, the activation is designed to produce much the same active coupling group as in the
• N 1 ----N 2 type backbones but where the reactive carbonyl or sulfonyl group is provided by the backbone itself rather than by a carbonyl or sulfonyl activating reagent, as in the methods shown in Figure 6.
• the activation can be performed readily by reacting the N 1 ----E type subunit with a carbodimide in the presence of p-nitrophenol, where the backbone electrophile is a carbonyl group, or by reacting with a carbodiimide in the presence of imidazole, 1,2,4 triazole or tetrazole, where the backbone is a sulfonyl.
• Subunit activation reactions involving carbonyl electrophilic groups are detailed in Examples 16 and 17.
• the general reaction conditions used to activate the N-amino-morphilino and linear chain backbone carbonyl groups are generally applicable to the other N 1 ----E type backbone structures shown in
• the activated complex is purified by conventional methods, such as silica chromatography, or, in the case of a support-bound activated chain, simply washed, and then reacted with a second subunit whose selected recognition moiety R 2 will form the next in-sequence recognition moiety in the completed polymer.
• the coupling reaction yields a dimer whose subunits are therefore coupled through an E-N 1 bond, as indicated in the figure.
• both subunits must be suitably base protected during the activation and coupling reactions.
• the polymer can be extended by repeating the above steps of (a) activating the free E electrophile in the second subunit, (b) separating the activated species from the activating agent, and (c) coupling the activated compound with the next-in-sequence subunit, whose backbone is unprotected.
• the second coupling method which is illustrated in Figure 7B, is directly analogous to the method described above with respect to Figure 5B.
• a first subunit having an E-protected backbone is reacted with a second subunit with an activated E group and a protected N 1 nucleophile, to form a dimer linked through an E-N 1 bond and protected at both free backbone end groups.
• the P 2 protective "group” takes the form of an acid-stable linkeage to a solid support.
• the N 1 -protected subunit is prepared and activated as above. Coupling conditions generally follow those used in the above, cyclic subunit coupling reactions.
• n 1 -protected and E-unprotected subunits are reacted together in the presence of a suitable E-activating agent, such as a carbodiimide, as indicated
• Figure 8 shows the dimeric structures produced by coupling the cyclic amd acyclic backbone subunits indicated at E-K in Figures 3 and 4, and indicated at
• E-E through K-K repsectively.
• the nucleosides subunits in structure F-F in Figure 3 are joined by an ester linkage.
• the structures, when joined to form polymers show Watson/Crick base pairing with complementary polynucleotides.
• achiral subunit linkages it may be desirable to introduce one or more charged achiral subunit linkages in the polymer molecules.
• the backbone charge may be used to enhance polymer solubility in many solution applications or to adjust polymer-target binding constants, as will be described further below.
• Polymers having regularly spaced charged achiral backbone linkages, e.g., between every second or third subunit, are suitable for the novel diagnostic system which is described below.
• polymeric units composed of two or more subunits which are internally joined by achiral uncharged linkages are to be linked by a charged achiral linkage. These uncharged units are formed by one of the methods described in Sections A and B above.
• the dimer subunits which are to be linked are selected such that that the free N 2 group of one dimer can be coupled to the free N 1 group of the other dimer through a suitable charged achiral linkage.
• the preferred linkage is a phosphodiester linkage which requires that the free N 2 group on one subunit and the free N 1 group on the other subunit both be hydroxyls. As can be seen in Figure 3, this condition is met if dimers formed from either structure A or structure B subunits, which both have a free N 2 hydroxyl, are linked to dimers formed from structure A, C, or D subunits which all have a free N 1 hydroxyl.
• dimer A which is protected at its N 1 position, as indicated, is carried through a series of reactions which lead to an reactive phosphoester coupling species linked to the N 2 hydroxyl through a phosphoester bond, as indicated in Figure 9.
• the preferred coupling method which is detailed in U.S. patent application for "Polynucleotide Assay Reagent and Method", Serial Number 712,396, filed March 15, 1985, is detailed in Examples 23 and 24 below, with respect to the formation of a tetramer have alternating uncharged, stereospecific methylphosphonate bonds, and charged achiral phosphodiester bonds.
• the illustrated method involves first forming nucleotide dimers linked by methylphosphonate bonds, isolatating stereoisomeric forms of the dimers and activating one of the stereoisomeric dimers to form a reactive N 1 -protected N 2 -(p-chloro ⁇ henyl-2-cyanoethyl)--phosphate.
• the activated dimer is then reacted with the second dimer to form a tetramer which is linked alternately by uncharged, stereoisomeric linkages and charged achiral intersubunit linkages.
• the phosphodiester linkage method may be incorporated, either is solution or support-type polymer synthesis method, according to the general procedures outlined in Sections A and B for polymer coupling involving achiral, but uncharged linkage reactions.
• the phosphodiester bonds can be used to couple dimeric or polymeric units which are themselves coupled by uncharged achiral bonds, formed as above, or for coupling dimeric units linked by uncharged, chiral but stereoisoeric linkages, such as the separated stereoisomeric forms of methylphosphonate-linked dimers.
• solubility enhancement is generally achieved with 1-3 charged backbone linkages per polymer of about 20 subunits, and preferably no more than about one charged linkage per four subunits.
• achiral backbone linkages are considered substantially uncharged if they contain less than about one charge backbone linkage per dimeric unit, and preferably one or fewer backbone linkage per tetrameric unit.
• the design considerations applied in preparing a polynucleotide binding polymer for use in the invention are governed by the nature of the target analyte and the reaction conditions under which the analyte is to be assayed.
• a first consideration there is selected a non-homopolymeric target base sequence against which the polymer is directed.
• This target sequence is preferably unique to the analyte being assayed, i.e., is calculated to occur only with some defined small probability (such as 1% or less) in an assay mixture containing a given number of unique-sequence bases.
• P that a 9-base target sequence will be found in a 20 kllobase polynucleotide is about 20x10 3 /2x10 5 or 0.08
• the probability that a 16-base target sequence will be present is about 20x10 3 /4.3x10 9 or
• a polymer having 9-16 recognition moieties specific for a defined 9-16 base target sequence should have high specificity for the target sequence in an assay mixture containing only viral genomes, whose greatest complexities correspond to about 400K of unique-sequence bases.
• the polyrner/analyte binding affinity, and particularly the temperature at which the polymer just binds with the target sequence can be selectively varied according to (a) polymer length, (b) the number of hydrogen bonds that can be formed between the recognition moieties and the corresponding, in-sequence bases of the analyte target sequence, and (c) backbone charge density. From a number of studies on model homopolymer duplexes, it is known that the melting temperature of oligonucleotide duplexes in the 10 to 20 bp range increases roughly 3°C per additional base pair where the complementary bases are capable of forming two hydrogen bonds, and about 6°C per additional base pair where the complementary bases are capable of forming three hydrogen bonds.
• the length of a target sequence which is initially selected to insure high binding specificity with the polymer, may be extended to achieve a desired melting temperature with the complementary-base polymer, under selected assay conditions.
• the recognition moieties used in constructing the polymer are the standard nucleic acid bases, as illustrated above, the target sequence may be selected to have a high percentage of guanine plus cytosine bases for achieving a relatively high polyrner/analyte melting temperature, or a relatively high percentage of adenine plus thymine bases, for achieving a relatively low melting temperature.
• the backbone charge density of the polymer must be substantially less than that of the polynucleotide analyte, to allow preferential binding of polycationic reporter molecules to the analyte, under conditions where reporter binding to the polymer does not occur, as already noted. This requirement is met where the spacing between the adjacent negative charges in the polymer backbone is at least twice as great as the spacing between adjacent charged phosphodiester linkages In the analyte.
• the charge density of the backbone also has an important effect on the polyrner/analyte melting temperature, particularly under low salt conditions, where any charge-charge repulsion between the analyte and polymer backbones can act to lower the temperature at which the two can anneal.
• a polymer having a less-charged backbone would be expected to show (1) a higher analyte/polymer inciting temperature, and (2) less dependence of the melting temperature on salt concentration.
• an uncharged achiral polymer such as the several polymers described above with respect to Figures 6 and 8, will allow the analyte/polymer annealing reaction in the diagnostic method to be carried out under a wider range of salt-concentrations than a partially charged polymer, such as a polymer formed from alternating charged achiral phosphodiester bonds and uncharged linkages which may be either achiral or chiral, bu stereospecifically defined.
• the polymer After selecting a desired polymer length and recognition moiety sequence, according to factors considered in Section IV, the polymer is assembled, using the general subunit coupling procedures detailed above.
• One method of polymer assembly involves initial preparation of an appropriate set of dimers, linking selected dimers to form tetramers, linking of these to form octamers, and so on. This method is carried out in solution, substantially according to methods described with reference to Figures 5A and 7A above. It should be noted that all couplings need not necessarily be between oligomers of equal size.
• each coupling product is roughly twice the mass of the precursors and so purification of the product of each coupling is a simplified matter.
• Example 18 below details the assembly of an 8-subunit carbamate-linked polymer formed by this method.
• Stepwise Assembly on a Solid Support One preferred method for polymer synthesis is stepwise assembly on a solid support.
• the first subunit in the polymer is attached through its N 2 backbone group to a solid support.
• a solid support such as glass beads derivatized with cleavable, preferably acid-stable, long-chain linkers are employed as the support material, and prepared for attachment of N 2 nucleophile, such as a 5' hydroxyl of a nucleoside, as descibed in Example 19.
• the glass beads are reacted with a subunit which has a preferably acid-labile N 1 protected group, and an activated N 2 or E backbone group, as detailed in Section III above.
• any unreacted linker nucleophiles are capped by addition of a suitable capping reagent, such as p-nitrophenyl acetate, and thereafter the support is washed and filtered.
• a suitable capping reagent such as p-nitrophenyl acetate
• the protecting group on the N 1 terminal subunit is removed, typically by acid treatment, and after neutralization, the support is then reacted with an excess of the next-in-sequence subunit (or polymer unit) which is activated at its free N 2 backbone moiety. The excess of activated subunit maximizes the number of support-bound subunits which are chain-elongated.
• one feature of the solid support assembly method is the need for high coupling efficiencies at each subunit addition step, and the concentration of added activated subunit is selected to maximize this efficiency. Chain elongation is continued in this manner, with capping of failure sequence, after each subunit addition, until the polymer of the desired length and sequence is achieved.
• the general method is illustrated in Example 20 for the preparation of a
• the polymer may be capped with a suitable charged or uncharged group coupled to the terminal N 1 group. If the backbone assembly has been carried out exclusively with uncharged achiral linkages, the capping reagent is preferably a charged group which imparts an end terminal charge to the polymer.
• the polymer After capping the polymer, the polymer is cleaved from the support, e.g., by treatment with a nucleophile, such as ammonium hydroxide, and the polymer is purified, such as by anion exchange chromatography.
• a nucleophile such as ammonium hydroxide
• the assembled, purified polymers are attached to a solid support, by methods to be considered below.
• Examples 18 for a solution synthesis from preassembled dimeric units, in Examples 20-23 for the preparation of a variety of uncharged achiral linkages, and in Example 24, for the preparation of an alternating charge type polymer.
• the reagent of the invention is formed by coupling multiple binding polymers from above to a solid support.
• the polymers may be synthesized in a stepwise or block fashion, on the support, as described above for the carbamate-linked polymers.
• the polymers may be coupled directly to (or formed directly on) the support, e.g., through an OH end group on the polymer to an OH-reactive group on a solid support, such as activated agarose, cellulose, or the like.
• a solid support such as activated agarose, cellulose, or the like.
• direct coupling often places the support-proximal subunits too close to the support to allow base- complementary binding between the analyte and the proximal subunit recognition moieties. Therefore, the polymer molecules preferably are each linked to the solid support through a spacer arm adapted to distance the polymer from the surface region of the support so as to allow substantially unhindered binding between the polymer and analyte target sequence.
• the spacer arm is preferably an unbranched chain having a total chain length of at least 6 atoms, and has suitable reactive end groups for attachment to the support, at one end, and to the polymer at the other end.
• a variety of types of spacer arms, particularly carbon-containing chains of various lengths and hydrophilicity, are well known, as are reactive groups used in spacer-arm coupling reactions.
• Example 25 below describe the synthesis of an arninohexyl spacer arm, its attachment to the 5' end of mixed methylphosphonate/phosphodies ter polymer, and coupling to a solid support.
• Example 26 below details the preparation of a polymer support having multiple surface-bound, linear-chain spacer arms, for use in forming a diagnostic reagent having carbamate-linked polymers.
• Example 26 The method of Example 26 is illustrated in Figure 10.
• the support shown in the figure is an aininomethylated polystyrene which is first reacted with succinic anhydride to form a carboxylated derivative. Activation of the support with di(succinimido) carbonate and reaction with 6-aminohexanol leads to the 13-atom terminal-hydroxyl spacer arm shown.
• Preferred solid supports include agarose, cellulose, nitrocellulose, latex, polystyrene, and other commercially available strip or particle-bead support material having surface-reactive or activatable groups which allow efficient coupling of polymer molecules, particularly through polymer-bound spacer arms.
• the concentration of polymers coupled to the support surface is preferably selected so as to allow a 10-1000 fold molar excess of polymer molecules to analyte molecules when a suitable sample volume of assay material is mixed with the support, in the diagnostic procedure, as will be described below.
• a procedure for coupling a target binding polymer to agarose beads through the aminohexyl spacer arm from Example 25 is described in the same example.
• the reporter of the diagnostic system of the invention is composed of two parts: (1) a polycationic moiety or tail designed to bind electrostatically to a fully charged polynucleotide, under conditions where the reporter does not bind to the less charged binding polymer carried on the diagnostic reagent, and (2) one or more reporter groups attached to the tail adapted to produce a signal by which the presence of the reporter can be detected.
• Polycationic as the term is used herein, encompasses tails having two or more suitably spaced cationic groups.
• the cationic tail is preferably constructed to provide at least two positively charged groups which are spaced for binding to adjacent negative charges on the sugar-phosphate backbone of the polynucleotide analyte.
• the spacing between adjacent charges on the cationic tail is such that electrostatic binding to the reagent polymer backbone which involves more than half of the reporter charges is energetically unfavorable.
• the distance between adjacent negative charges in the polymer backbone is approximately twice that in a polynucleotide backbone.
• binding between substantially all of the charged groups of the cationic tail and the alternately spaced negative charges of the polymer backbone would require energetically unfavorable contortion of the polymer backbone.
• the spacing between adjacent positive charges in the cationic tail should be close to the minimum spacing which provides strong electrostatic binding between the reporter tail and the polynucleotide backbone.
• the charge-spacing requirement in the reporter becomes much less critical, of course, where the reagent polymer has a density of negative charge less than one per two subunit linkages or where the reagent polymer has an uncharged backbone.
• the cationic reporter can most effectively discriminate between the fully charged polynucleotides and the polymer when its cationic moieties are unable to hydrogen bond to the uncharged linkage, such as to the double-bonded oxygen of the methylphosphonate linkage. For this reason, it is generally advantageous to use quaternary ammonium ions for the cationic groups in such a reporter.
• the number of cationic moieties in the reporter tail may vary from two up to about 8 or more, according to the total electrostatic attraction required to bind the reporter to the polynucleotide analyte under binding conditions where the reporter does not bind to the reagent polymer backbone.
• reporters having relatively large reporter groups, such as enzymes multiple electrostatic binds may be required to attach the reporter tail to the analyte backbone.
• a reporter tail having a number of spaced cationic moieties is particularly suitable for use with a reagent whose polymer backbone is uncharged and thus cannot form electrostatic bonds to the tail.
• an N-methyl amino acid is N-protected with di-t-butyl dicarbonate (BOC), activated with carbonyl diimidazole, then coupled through an amide linkage to diinethylamine.
• BOC di-t-butyl dicarbonate
• the amide is reacted with an N-protected, carbonyl diiamidazole-activated amino acid from above, to form a diamide compound which is shown at the center in Figure 11.
• the deprotection reaction and reaction with N-protected diimidazole-activated amino acid are repreated until the desired-length polyamide is formed. Details of the synthetic reactions are set forth in Examples 28-30.
• a reporter group is most readily attached, typically, to a primary amine group in the polycation.
• an amino acid e.g., 4-amino butyric acid
• BOC-protected is BOC-protected, activated with diimidazole, and reacted with the deprotected polyamine, as illustrated in Figure 12.
• the resulting BOC-protected compound can then be reduced, after treatment with trifluoroacetic acid to remove the BOC group, by reaction with borane-tetrahydrofuran.
• Figure 13 shows a reaction scheme for converting polyamine, such as synthesized above, to a polyquaternary ammonium salt. The procedure involves protection of the terminal 1° amine followed by reaction with methyl iodide, to form the poly quaternary ammonium salt, and deprotection with trifluoroacetic acid.
• Example 33 gives details of the method.
• Preferred solid supports include agarose,cellulose, nitrocellulose, latex, polystyrene, and other commercially available strip or particle-bead support material having surface-reactive or activatable groups which allow efficient coupling of polymer molecules, particularly through polymer-bound spacer arms.
• concentration of polymers coupled to the support surface is preferably selected so as to allow a 10-1000 fold molar excess of polymer molecules to analyte molecules when a suitable sample volume of assay material is mixed with the support, in the diagnostic procedure, as will be described below.
• a procedure for coupling a target binding polymer to agarose beads through the aminohexyl spacer arm from Example 25 is described in the same example.
• the reporter of the diagnostic system of the invention is composed of two parts: (1) a polycationic moiety or tail designed to bind electrostatically to a fully charged polynucleotide, under conditions where the reporter does not bind to the less charged binding polymer carried on the diagnostic reagent, and (2) one or more reporter groups attached to the tail adapted to produce a signal by which the presence of the reporter can be detected.
• Polycationic as the term is used herein, encompasses tails having two or more suitably spaced cationic groups.
• the cationic tail is preferably constructed to provide at least two positively charged groups which are spaced for binding to adjacent negative charges on the sugar-phosphate backbone of the polynucleotide analyte.
• the spacing between adjacent charges on the cationic tail is such that electrostatic binding to the reagent polymer backbone which involves more than half of the reporter charges is energetically unfavorable.
• the distance between adjacent negative charges in the polymer backbone is approximately twice that in a polynucleotide backbone.
• binding between substantially all of the charged groups of the cationic tail and the alternately spaced negative charges of the polymer backbone would require energetically unfavorable contortion of the polymer backbone.
• the spacing between adjacent positive charges in the cationic tail should be close to the minimum spacing which provides strong electrostatic binding between the reporter tail and the polynucleotide backbone.
• the charge-spacing requirement in the reporter becomes much less critical, of course, where the reagent polymer has a density of negative charge less than one per two subunit linkages or where the reagent polymer has an uncharged backbone.
• the cationic reporter can most effectively discriminate between the fully charged polynucleotides and the polymer when its cationic moieties are unable to hydrogen bond to the uncharged linkage, such as to the double-bonded oxygen of the methylphosphonate linkage. For this reason, it is generally advantageous to use. quaternary ammonium ions for the cationic groups in such a reporter.
• the number of cationic moieties in the reporter tail may vary from two up to about 8 or more, according to the total electrostatic attraction required to bind the reporter to the polynucleotide analyte under binding conditions where the reporter does not bind to the reagent polymer backbone.
• reporters having relatively large reporter groups, such as enzymes multiple, electrostatic binds may be required to attach the reporter tail to the analyte backbone.
• a reporter tail having a number of spaced cationic moieties is particularly suitable for use with a reagent whose polymer backbone is uncharged and thus cannot form electrostatic bonds to the tail.
• an N-methyl amino acid is N-protected with di-t-butyl dicarbonate (BOC), activated with carbonyl diimidazole, then coupled through an amide linkage to dimethylamine.
• BOC di-t-butyl dicarbonate
• the amide is reacted with an N-protected, carbonyl diiamidazole-activated amino acid from above, to form a diamide compound which is shown at the center in Figure 11.
• the deprotection reaction and reaction with N-protected diimidazole-activated amino acid are repreated until the desired-length polyainide is formed. Details of the synthetic reactions are set forth in Examples 28-30.
• a reporter group is most readily attached, typically, to a primary amine group in the polycation.
• an amino acid e.g., 4-amino butyric acid
• BOC-protected is BOC-protected, activated with diimidazole, and reacted with the deprotected polyamine, as illustrated in Figure 12.
• the resulting BOC-protected compound can then be reduced, after treatment with trifluoroacetic acid to remove the BOC group, by reaction with borane-tetrahydrofuran.
• Figure 13 shows a reaction scheme for converting polyamine, such as synthesized above, to a polyquaternary ammonium salt. The procedure involves protection of the terminal 1° amine followed by reaction with methyl iodide, to form the poly quaternary ammonium salt, and deprotection with trifluoroacetic acid.
• Example 33 gives details of the method.
• the one or more reporter groups in the reporter should be (1) readily attached to the cationic tail, and
• reporter groups capable of generating an easily detected signal, either when the reporter is bound to a polynucleotide backbone, or after the reporter has been eluted from the analyte.
• Small reporter groups that include chrotnophores, such as nitroaniline or other strongly absorbing dyes, and fluorophores, such as dansyl or rhodamine-based fluorescent molecules, are suitable and have the advantage that they can be readily detected by photometric equipment, or in the case of dyes, by visual inspection. Radioisotopic reporter groups may provide advantages in diagnostic sensitivity, but reporter detection may be more complex and expensive.
• Stable paramagnetic molecules such as nitroxide spin labels, may also be used, the binding of the reporter to the polynucleotide being detected by broadening of electronic spin resonance (esr) absorption lines characteristic of immobilized paramagnetic species.
• esr electronic spin resonance
• Another class of suitable reporter groups include ligand molecules, and preferably small antigenic molecules capable of binding specifically and with high affinity to anti-ligand molecules.
• Exemplary ligand/ anti-ligand pairs include antigen/antibody, lectin/ carbohydrate, and biotin/avidin.
• the anti-ligand molecule is part of a signal-producing binding conjugate which also includes a signal-producing group, such as a chromophore, fluorophore, or enzyme by which the presence of ligand groups can be detected, when ligand/ anti-ligand binding has occurred.
• a signal-producing group such as a chromophore, fluorophore, or enzyme by which the presence of ligand groups can be detected, when ligand/ anti-ligand binding has occurred.
• the reporter may have enzyme reporter moieties, particularly, as noted above, where the reporter tail has more than two cationic groups.
• Representative classes of enzymes are oxidoreductases, typified by luciferase; glucose oxidase; galactose oxidase and catalase; hydrolases, typified by various kinds of phosphatases; glycosyl hydrolases, such as ⁇ -galactosidase; peptidases; and lyases.
• the reporter group or groups are coupled to an amine of the polycationic tail, and preferably a primary amine, according to known coupling methods.
• a polyamine is reacted with a suitable bifunctional coupling agent, such as 4-fluoro-3-nitrophenylazide, and then coupled to a reporter group, such as an enzyme.
• a suitable bifunctional coupling agent such as 4-fluoro-3-nitrophenylazide
• a reporter group such as an enzyme.
• a variety of bifunctional reagents for coupling amines to reactive reporter groups such as amine, carboxyl, OH, and sulhydral groups, are well known.
• a detailed method for forming a tetracationic reporter with an alkaline phosphatase reporter group is given in Example 38.
• a reporter is prepared by reacting bis-3,3'-amihopropyl ⁇ methylamine with an amine-reactive dansyl group.
• the reaction scheme in the figure also indicates how the amino moieties of the reporter tail can be fully alkylated before or following reporter coupling to the tail. Details of the procedure are given in Example 34.
• the analyte may be one which normally exists in a single-stranded form, such as messenger RNA (mRNA), ribosomal RNA (rRNA) or a single-stranded RNA or DNA viral genome, or one which exists under physiological conditions in a double-stranded or duplex form, such as double-stranded viral RNA, RNA/DNA viral replicative intermediates, and duplex DNA, such as that derived from a virus, a bacterium, or eukaryotic cell.
• mRNA messenger RNA
• rRNA ribosomal RNA
• RNA or DNA viral genome or one which exists under physiological conditions in a double-stranded or duplex form, such as double-stranded viral RNA, RNA/DNA viral replicative intermediates, and duplex DNA, such as that derived from a virus, a bacterium, or eukaryotic cell.
• a sample to be assessed for analyte is collected, typically by conventional clinical sample-handling techniques.
• the analyte is a virus or bacteria-derived polynucleotide
• assaying for the presence of a bacterial pathogen it is often useful to filter the sample through a 1.0 micron pore-sized membrane to remove eucaryotic cells, which may also be present in the sample.
• Typical sample preparation methods are described for diagnosis of viral pathogens in Examples 36 and 37.
• the sample should be treated to free the organism's nucleic acid.
• detergents and/or chaotropic salts are generally adequate.
• alkali when the analyte is DNA
• suitable enzymes e.g., lysozyme for many bacteria
• the freed nucleic acids can be conveniently separated from proteins and other contaminants by addition of a chaotropic salt (sodium trichloroacetate) followed by selective precipitation of the nucleic acid with ethanol.
• a chaotropic salt sodium trichloroacetate
• Example 36 One efficient method for freeing and isolating nucleic acid material from viral or cell components has been described by the inventor in Anal Biochem (1983) 133:79.
• the method which is detailed in Example 36, involves suspending the sample in 4M trichloroacetate, 100 mmol EDTA, to denature and solubilize proteinaceous material, then precipating freed nucleic acid material in the salt solution by .the addition of an equal volume of cold ethanol.
• a carrier polynucleotide such as polyuridylic acid, may be added to facilitate nucleic acid precipitation. After a short chilling time, the precipitated nucleic acid is pelleted by centrifugation, and washed with aqueous ethanol to remove salt.
• the nucleic acid fraction is resuspended in annealing buffer having a selected salt concentration and a divalent cation chelating agent.
• An annealing buffer containing about 100 mmol or less of monovalent salt, such as NaCl, and about 10 mmol chelating agent, such as EDTA, is generally suitable for binding of a polynucleotide which exists normally in a duplex DNA form. Salt concentration significantly below 100 mmol may be difficult to achieve with precision. Higher salt concentrations, particularly above about 0.5 M, tend to allow duplex formation between complementary polynucleotide strands, leading to competition between the reagent polymer and the complementary strand for binding to the analyte polynucleotide.
• Duplex formation between complementary polynucleotides is also inhibited by the chelating agent, which acts to sequester Mg +2 and Ca ++ ions in the annealing mixture.
• the analyte is an RNA
• the annealing reaction is preferably carried out at a temperature which is about 5°C to 15°C below the melting temperature of the analyte/polymer duplex structure which forms during the reaction period. This annealing temperature favors faithful base-sequence pairing between the analyte target sequence and the polymer.
• the reaction temperature is preferably higher than the melting temperature of the native polynucleotide duplex, to avoid undesired pairing of the analyte with its complementary polynucleotide competing with the desired pairing of the analyte with the reagent polymer.
• annealing buffer concentration of about 100 mmol monovalent cation
• annealing temperatures in the range of 24° to 60°C are generally suitable.
• the actual optimal annealing temperature is a function of the length of the binding polymer, its ratio of A + T to C + G recognition moieties, and, for partially charged polymers, the salt concentration.
• the melting temperature of the analyte/polymer duplex structure may be substantially higher than a preferred reaction temperature, such as 37°C, in the particular annealing buffer employed, such as 100 mmol monovalent salt. In such cases, it may be convenient to lower the melting temperature of the polyrner/analyte duplex structure to the desired temperature by the addition of a denaturant such as formamide. To determine the amount of formamide needed to achieve the desired melting temperature, the melting curve of the polymer and the.
• target sequence which may be a synthetic oligonucleotide having the analyte target sequence
• target sequence is determined by conventional means, and at a number of different denaturant concentrations, and, in the case of added formamide, typically ranging between about 5% and 50% by volume of denaturant. From this determination, the amount of formamide needed in the annealing buffer in order to achieve a melting temperature about 5° to 15° above the desired reaction temperature is determined.
• the analyte sample in the reaction buffer is added to the diagnostic reagent, preferably under conditions where the binding polymers of the reagent are present in a 10-1000 molar excess over the molar concentration of analyte molecules in the assay mixture.
• the polymer/polynucleotide annealing reaction is carried out at the selected reaction temperature for a period sufficient to allow substantial polyrner/analyte annealing, typically between 10 minutes and 3 hours.
• the solid-support reagent is washed one or more times to remove unbound material.
• Reporter is then added to the washed reagent under preselected conditions to bind reporter molecules to the fully charged backbone of the reagent-bound analyte.
• the spatial/charge characteristics of the reporter which permit selected binding of the reporter to the polynucleotide backbone have been discussed above.
• the optimal salt concentration .of the binding medium is the maximum or near-maximum concentration of monovalent salt which permits adequate electrostatic binding of the reporter to the fully charged analyte backbone.
• This optimal salt concentration can be determined by equilibrium dialysis techniques, in which binding of the diffusable reporter to a nondiffusable polynucleotide is measured as a function of salt concentration of the suspending medium.
• Optimal ionic-strength conditions for reporter binding to the analyte may also be determined readily by binding the reporter to immobilized polynucleotide, under low salt conditions, and eluting the reporter with a salt gradient.
• each polymer has the sequence of recognition moieties complementary to the selected 16-base target sequence in Herpes simplex virus, Types I and II, as described in Example XXI. The base-complementary binding of one of these polymers to the target sequence in a Herpes simplex analyte polynucleotide is shown.
• the reporter shown in the figure is the dicationic reporter from Example 34, Each reporter is adapted to bind through electrostatic attraction to a pair of adjacent phosphodiester bonds in the polynucleotide through electrostatic attraction with adjacent phosphodiester bonds.
• the reporter molecules are shown in their expected binding configuration, where substantially every phosphodiester linkage is paired with a reporter cation, and the reporter molecules are arrayed head-to-head and tail-to-tail. Assuming a maximum density of bound reporter molecules, it can be appreciated that an N-base analyte can bind up to about N/2 reporter molecules.
• the assay method readily leads to binding of thousands to several hundred thousand or more reporter molecules to each reagent-bound analyte molecule.
• the sensitivity of detection can therefore be between 2 and 4 orders of magnitude greater than in existing types of polynucleotide-based diagnostics, where analyte detection is generally based on one or a few probe molecules per analyte molecule, with each probe typically containing roughly 100 reporter moieties.
• reporter groups In determining the amount of reporter associated with the reagent, it may be desirable, particularly in the case of fluorescent or chromophoric reporter groups, to elute the reporter from the reagent with a high salt solution and then assess the eluate for reporter.
• Other types of reporter groups such as enzymes, can be readily assessed with the reporters either bound to or eluted from the reagent. Methods for determination of a variety of different reporter groups, such as those mentioned above, are well known. Examples 36 and 37 illustrate diagnostic procedures based on determination of fluorescent and enzymatic reporters, respectively.
• the diagnostic reagent can be readily tailored, by reagent polymer design, for the detection of any ribo-or deoxyribopolynucleotide having a unique base pair sequence. Further, the reagent polymer can be tailored to bind a given target sequence with high sequence specificity at a convenient temperature.
• the reaction can be carried out under low-salt and/or denaturing conditions which prevent competition from complementary polynucleotide strands for analyte. binding to the reagent.
• This diagnostic system therefore provides the advantage, of the prior art solid-support, single-probe polynucleotide diagnostic system, in that competition between complementary strands is eliminated, but avoids the rather laborious step associated with that system in attaching single-strand test nucleic acids to the solid support.
• the system avoids the problems associated with the dual-probe polynucleotide diagnostic system described earlier, in that analyte detection is based on pseudo-first order kinetics, and only one sequence-specific binding polymer is required.
• reporter binding to the analyte is based on sequence-independent electrostatic interactions rather than sequence-specific binding, as in existing types of polynucleotide diagnostics. Accordingly, the reporter itself can be prepared relatively cheaply, can react with the analyte quickly and under a wide range of conditions, and, most importantly, can bind to the analyte at a density ranging up to multiple reporter moieties per polynucleotide subunit in the analyte.
• the sensitivity of the diagnostic system can be in the range of 2 to 4 or more orders of magnitude greater than existing tests, which rely on detection of one or a few probes, containing a limited number of reporter moieties, per analyte molecule.
• 2,6-Diamino-9-( ⁇ -D-ribofuranosyl)-9H-purine (2,6-diaminopurine riboside) is obtained from Pfaltz and Bauer, Inc., Division of Aceto Chemical Co., Inc., Waterbury, CT.
• nucleosides are prepared by the literature methods indicated:
• 1-(2-Deoxy- ⁇ -D-erythro-pentofuranosyl)-2-pyrimidinone (2-hydroxy ⁇ yrimidine deoxyriboside) is prepared by the method of P. Kohler, E. Volz, U. Sequin, and C. Tamm in Nucleic Acid Chemistry (L.B. Townsend and R.S. Tipson, eds) John Wiley and Sons, Inc. (1976).
• 1-(2-Deoxy- ⁇ -D-erythro-pentofuranosyl)-4-methoxy- 2-pyrimidinone is prepared by the following procedure:
• 2-Amino-9-(2-deoxy- ⁇ -D-erythro-pentofuranosy ⁇ )-1, 9-dihydro-6H-purine-6-thione (deoxythioguanosine) is prepared by the procedure of R.H. Iwamoto, E.M. Acton, and L. Goodman, J Med Chem (1963) 6: 684.
• 1-( ⁇ -D-Ribofuranosyl)-2-pyrimidinone (2-hydroxypyrimidine riboside) is prepared by the procedure of U. Niedballa and H. Uorbruggen, J Org Chem (1974) 39:3668.
• 2-Amino-9-( ⁇ -D-ribofuranosyl)-1,6-dihydro-6H-purine-6-thione is prepared by the procedure of J.J. Fox, I. Wempen, A. Hampton and I.L. Doerr, J Amer Chem Soc (1958) 80:1669.
• N-2 9-fluorenylmethoxycarbonyl derivative is prepared by the procedure below which is general for the protection of nucleoside amino groups: Guanosine (1 mmol) is suspended in pyridine (5 mL) and treated with trimethylchlorosilane (5 mmol). After the solution is stirred for 15 minutes 9-fluorenylmethoxycarbonyl chloride (5 mmol) is added and the solution maintained at room temperature for 3 hours. The reaction is cooled in an ice bath and water (1 mL) is added. After stirring for 5 minutes conc, ammonia (1 mL) is added and the reaction stirred for 15 minutes. The solution is evaporated to near dryness and the residue dissolved in chloroform (10 mL).
• N-Isobutyrylguanosine is prepared by the method of Letsinger and Miller, J Amer Chem Soc (1969) 91:3356.
• N-2 Acetylguanosine is obtained by the method of C.B. Reese and R.S. Saffhill, J Chem Soc Perkin Trans (1972) 1:2937.
• N-2 9-fluorenylmethoxycarbonyl derivative is prepared by the method of J. Heikkla and J. Chattopadhyaya, Acta Chem Scand (1983) 837:263.
• N-2 acetyl derivative is obtained from Research Plus Inc., Bayonne, N.J.
• N-6 2-(4-nitrophenyl)-ethoxycarbonyl derivative is prepared by the method of F. Himmelsbach and W. Pfleiderer, Tetrahedron Lett (1983) 24:3583.
• N-6 4-Nitrobenzoyl-2'-deoxyadenosine is prepared using the procedure above for FMOC-guanosine except that 4-nitrobenzoyl chloride is substituted for FMOC chloride.
• the N-6 2-(phenylsulfonyl)-ethoxycarbonyl derivative is prepared by the procedure for FMOC guanosine except the 2-(phcnylsulfonyl)-ethyl chloroformate (obtained from N. Balgobin, S. Josephson and B. Chattopadhyaya, Tetrahedron Lett (1981) 22 : 3667) is used as the acylating agent and N-methylimidazole or pyridine is used as the solvent.
• N-6 2-(4-nitrophenyl)-ethoxycarbonyl derivative is prepared by the method of F. Himmelsbach and W. Pfleiderer, Tetrahedron Lett (1983) 24:3583.
• N-6 4-Nitrobenzoyladenosine is prepared using the procedure above for FMOC-guanosine except that 4-nitrobenzoyl chloride is substituted for FMOC chloride.
• N-6 2-(phenylsulfonyl)-ethoxycarbonyl derivative is prepared by the procedure for FMOC guanosine except the 2-(phenylsulfonyl)-ethyl chloroformate (obtained from N. Balgobin, S. Josephson and B. Chattopadhyaya Tetrahedron Lett (1981) 22:3667) is used as the acylating agent and N-methylimidazole or pyridine is used as the solvent.
• the N-4 2-(4-nitrophenyl)-ethoxycarbonyl derivative is prepared by the method of F. Himmelsbach and W. Pfleiderer, Tetrahedron Lett (1983) 24:3583.
• the N-6 2-(phenylsulfonyl)-ethoxycarbonyl derivative is prepared by the procedure for FMOC guanosine except the 2-(phenylsulfonyl)-ethyl chloroformate (obtained from N. Balgobin, S. Josephson and B. Chattopadhyaya Tetrahedron Lett (1981) 22:3667) is used as the acylating agent and N-methylimidazole or pyridine is used as the solvent.
• the N-4 2-(4-nitrophenyl)-ethoxycarbonyl derivative is prepared by the method of F. Himmelsbach and W. Pfleiderer, Tetrahedron Lett (1983) 24:3583.
• the N-6 2-(phenylsulfonyl)-ethoxycarbonyl derivative is prepared by the procedure for FMOC guanosine except the 2-(phenylsulfonyl)-ethyl chloroformate (obtained from N. Balgobin, S. Josephson and B. Chattopadhyaya Tetrahedron Lett (1981) 22:3667) is used as the acylating agent and N-methylimidazole or pyridine is used as the solvent.
• N-2,N-6-bis(9-fluorenylmethoxycarbonyl) derivative of 2,6-diaminopurine riboside is prepared by the general procedure.
• the N-2,N-6-bis(isobutyryl) derivative is prepared by the general procedure.
• the bis N-2,N-6-(9-fluorenylmethoxycarbonyl) derivative of 2,6-diaminopurine-2'-deoxyriboside is prepared by the general procedure.
• N-2 9-fluorenylmethoxycarbonyl derivative of thioguanosine is prepared by the general procedure.
• N-2 9-fluorenylmethoxycarbonyl derivative of 2'-deoxythioguanosine is prepared by the general procedure.
• Example 3 Preparation of 5'-amino-2',5-dideoxyribonucleoside subunits.
• Carbon tetrabromide, sodium azide, p-toluenesulfonyl chloride (tosyl chloride), triphenyl phosphine and 10% palladium on carbon are purchased from Aldrich Chem Co.
• Lithium azide is obtained from Kodak Laboratory and Specialty Chemicals.
• nucleosides employed in this example are thymidine, N6-benzoy1-2'-deoxyadenosine, N4-benzoyl-2'-deoxycytodine, and 2'-deoxyinosine, 2-hydroxy-pyrimidine-2'-deoxyriboside and the
• N2-N6-bisisobutyryl derivative of 2,6-diamino purine-2'-deoxyriboside see Example 1.
• the required dried nucleoside (1 mmol) is weighed into a reaction vessel containing triphenyl phosphine (1.01 mmol) and lithium azide (5 mmol). After the solids are suspended in DMF, carbon tetrabromide (1.0 mmol) is added to the vessel. The solution is stirred at room temperature for
• the 5'-azido nucleoside (1 mmol) is dissolved in ethanol. Hydrogenation in the presence of 10% palladium on carbon (catalytic amount) under a hydrogen atmosphere (35 psi) occurs over 10 h. The solution is filtered and evaporation under reduced pressure affords a crude solid. The solid is purified by trituration with the appropriate solvent.
• the 5'-azido derivative of 5-bromo-2'-deoxy uridine is prepared via the method described above.
• the 5'-azido-t-bromo-2'-deoxyuridin (1 mrnol) is treated with triphenyl phosphine (1.5 mmol) in pyridine at room temperature for 2 h.
• Concentrated ammonia (1 mL) is added to the reaction vessel. After 14 h the solvent is removed under vacuum. The residue is dissolved in THF and this solution is added to hexanes. The precipitate is collected and the solid triturated with the appropriate solvent to afford the 5'-amino-5-bromo-2'-deoxyuridine.
• 5'-amino-2',5'-dideoxyguanosine is to treat the protected 2'-deoxyguanosine (protected at either the N-2-acetyl or the N-2-FMOC derivative) (1 mmol) with tosyl chloride (1.3 mmol) in pyridine at 0°C overnight.
• the solution is evaporated to dryness and the residue is dissolved in chloroform.
• the resulting solution is washed twice with aqueous sodium bicarbonate and dried over sodium sulfate.
• the solvent is evaporated and the residue chromatographed on silica gel eluting with methanol/chloroform mixtures.
• the resulting tosylate (1 mmol) is treated with sodium azide (6 mmol) in DMF at 80-100°C for a few h.
• the solvent is removed by rotovap and the residue is chromatographed on silica gel eluting with chloroforrn/methanol solvent mixtures.
• the azide is reduced to the desired amine using the above procedure.
• Alternate protecting groups for the base nitrogens of 2'-deoxycytidine, 2'-deoxyadenosine, 2'-deoxyguanosine, and 2,6-diaminopurinedeoxyriboside are 2-(phenylsulfonyl) ethoxy carbonyl for 2'-deoxycytidine and 2'-deoxyadenosine and the use of the 9'-fluorenylmethoxycarbonyl (FMOC) to protect 2'-deoxyguanosine and 2,6-diarninopurine deoxyriboside, as in Example 2.
• Example 4 Preparation of 3'-amino-2',3'-dideoxyribonucleoside subunits. Thymidine is transformed to 5'-O-acetyl-3'-azido-2',3'-dideoxythymidine and this is converted to 3'-azido-2',3'-dideoxyadenosine and 3'-azido-2',3'-dideoxyguanosine via the methods of M. Imazawa and F. Eckstein, J Org Chem (1978) 43:3044.
• the base moiety of the 3'-azidoadenosine is protected as either the benzoyl or the 2-(phenylsulfonyl)ethoxycarbonyl derivative (as shown in Example 1).
• N-2 of the 3'-azidoguanosine is protected as either the acetyl or FMOC derivative (see Example 1).
• the reduction of these 3'-azido functions to the 3'-amino-2',3'-dideoxyribonucleosides is performed as shown in Example 3.
• Ammonium biborate, sodium m-periodate, sodium cyanoborohydride, uridine, N4-benzoyl cytidine, and N6-benzoyl adenosine are obtained from Sigma Chemical Co.
• N2-isobutyryl guanosine is prepared by the general method of Letsinger and Miller (J Amer Chem Soc (1969) 91: 3356).
• 2-Phenyl-2-- ⁇ ropanol and bis (p-nitrophenyl) carbonate are obtained from Aldrich Chemical Co.
• the morpholino de'rivative of uridine is prepared by dissolving 1 mmol of uridine plus 2 mmol of ammonium biborate, (NH 4 ) 2 B 2 O 7 , in 5 ml of water. While stirring in an ice bath protected from direct light 1.2 mmol of sodium m-periodate in 5 ml of water is added. After 90 min, 0.2 ml of 1,2-propanediol is added and stirring is continued for 10 min at rt. Thereafter, while stirring in a well-ventilated hood, 0.25 g of sodium cyanoborohydride dissolved in 3 ml of water is added and the mixture stirred for 4 hr at rt.
• ammonium biborate (NH 4 ) 2 B 2 O 7
• reaction mixture is reduced to an oil under vacuum in a warm water bath, resuspended in a minimal volume of methanol, layered on a silica gel chromatography column, and the column eluted with methanol/1% triethylamine.
• the morpholino product elutes from the column as a sharp band moving significantly slower than the original ribonucleosideand its oxidation products.
• the morpholino product has a UV spectrum essentially identical to the parent ribonucleoside, but its mass is lower by 17 daltons (determined by mass spectral analysis using fast atom bombardment activation).
• the morpholino nitrogen is next protected by reacting the product with 2-phenylisopropyl phenyl carbonate.
• the required active carbonate is prepared and reacted with the morpholino subunit essentially by the methods of. Sandberg and Ragmarsson (Int J Peptide Protein Res (1974) 6:111).
• the hydroxyl at the position corresponding to the original 5' can be activated by dissolving the N-protected subunit in a minimal volume of dry dimethylformamide and adding 2 equivalents of bis (p-nitrophenyl) carbonate plus 0.2 equivalent of triethylamine, N-methylimidazole, or N,N-dimethylamino pyridine. After 3 h at rt, the reactions mixture is reduced in volume under vacuum in a warm water bath. The thick syrup is resuspended in a small volume of dichloromethane and layered on a silica gel column, which is subsequently eluted with a mixture of dichloromethane/ether (1:1 by vol) 0.2% in
• the preferred base-protective groups for the common starting ribonucleosides are: the phenylsulfonylethoxycarbonyl moiety for cytidine and adenosine and the 9-fluorenylmethoxycarbonyl moiety for guanosine.
• Triethylamine, pyridine/sulfur trioxide complex, p-nitrophenol, dicyclohexylcarbodiimide, and 40% aqueous dimethylamine are obtained from Aldrich.
• the analogous series of reactions may be carried out on the other properly protected 2'-deoxynucleosides.
• the active ester (1 mmol) is treated with 40% aqueous dimethylamine ( 2 mmol) in methanol to form the N , N-dimethylamide of the N-protected 3'-O-tert-butyl dimethylsilyl-2',5'-dideoxyadenosine-5'-acetic acid.
• the solvents are removed by evaporation under reduced pressure and the residue is desilylated by using the 2M
• HF/1M tert-butylammonium fluoride (TBAF) reagent described in B.L. Gaffney and R.A. Jones, Tetrahedron
• Example 7 Preparation of Purine and Pyrimidine Pyrrolidones Potassium t-butoxide, anisoyl chloride, 6-chloropurine, 10% palladium on charcoal, phthaloyl chloride, 2-arnino-6-chloro ⁇ urine, 20% aqueous tetraethylamrnonium hydroxide, 25% aqueous trimethylamine, 2-pyrimidinone, N-bromosuccinimide, trifluoroacetic acid, 4-nitrophenol, and N,N-disuccini ⁇ r ⁇ ydyl carbonate are obtained from Aldrich. Lithium azide is obtained from Eastman Kodak, Rochester, New York. C18 reverse phase silica gel is obtained from Whatman, Hillsboro, Oregon.
• the mixture from the previous paragraph is dissolved in pyridine or N-methylimidazole (10 mL) and treated with anisoyl chloride (2.8 rnmol) at room temperature. After stirring for 2 h, the mixture is quenched with ice (0.5 g). After 5 min, 1 mL of 29% ammonia was added. After 15 min at rt the solution is dissolved in ethyl acetate (15 mL) and washed twice with brine (15 mL). The washings are combined and washed with ethyl acetate (2 x 30 mL), the combined organic layers dried with sodium sulfate and evaporated under reduced pressure. The residue is coevaporated several times with toluene and the residue chromatographed on silica gel with a gradient of methanol in methylene chloride (0-20%).
• 6-azidopurine pyrrolidone The 6-chloropurine pyrrolidone (1 mmol) is treated with lithium azide (2 mmol) in dimethyl sulfoxide (2 mL) at 30-100°C for several h. At the end of this time the mixture is evaporated under reduced pressure, dissolved in chloroform, washed with 10% sodium bicarbonate, and the organic layer dried over sodium sulfate and concentrated under reduced pressure. The residue is chromatographed on silica using a gradient of methanol in chloroform (0-25%).
• the azide from the previous example is hydrogenated by shaking the azide (1 mmol) with 30 pounds of hydrogen pressure in a solution of ethanol (10 mL) containing palladium on charcoal (100 mg, 10% by weight Pd) for 24 h. The solution is filtered through celite and the solvent evaporated. The residue is used directly for the next step.
• N-6 phthaloyladenosine pyrrolidone The phthaloyl group is introduced at the N-6 position by the acylation of the adenosine pyrrolidone (1 mmol) with phthaloyl chloride (1.4 mmol) using the procedure above for the anisoylation of cytidine except that no ammonia was added in the workup.
• the pyrrolidone tosylate is alkylated with 2-amino-6-chloropurine as per the preparation of the 6-chloropurine derivative. 7.8 Preparation of guanine pyrrolidone
• the chloropurine pyrrolidone (1 mmol) from the previous paragraph is dissolved in diglyme (10 mL) and 25% aqueous trimethylamine (2 mL). The solution is stirred at rt for 5 h, water (10 mL) is added, and the mixture concentrated to 10 mL under reduced pressure. Acetic acid (2 mL) is added, and the mixture was evaporated under reduced pressure to an oil. The residue which contains tetraethylammonium acetate is used directly for the next step.
• Guanine pyrrolidone (1 mmol) from the previous paragraph is reacted with acetic anhydride (5 mL) at reflux for 2 h.
• the solvent is evaporated and the residue coevaporated with dimethylformamide.
• Theresidue is dissolved in methanol (5 mL) saturated with ammonia at 0°C, and the solution is stirred for 2 h at this temperature.
• the solvent is evaporated under reduced pressure and the residue purified by chromatography on a short column of silica using a gradient of methanol in chloroform (5-50%).
• the acetyl group is introduced by the method above for N-2 acetylguanine pyrrolidone except that the methanolic ammonia treatment is carried out for 8 h.
• the solvents are evaporated and the residue is phthaloylated as for the adenosine derivative.
• This compound is obtained by the alkylation of 2-pyrimidinone by the procedure used for the preparation of the 6-chloropurine derivative.
• Example 8 Preparation of Purine and Pyrimidine T-BOC Amino Acids
• the general procedure described below for the cytosine pyrrolidone may be applied to all properly protected pyrrolidone derivatives.
• the product, referred to as the t-BOC acid is formed by cleavage of the pyrrolidone ring to an acid and a t-BOC amine.
• N-4-Anisoylcytosine pyrrolidone (1 mmol) is dissolved in methylene chloride (0.5 M solution) containing di-tert-butyl dicarbonate (2 mmol), triethylamine (1 mmol), and dimethylaminopyridine (1 mmol). The solution is stirred for 10 h at rt. The volatiles are removed and the residue purified on silica using a gradient of methanol in chloroform (0-20%). The residue is dissolved in tetrahydrofuran (0.2 M solution) to which is then added lithium hydroxide ( 3 mmol, as a 1 M solution).
• the cytosine t-BOC acid (1 mmol) is dissolved in aqueous acetic acid and treated with sodium nitrite (1 mmol) at 4°C. The mixture is stirred for 1 h and evaporated to dryness under reduced pressure. The product is purified by chromatography in C18 reverse phase silica gel using water and methanol (or trifluoroethanol) mixtures.
• This compound is obtained from the uracil t-BOC acid by the following procedure:
• the uracil t-BOC acid (1 mmol) is dissolved in DMF (3 mL) and treated with N-bromosuccinimide (1.2 mmol). The solution is allowed to stand at room temperature for 16 h. After removal of the solvents under reduced pressure the product is purified by chromatography on C18 reverse phase silica gel using water and methanol (or trifluoroethanol) mixtures.
• the cytosine t-BOC acid (1 mmol) from the previous paragraph is dissolved in N-methylimidazole or pyridine (5 mL) and treated with chlorotrimethylsilane (5 mmol). After 15 min at room temperature the solution is treated with 2-(4-nitro ⁇ henyl) ethylchloroformate (3 mmol, obtained from F. Himmelsbach and W. Pfleiderer, Tetrahedron Lett (1983) 24: 3583). The reaction iss maintained at room temperature for 8 h, then cooled in an ice bath, and water (1 mL) was added. After 5 min, 1 mL of concentrated ammonia is added and the mixture stirred at rt for 15 min.
• the reaction is then evaporated to dryness and the residue dissolved in water.
• the solution is made acidic with 2 M HCl and extracted with chloroform.
• the combined organic extracts are dried over sodium sulfate and evaporated under reduced pressure.
• the residue is purified by chromatography on silica using a gradient of methanol in chloroform (5-50%).
• Lithium borohydride, di-tert-butyl dicarbonate and bis (triphenylphosphine) palladium II chloride were obtained from Aldrich Chemical Co., Milwaukee, WI. 2-Amino-5-bromopyrimidine is prepared as per T. Nishikawa, Chem. Pharm. Bull, 9:38 (1961).
• 2-amino-5-bromopyrimidine is benzoylated at the exocyclic arnino group by the. general method in Example 2 using benzoyl chloride.
• the product benzamide (25 mmole) is added to a 45 mL pressure vessel containing triethylamine (10 mL), benzene (10 mL), and bis (triphenylphosphine) palladium II chloride (0.375 mmole).
• the bomb is flushed with argon, sealed, and pressurized to 600 psi with carbon monoxide and then pressurized to 1200 psi with hydrogen.
• the reaction vessel is heated in an oil bath with stirring at 145°C.
• the reaction is filtered and the solvents removed under reduced pressure.
• the residue is dissolved in methanol which is saturated with ammonia at 0°C and stirred at room temperature for 10 h. After evapoaration of the solvents, the residue iss purified by chromatography on C18 silica gel using methanol water mixtures buffered to pH 7 with ammonium acetate (0.2 M).
• the product may be purified by chromatography on silica gel using a gradient of methanol in chloroform (0-50%).
• Ethyl 6-hydroxynicotinate is prepared as per H.
• Lithium borohydride is obtained from Aldrich.
• Manganese dioxide is prepared as per Uereshchagin et al, Zhurnal Arganicheskoi Khimil,8:1129 (1972).
• Dowex resin is obtained from Bio-Rad
• the benzylic alcohol (66 mmol) prepared in the previous paragraph is dissolved in ether (250 mL) and treated slowly (exothermic) with a slurry of manganese dioxide (54 g) in ether (100 mL). After twelve hours at room temperature, the mixture is filtered, the solvent removed under reduced pressure, and the residue distilled in vacuo to give 6-hydroxynicotinaldehyde.
• the aldehyde from the previous paragraph is reacted with 4-amino butyric acid as for the preparation of the cytidine analog in Example 11.1
• the amino acid from the previous paragraph was converted to the corresponding BOC-derivative as for the preparation of the cytidine analog in Example 10.1
• N-2 9-Fluorenylmethoxycarbonyl-2'- deoxyguanosine (1 mmol) is dissolved in anhydrous pyridine (2.0 mL) and kept at 0°C. Dirnethoxytrityl chloride (1.2 rnmol) is added in portions (0.15 rnmol) during an 8 hour period. After an additional 2 hours methanol (0.5 mL) was added and the solution is concentrated at reduced pressure. The residue is treated with a mixture of sodium bicarbonate (2 mL, 5%) and methylene chloride (5 mL).
• the organic layer is washed twice with aqueous NaOH (5 mL, 0.1 M), water (2 mL), dried over sodium sulfate and evaporated.
• the residue is applied to a silica gel column and eluted with a gradient of isopropanol in chloroform (0-10%).
• the fractions containing the product are pooled, evaporated, dissolved in chloroform (10 mL) and the aqueous NaOH washes are repeated to remove traces of 4-nitrophenol.
• the organic layer is washed with water, dried over sodium sulfate and evaporated.
• the product is homogeneous by TLC and is used directly for preparation of the dimeric carbonates.
• the calculated amount of dicyclohexylcarbodiimide is added to the solution at 0°C. After 0.5 h the mixture is allowed to come to rt and was held there for 1 h.
• the dicyclohexylucea which separated is filtered and washed with solvent. The combined filtrate and washings are evaporated to dryness under reduced pressure.
• the ester may be used directly for coupling reactions or may be purified by short column chromatography on silica using an isopropanol-in-chloroform gradient (0-50%).
• the residue is desilylated by using the 2 M HF/1M tert-butylammonium fluoride (TBAF) reagent described in B.L. Gaffney and R.A. Jones, Tetrahedron Lett (1982) 23:2257.
• TBAF 2 M HF/1M tert-butylammonium fluoride
• To the 2M HF/1M tert-butylammonium fluoride in pyridine (1 mmol of TBAF) is added the deprotected nucleoside from the previous paragraph. After stirring for 24 h, the reaction is partitioned between methylene chloride and aqueous sodium bicarbonate. The organic layer is washed with water, dried over sodium sulfate, and evaporated to dryness.
• the residue is purified by chromatography on silica using a gradient of methanol in methylene chloride (5-25%).
• the 3'-hydroxydinucleoside carbonates are converted to the 3'-(4-nitrophenyl)-carbonates by the method in Example 11. These derivatives may be reacted with the 5'-hydroxyl of a nucleoside or oligonucleoside carbonate to prepare higher order oligonucleoside carbonates.
• the 5'-tritylated aminonucleoside (1 mmol) is evaporated twice from DMF, then treated with bis-(p-nitrophenyl) carbonate (2 mmol) in the presence of triethylamine (or N,N-diinethylaminopyridine, or N-methyl imidazole) (catalytic amount) using DMF as the solvent. After 3 h, the solvent is evaporated and the residue dissolved in chloroform. This solution is washed twice with 0.01 N aqueous NaOH, once with water, then dried over Na 2 SO 4 .
• the solvent is removed by rotovap and the residue is chromatographed on silica gel eluting first with a chloroform/0.1% DMA mixture, then with a chloroform/methanol/0.1% DMA solvent system. The appropriate fractions are combined and evaporated to dryness.
• the residue is dissolved in a minimum of THFand this solution is added to an excess of hexanes.
• the precipitated activated nucleoside is collected by filtration and dried under vacuum.
• the required 5'-aminonucleoside (1.1 mmol), as prepared in Example 3 above, is twice evaporated from DMF.
• the activated nucleoside (1 mmol) is added to the reaction vessel and the solids are dissolved in DMF.
• the solution is concentrated to a small volume and allowed to stand overnight.
• the solvent is completely removed under vacuum and the resulting residue is dissolved in chloroform.
• This solution is twice washed with 0.01 N aqueous sodium hydroxide, once with water, then, dried over solid sodium sulfate.
• the solvent is removed by rotovap, and the residue is chromatographed on silica gel eluting with the appropriate methanol/chloroform/1% triethylamine solvent system. The fractions containing the dimer nucleoside are combined, then evaporated to dryness.
• the residue is dissolved in a minimum of THF and this solution is added to hexanes. The precipitate is collected and dried under vacuum.
• N,N-dimethylaminopyridine (DMAP) is purchased from Aldrich Chemical Co.
• Example 13 with the following alterations in procedure.
• the 5'-aminonucleosides employed have as base-protecting moieties either 2-(phenylsulfonyl)ethoxycarbonyl (for deoxycytidine and deoxyadenosine) or 9-FMOC (for guanosine and 2,6-diamino-2'-deoxyriboside) groups.
• the preparation of these molecules are described above
• N-methylimidazole is purchased from Aldrich Chemical Co.
• the chloroform solution is washed twice with 0.01 N aqueous NaOH, once with water, and then dried over Na 2 SO 4 .
• the solvent is removed by rotovap and the residue is chromatographed on silica gel eluting with chloroform/methanol solvent mixtures. The fractions containing the desired dimer are combined, then rotovaped to dryness.
• the residue is dissolved in a minimum of THF and the solution is added to an excess of hexanes. The precipitate is collected and dried under vacuum.
• Morpholino subunits linked by thiocarbamate moieties are prepared as related above in this example with the following experimental alterations.
• the base-protecting groups are either 1-(phenylsulfonyl) ethoxycarbonyl (for deoxycytidine and deoxyadenosine) or 9-FMOC (for deoxyguanosine and 2,6-diamino-2'-deoxyriboside) groups.
• the preparation of these molecules is described above (Example 5).
• N-protected morpholino nucleoside (1 mmol) is achieved with p-nitrophenylchlorothioformate (1.2 mmol) in the presence of triethylamine (2 mmol) and DMAP or N-methyl imidazole (catalytic amount) in DMF.
• the coupling step employs this activated monomer (1 mmol) with the requisite N'-free morpholino nucleoside (1.1 mmol) using DMAP or N-methyl imidazole as catalyst and DMF as the solvent while warming the solution to 35-40°C.
• the 0.01 N aqueous NaOH washes are omitted, employing in their place water washes.
• the coupling of two subunits is performed by reaction of the 5'-N,N-acetarnide-3'-hydroxy derivative with the with the 3'-silylated-5'-active ester. These are prepared as in Example 6.
• the reagents (1 mmol each) are coevaporated several times with dimethylformamide, then dissolved in dimethylformamide (5 mL) and treated with N,N-dimethylarninopyridine (0.2 mmol) or N-methylimidazole (1 rnmol).
• the solvent is removed under reduced pressure and the reaction allowed to stand at room temperature for 2 h.
• the residue is dissolved in chloroform and washed with dilute HCl, water, and the organic phase dried with sodium sulfate and solvents evaporated under reduced pressure.
• the residue is purified by chromatography on silica gel using a gradient of methanol in chloroform.
• the chain may be elongated by desilylation as in Example 6, and treatment of the resulting 3'-free hydroxy compound with the active ester as in the previous paragraph.
• Example 17
• a fully protected t-BOC N-hydroxysuccinimidoyl ester or p-nitrophenyl ester prepared as in Example 11.3 and 11.4 (1 mmol) is dried by several coevaporations with dry dimethyformamide.
• the protected amino acid trifluoroacetate salt from Example 9 (1 mmol) is treated similarly.
• the two components are separately dissolved in dry dimethylformamide (2 mL), mixed, and treated with diisopropylethylamine (1.0 mmol). The solution is stirred at room temperature for 1 h, then the solvent is removed by evaporation under reduced pressure, the residue dissolved in chloroform and washed with dilute HCl.
• the organic layer is dried over sodium sulfate, evaporated to dryness under reduced pressure, and the residue purified by chromatography on silica gel using a gradient of methanol in chloroform (5-50%).
• the t-BOC dimer acid may be purified by chromatography on C18 reverse phase silica gel using water and methanol (trifluoroethanol) mixtures.
• the t-BOC dimer active ester and the dimer acid trifluoroacetate are coupled to the t-BOC tetramer acid by the general procedure. Purification is best effected by chromatography on C18 reverse phase silica gel using water and methanol (or trifluoroethanol) mixtures buffered to pH 7.0 with triethylammoniurn acetate. In this manner chains of any length may be prepared by coupling an active ester with a free amine component.
• DEAE cellulose is purchased from Sigma Chemical Co.
• Preparative TLC plates are a product of EM Science purchased from UWR Scientific. HPLC equipment, columns, and supplies are available from Beckman Instruments, Inc.
• the requisite carbamate-linked dimer (0.2 mmol) prepared as described in example 12, is treated with 4 mL of a 1/1/1 mixture of methanol/THF/glacial acetic acid at rt for 12 h, The solvent is removed under vacuum and the residue is taken up in a minimum of THF.
• the THF solution is added to a large volume of hexanes and the resulting precipitate is collected and dried.
• the acetate salt is dissolved in a 4/1 THF/ethanol mixture and DEAE cellulose (0.8 mmol of the base) is added to the vessel. After stirring for 20 min, the heterogeneous mixture is filtered and the filtrate evaporated to dryness.
• the residue is dissolved in a minimum of 4/1 THF/ethanol and this solution is added to hexanes.
• the solid is collected and dried. The precipitation procedure is repeated once.
• N-5'-trityl dimer (0.1 mmol) (as prepared in Example 12) is evaporated twice from DMF, then treated with bis (p-nitrophenyl) carbonate (2 mmol) in the presence of triethylamine (or DMAP or N-methyl imidazole) (catalytic amount) using DMF as the solvent. after 3 h the solvent is evaporated and the residue dissolved in chloroform. This solution is washed twice with 0.01 N aqueous NaOH, once with water, then dried over Na 2 SO 4 . The solvent is removed by rotovap and the residue is chromatographed on silica gel eluting with a chloroforrn/isopropanol or methanol/0.1% DMA mixture.
• the octamer is configured for further use as follows.
• the N-5'-trityl octomer nucleoside is treated with 1/1/1 THF/methanol/glacial acetic acid and purified employing the conditions listed above.
• the 5'-amino octomer nucleoside (0.01 mmol) is treated with succinic anhydride (0.02 mmol) in pyridine at room temperature for two hours.
• the solvent is removed by rotovap and the residue is evaporated several times from ethanol.
• the residue is taken up in 3/1 THF/ethanol and added to a 2/1 hexane/benzene mixture.
• the solid is collected and dried.
• N-5'-succinylated octamer nucleoside (0.01 mmol) is treated with a 1/1 mixture of pyridine/concentrated ammonia (1 mL). After standing overnight the solvent is removed by rotovap and the residue is evaporated from ethanol several times. The crude solid is purified using reverse phase (RP-18) HPLC chromatography. The elutants are evaporated and the residue is taken up in DMSO and precipitated from a 1/1 hexane/benzene solvent mixture. The solid is collected and dried.
• RP-18 reverse phase
• Example 20 A mixture of 1 ml of the sulfonyldiethanol solution plus 0.2 g of dicyclohexylcarbodiimide is added to 1 g of the dry controlled pore glass support carrying carboxylic acid residues and the slurry mixed by rocking or tumbling (not stirring) overnight at rt. Thereafter, the glass support is thoroughly washed with methanol and dried.
• Example 20 A mixture of 1 ml of the sulfonyldiethanol solution plus 0.2 g of dicyclohexylcarbodiimide is added to 1 g of the dry controlled pore glass support carrying carboxylic acid residues and the slurry mixed by rocking or tumbling (not stirring) overnight at rt. Thereafter, the glass support is thoroughly washed with methanol and dried.
• Example 20 A mixture of 1 ml of the sulfonyldiethanol solution plus 0.2 g of dicyclohexylcarbodiimide is added to 1 g
• DBU 1,8-diazabicyclo[5.4.0]undec-7-ene
• the 2'-deoxycytidine subunit(0.1 mmol) prepared as in Example 4.2 (wherein the N4 carries a p-nitrophenethoxycarbonyl moiety, the 5' oxygen carries a di(p-methoxy) trityl moiety (DMT), and the 3' oxygen carries a p-nitrophenoxycarbonyl moiety) is dissolved in a minimal volume of dry tetrahydrofuran (THF) or dimethylformamide and added to 0.5 g of thoroughly dried controlled pore glass support carrying a cleavable linker, prepared as in Example 19.
• THF dry tetrahydrofuran
• Catalyst (either 1 nunol of N-methylimidazole or 0.1 mmol of DMAP) is introduced and the slurry is mixed by rocking or trembling (not stirring) for 2 hours. The slurry is next filtered, and the solid washed thoroughly with THF. Any unreacted hydroxyls are capped by adding two ml of THF 1 M in methyl p-nitrophenyl carbonate and 0.5 M in DMAP and mixing for 20 min at rt. Thereafter, the glass support is washed with THF and filtered.
• Example 21 Preparation of a 19-subunit carbamate-linked polymer targeted against a conserved sequence in the AIDS viral genome. Stepwise assembly of oliqomer blocks on a solid support: addition of the first subunit and chain extension.
• the 5'-amino-2',5'-dideoxycytidine subunit (0.2 mmol), prepared as in Example 3 (wherein the N4 carries a benzoyl moiety, the 5'-amine carries a p-methoxytrityl moiety, and the 3' oxygen carries a p-nitrophenbxycarbonyl moiety) is dissolved in a minimal volume of dry THF and added to 0.5 g of dried controlled pore glass support carrying a cleavable linker, prepared as in Example 19. Catalyst (either 1 mmol), prepared as in Example 3 (wherein the N4 carries a benzoyl moiety, the 5'-amine carries a p-methoxytrityl moiety, and the 3' oxygen carries a p-nitrophenbxycarbonyl moiety) is dissolved in a minimal volume of dry THF and added to 0.5 g of dried controlled pore glass support carrying a cleavable linker,
• N-methylirnidazole or 0.1 mmol of DMAP is introduced and the slurry mixed by rocking or tumbling for 2 h. The slurry is next filtered, and the solid washed thoroughly with THF. The mono-p-methoxy trityl is removed by washing with dichloromethane, followed by treatment with 5 ml of 0.2 M dichloroacetic acid in dichloromethane at rt for 1 min. The support is then washed with dichloromethane and filtered. The 5' amino termini are converted to their free ar ⁇ ine form by a brief wash with 3 ml of THF containing 1% by volume of diisopropylethylamine, followed by washing with THF and filtration.
• Any unreacted amine moieties are capped by adding 2 ml of THF 2 M in p-nitrophenyl acetate and mixing at rt for 20 min. Thereafter, the glass support is washed with THF and filtered.
• the mono-methoxytrityl at the 5' terminus is removed with dichloroacetic acid, as before.
• Subsequent activated dimeric subunits prepared as in Example 17 (wherein the exocyclic ring nitrogen of cytosine is protected with a benzoyl moiety and the exocyclic ring nitrogen of A is protected with a benzoyl or a p-nitrobenzoyl moiety), and added in a like manner and in the following order: A-T, C-A, T-A, T-T, T-T, A-C, A-C, C-A (5' to 3').
• Subunits having base exocyclic ring nitrogen protective groups removable by strong nonnucleophilic bases can also be used for assembling polymers by the procedure above.
• polymers having these alternative protective groups are generally deprotected by treatment with DBU rather than by ammonium hydroxide.
• Example 11.3 (wherein the N4 of the cytosine carries a 2(P-nitrophenyl)ethoxycarbonyl moiety, the amine of the backbone carries a t-butoxycarbonyl moiety, and the carboxyl is in the form of a p-nitrophenyl ester) is dissolved in a minimal volume of dry THF and added to 0.5 g of dried controlled pore glass support carrying a cleavable linker, prepared as in Example 19. Catalyst (either 1 mmol of
• N-methylimidazole or 0.1 rnmol of DMAP is introduced and the support mixed for 2 h, filtered, and the solid is washed thoroughly with THF.
• the t-BOC is removed by washing the support with dichloromethane followed by treatment at rt with 5 ml of 20% by volume trifluoroacetic acid in methylene chloride for 30 min.
• the support is washed with dichloromethane and filtered.
• the support-bound amino terminus is converted to the free amine form by a brief wash with 3 ml of THF containing 1% by volume of diisopropylethylamine, followed by a THF wash.
• the activated dimeric subunit (0.1 mmol) having the sequence (amino terminus)-G-A-(carboxy terminus) prepared as in Example 17 (wherein the N2 of guanine carries an FMOC moiety, the N6 of adenine carries a p-nitrophenethoxycarbonyl moiety, the backbone amino terminus carries a t-BOC moiety, and the carboxy terminus is in the form of a p-nitrophenyl ester) is dissolved in a minimal volume of dry THF and added to the glass support and mixing is carried out for 2 h (no catalyst is added for this or subsequent coupling steps). The support is washed with THF.
• Any unreacted amine moieties are capped by adding 2 ml of 2 M p-nitrophenyl acetate in THF and mixing at rt for 20 min. Thereafter, the glass support is washed with THF.
• Example 17 are added in a like manner in the following order: (C-terminus) T-A, A-C, A-T, T-T, T-T, C-A, C-A, C-A,
• A-C (N-terminus).
• Subunits having exocyclic ring nitrogen protective groups removable by good nucleophiles can also be used for assembling polymers by the above procedures.
• polymers having these alternative protective groups are generally deprotected by treatment with ammonium hydroxide rather than by DBU.
• Thymidine N-benzoyldeoxyadenosine, N-benzoyldeoxycytidine, N-isobutyryldeoxyguanosine and their 5'-O-(di-p-methoxytrityl) 5'-ODMT-nucleoside) derivatives are obtained from Pharmacia P-L Biochemicals (Piscataway, NJ).
• ⁇ -benzoylpropionic acid and dicyclohexylcarbodiimide (DCCD) are obtained from commercial sources.
• a selected 5'-O-dimethoxytrityl nucleoside (1mmol) is reacted with ⁇ -benzoylpropionic acid (3 mmol) and DCCD (4 mmol) in 6 ml pyridine.
• the reaction mixture is stirred at 25°C for three hours, after which 1.5 ml water is added and the mixture stirred for 5 hours at 25°C.
• the reaction mixture is filtered, and after evaporation of the filtrate, the residue is freed of pyridine by several coevaporations with ethanol.
• the purified residue is taken up in ethyl acetate and chromatographed on silica gel using ethyl acetate.
• the concentrated ethyl acetate eluate is treated with hexane to precipitate the resultant 3'-O- ⁇ -benzoylpropionyl-nucleoside (3'-O ⁇ B-nucleoside).
• p-Chlorophenylphosphorodichloridate is obtained from Aldrich (Milwaukee, WI). Benzenesulfonic acid, tetrahydrofuran, triethylamine, and 3-hydroxypropane-nitrile are obtained from commercial sources.
• a solution of p-chlorophenylphosphoro-ditriazolide is prepared by sequential reaction of 3 mmol triazole in 10 ml tetrahydrofuran with 3 mmol triethylamine and 1.5 mmol p-chlorophenylphosphoro-dichloridate.
• the reaction is terminated by pouring the mixture into 20 ml of 5% aqueous sodium bicarbonate at 0°C, extracting thoroughly with chloroform, drying the extracts with sodium sulfate, and removing the solvents under reduced pressure.
• the 5'-ODMT nucleoside 3'-O-(p-chlorophenyl-(2-cyanoethyl))-phosphate product is obtained by chromatography on silica gel using successive elutions of ether, ethyl acetate, and tetrahydrofuran.
• a solution of methylphosphonoditriazolide is prepared by reacting 1,2,4-triazole (3 mmol) and triethylamine (3 mmol) in 20 ml anhydrous tetrahydrofuran in the presence of methylposphonodichloridate (1.2 mmol) for 2-10 hours at 25°C. Following filtration, a solution of a selected 5'-ODMT nucleoside (1 mmol) in 10 ml dry pyridine is added to the filtrate, and the mixture is concentrated to 8 ml and allowed to stand at 25°C for up to 2 hours.
• stereoisomeric Methylphophonate Dimers The stereoisomeric dimers produced in the above section are separated by silica gel column chromatography, carried our at atmospheric pressure in glass columns with packed silica gel 60, using ethyl acetate: tetrahydrofuran mixtures (0-100% tetrahydrofuran) or chloroform/methanol mixtures (0-20% methanol). The faster moving stereoisomer fractions are combined, and precipitated from the tetrahydrofuran solution by the addition of hexane. The slower-moving stereoisomer is not used further.
• First and second stereospecific methylphosphonate dimers each having a selected 2-base combination and 3' O ⁇ D and 5' ODMT protecting groups, are each prepared as in Examples 24.1 and 24.2.
• the 5' ODMT protecting group on the first dimer is removed to give the pure 5' hydroxy compound.
• the cyanoethyl group of the second dimer is removed by treatment of 1 mmol of the dimer with a solution of pyridine (8.5 ml), water (2.9 ml), and triethylamine (2.9 ml) for 1 hour at 25°C, and evaporating the solvents to give the 3' hydroxynucleotide.
• the dimer condensation reaction is carried out by dissolving the 5'-OH dimer (1 mmol) and the 3'-hydroxynucleotide dimer (1 mmol) in 8 ml of pyridine and treating with mesitylenesulfonyl tetrazolide (3-6 mmol) for 3.5 hours at 25°C.
• the reaction mixture is combined with 4 ml of cold 50% aqueous pyridine and poured into 80 rnl of aqueous sodium bicarbonate.
• the reaction product is extracted thoroughly with chloroform, and after drying over sodium sulfate and evaporation of the organic solvent, is purified on silica gel using a rnethanol/chloroform mixture.
• Tetramers possessing the 3'-O-PO-(OpCP) (OCE) protecting group may be prepared by substantially the same method beginning with a dimer possessing the 3'-O-PO-(OpCP) (OCE) group.
• a bi-functional hexane linker arm 6-(2-(methyl- sulfonyl)-ethoxycarbonylamino)-hexanol is prepared by reacting 6-aminohexanol (1 mrnol) with 2-(methylsulfonyl) ethyl p-nitrophenylcarbonate (1 mmol) in 1 ml dimethylformamide for up to 4 hours at 25°C. The reaction mixture is poured into water, extracted thoroughly with benzene, the benzene washed with water, and the organic solvent then dried with sodium sulfate and evaporated to give the carbamate alcohol, which is purified by silica gel chromatography using a methanol/chloroform solvent mixture.
• Triethylammonium bicarbonate and tetrabutylammonium fluoride are obtained commercially.
• a fully protected oligonucleotide analog is prepared by the methylphosphonate-dimer condensation scheme described in Example VI.
• the oligonucleotide (1 mmol) is dissolved in 10 ml of chloroform: methanol (7:3, v/v) containing 2% benzenesulfonic acid, and kept at 0°C for about 40 minutes.
• the reaction mixture is washed with a 5% sodium bicarbonate solution and then water.
• the chloroform layer is dried over sodium sulfate, filtered, and evaporated under reduced pressure.
• the residue is chromatographed on silica gel using a chloroform/methanol solvent mixture.
• the protected oligonucleotide (1 mmol) is treated with 4 ml hydrazine hydrate in 14 ml of 20% acetic acid/pyridine for 16-24 hours at 25°C.
• the residue is treated with a solution containing 0.017 M tetrabutylammonium fluoride in 30 ml tetrahydrofuran/ pyridine/water (8:1:1, v/v/v) for 24 hours at 25°C.
• the solution is then treated with 60 ml 50% concentrated ammonium hydroxide in pyridine for 10 hours at 4°C.
• the resulting oligomer is purified on a reverse-phase HPLC column using an agueous acetonitrile mixture in 0.1 M ammonium acetate buffer, pH 5.8, as the chromatography solvent.
• Affi-gel 10 is obtained from Bio-Rad (Richmond, CA). 10 ml of the packed gel is washed with isopropyl alcohol (3 bed volumes), and then with ice-cold deionized water (3 bed volumes). A 5'-O-(6-aminohexyl)-oligonucleotide (150 mmol) is prepared as described in Example 26. The oligonucleotide (150 M) in 5 ml 0.1 M sodium bicarbonate buffer, pH 8.0, is slurried with the washed gel for 1-4 hours at 25°C. The mixture is then treated with 1 ml 1 M ethanolamine : HCl buffer, pH 8.0, to cap any unreacted active esters on the gel. The gel is washed with water until all the buffer has been removed, and stored at 4°C in the presence of 0.02% sodium azide.
• Example 26 Preparation of the Reagent Support
• Aminomethylated polystyrene is prepared as described by B.A. Mukhitdinova, E.E. Eighozin, and G.A. Makhmudova, Izv Akad Nauk Kaz SSR., Ser Khim (1980) 48.
• Disuccinimido dicarbonate and 6-aminohexanol are obtained from Aldrich.
• Aminomethylated polystyrene (1 g, 3.0 meq/g) is suspended in water/acetonitrile (10 ml, 3:1 v/v) and treated with succinic anhydride (20 mmol) at 4°C. The pH of the solution is kept at 6.0 by the addition of 20% NaOH.
• the support from above is suspended in dimethylformamide (10 ml) and reacted with 6-aminohexanol (20 mmol) for 24 hours at.25°C.
• the support is isolated by filtration and the support having the bound alcohol chain is washed thoroughly with dimethylformamide.
• N-methyliinidazole, tetrabutylammonium chloride, tetrabutylammonium fluoride, and imidazole are obtained from Aldrich.
• Bis (p-nitrophenyl) carbonate is obtained from Sigma (St. Louis, MO).
• the supported alcohol (10 mmol) is reacted with a coupling reagent such as carbonyl diimidazole (50 mmol) in dimethylformamide (30 ml) for 3 hours at 25°C.
• the activated support is isolated by filtration and thoroughly washed with dimethylformamide.
• the support is resuspended in 30 ml of dimethylformamide and treated with a selected polycarbamate polymer (50 mmol) prepared as in Example 21. After 3 hours, the supported alcohol is filtered and thoroughly washed with dimethylformamide.
• a selected probe is specific for a target sequence comprising residues 8441 to 8456 of the ORF-2 gene of ARU-2, the etiological agent of AIDS
• the supported polycarbamate (10 mmol) is suspended in acetonitrile (30 mmol) and treated with tetrabutylammonium chloride (3 mmol per meq of protecting group) and potassium fluoride dihydrate (4 mmol per meq of protecting group) and heated at 50°C for 12 hours. At the end of this time water (30 ml) is added and the supported probe is thoroughly washed with water.
• the protecting group may also be removed with tetrabutylammonium fluoride in tetrahydrofuran (3 mmol per meq of protecting group) under the same conditions.
• the dioxane is removed under reduced pressure and the pH of the solution is adjusted to pH-2.5 by the addition of potassium bisulfate.
• the aqueous phase is thoroughly extracted with ethyl acetate and the organic layers combined and dried over sodium sulfate. Removal of the solvents under reduced pressure gives the free acid which is purified by recrystallization from chloroform/hexane, or by chromatography on silica gel using chloroform/methanol mixtures.
• N,N'-carbonyl diimidazole is obtained from
• a solution of the BOC-protected amino acid (or oligopeptide acid, 1 mmol) is treated with carbonyl diimidazole (1 mmol) at -20°C for 6 hours.
• a solution of dimethylamine (excess) or oligopeptide amine (1 mmol) prepared as in Example 30, in DMF (1 ml) is added at -20°C and the reaction then stirred at 25°C for 12 hours.
• the solvent is removed by reduced pressure and the residue is chromatographed on silica gel using methanol/chloroform to give
• N,N-Ditnethyl 4-(methylamino)-butyramide Trifluoroacetic acid is obtained from Aldrich.
• polyamides of various lengths may be prepared.
• the oligomeric polyamide to be reduced is treated with trifluoroacetic acid as in the general procedure in order to remove the BOC group.
• the free amine (1 mmol) in tetrahydrofuran (1 ml) is added dropwise to a solution of borane (2 mmol per amide residue) in tetrahydrofuran
• the residue is dissolved in 1 N HCl (4 ml) and applied to a Dowex 50W ion exchange column. After washing with water, and then 2 M HCl, the product is recovered as the hydrochloride by elution with 6 N HCl and removal of the solvent under reduced pressure.
• Example 33 General Procedure for the Incorporation of a Terminal Primary Amino Group into the Polyamine 4-aminobutyric acid is converted to the BOC-derivative. This is reacted with carbonyl diimidazole as in Example 28 and treated wtih the dimeric amide from Example 29. Cleavage of the BOC-group and reduction as in Example 31 produced the polyamine.
• the primary amino group of the polyamine is protected as the BOC-derivative as in the general procedure and converted into the ammonium salt using methyl iodide as per Example 33.
• the solvent is evaporated and the residue is dissolved in trifluoroacetic acid (5 ml). After 1 hour, the solvent is evaporated and the residue dissolved in pyridine (5 ml).
• ethyldiisopropylamine (2mmol per mmol of primary, secondary, and tertiary amine function) and the dansyl group is introduced by treatment of the solution with 5-dimethylamino-naphthalene-sulfonyl chloride (0.9 mmol) (obtained as in Example XX) at 0°C, then allowing the mixture to stand overnight at 4°C.
• the reaction product is purified as in the previous paragraph by ion exchange chromatography, and isolated as the hydrochloride salt.
• the dansylated reporter may be treated directly with methyl iodide in dimethylformamide and purified by ion exchange chromatography, as above.
• the residue is dissolved in water (10 ml) and applied to a Dowex 50-W (Bio-Rad) ion exchange column and washed with water (10 ml), 0.5 N HCl (5 ml), and finally the product is eluted with 6 N HCl.
• the hydrochloride salt of the product is obtained by removal of the solvent under reduced pressure.
• the 16-base sequence at positions 462 to 477 of the 2gD gene of Herpes simplex virus, types I and II, 5'-GCGGGGCTGCGTTCGG-3', comprises the selected target sequence (Lasky & Downbenko, DNA (1984) 3:23).
• a complementary reagent polymer composed of alternating methylphosphonate/phosphodiester linkages is constructed substantially according to the methods of Examples 23 ans 24. The polymer is converted to the 5'-O-(6-aminohexyl)-oligonucleotide analog and coupled through the aminohexyl spacer arm to an Affi-Gel 10 solid support material, by conventional coupling methods.
• the melting temperature of the polymer/analyte duplex is determined using a synthetic oligonucleotide having the 5'-GCGGGGCTGCGTTCGG-3' target sequence.
• This target sequence which is purchased, or constructed by conventional methods, is mixed with a substantially equimolar amount of the polymer (before polymer attachment to the solid support) in annealing buffer (10 mM EDTA, 100 mM sodium phosphate, pH 7.2). This solution is heated to 90°C and slowly cooled to room temperature to effect annealing. The temperature is then slowly raised and absorbance is recorded as a function of the temperature.
• annealing buffer (10 mM EDTA, 100 mM sodium phosphate, pH 7.2
• Tm is taken as the temperature at which half the total absorbance change has occurred.
• An analyte sample taken as a skin scrape of an infected area, is suspended in 0.1 ml of EDTA-detergent solution (10 mM EDTA, 1% w/v sodium dodecyl sulfate, pH to 7.0), homogenized briefly in a micro tissue grinder (Kontes #K-885470) and the homogenate filtered centrifugally in a microfilter (UWR Scientific #28151-807). One-half ml of 4.5 M sodium trichloroacetate is added, followed in a few seconds by 0.6 ml. of ethanol. This preparation is placed on ice for 30 min and then centrifuged for 5 min at 10,000 g.
• the supernatant is carefully decanted and discarded and the tube is gently rinsed with aqueous 80% ethanol.
• the pelleted material (often not visible) is resuspended in 0.05 ml of annealing buffer (10 mM EDTA, 100 mM sodium phosphate, pH 7.2) and added to an appropriate amount of diagnositc reagent from Example XXI (estimated reagent polymer/ analyted molar ratio > 100).
• Annealing is carried out at a temperature 8°C below the Tm of the polymer/target duplex (predetermined as described in Example 35) for 30min and then the diagnostic reagent is washed three times with 2 ml volumes of annealing buffer.
• This washing is conveniently carried out centrifugally in a microfilter.
• the diagnostic reagent is suspended in 0.2 ml of reporter solution containing 1 mg of the fluorescent-diquaternary ammonium reporter, whose synthesis is described in Example 34.
• the reporter solution contains only NaCl at a suitable concentration, predetermined as described above.
• the diagnostic reagent is next washed three times with 2 ml volumes of reporter-free binding solution.
• reporter is eluted from the diagnostic reagent with 0.1 ml of 2 M NaCl and the elutant assessed for fluorescence in a spectrofluorometer. The fluorescence from a control sample lacking analyte is subtracted to provide a quantitative measure proportional to the analyte present in the initial sample.
• Example 37 Preparation of Diagnostic Reagent for Detection of the AIDS Virus
• a complementary polymer having carbarnate-linked subunits is constructed substantially according to methods detailed in Example 21. Briefly, the
• Example X 2'deoxyribonucleosides dA, dC, and dG are protected as in Example X. These protected nucleosides plus thymidine are then converted to their 5'amino derivatives. Polymeric support is then prepared as in Example 25 or 26, and subunits are linked sequentially to this support by the method described in those examples to give a support-bound protected polymer having the sequence: Support CTGCTCCCACCCCATC-3'. In the final step the base-protective groups are removed to give the desired carbamate-linked diagnostic reagent.
• the melting temperature of the polyrner/analyte is determined as follows.
• An RNA transcript is prepared from single-stranded polynucleotide containing a sequence complementary to the target sequence.
• This target-containing RNA is suspended in annealing buffer (10 mM EDTA, 100 mM sodium phosphate, pH 7.0) and added to the above diagnostic reagent.
• the mixture is warmed to 90°C and slowly cooled to room temperature to effect annealing.
• the diagnostic reagent is placed in a small water-jacketed chromatography column through which annealing buffer is slowly pumped.
• the temperature is slowly raised while monitoring the effluent for released RNA.
• the release temperature (Tr) is the temperature at which the RNA is eluted from the column. This Tr value often differs by one to a few degrees C from the corresponding Tm determined by the hyperchromic shift method described in Example XXI.
• the solvent is removed under reduced pressure and the solid is triturated with hexane to remove unreacted phenylazide.
• the solid is next suspended in 10 ml of 0.1 M NaCl and cacodylic acid is added to lower the pH to 7.2.
• 5 mg of alkaline phosphatase (Sigma Chem Co., #P5778) is added to 1 ml of the foregoing tail solution and illuminated for 1 hr with a high flux of 366 nm light.
• the resulting reporter is dialyzed for 18 hr against a large volume of buffer (0.1 M NaCl, 0.05 M sodium cacodylate, pH 7.0) to remove cationic tail not linked to the enzyme.
• Bovine serum albumin 1% w/v
• sodium azide 0.02% w/v
• the pelleted nucleic acid (often not visable) is washed with aqueous 80% ethanol, drained well, and resuspended in 0.1 ml of annealing buffer (10 mM EDTA, 100 mM sodium phosphate, pH 7.2) and added to an appropriate amount of diagnostic reagent from Example. 37 (estimated polymer/ target molar ratio > 100).
• Annealing is carried out at a temperature 7°C below the Tr of the polymer/target duplex (predetermined as in Example 37) for one hr and then the diagnostic reagent is washed three times with 2 ml volumes of annealing buffer. This washing is conveniently carried out centrifugally in a microfilter.
• the diagnostic reagent is suspended in 0.2 ml of an enzymatic-tetracationic reporter solution prepared as in Example 38. After 30 sec the diagnostic reagent is washed three times with 2 ml volumes of reporter-free binding solution. Thereafter, the diagnostic reagent is suspended in developing solution (15 mM p-nitrophenyl phosphate, 0.5 mM MgCl, 1.0 M diethanolamine, pH 9.8) and incubated for 3 hr at 37°C. Reporter-generated p-nitrophenol is quantitated spectrophotometrically. Corresponding absorbance from a control sample lacking analyte is subtracted to provide a quantitative measure proportional to the analyte present in the initial sample.
• the diagnostic reagent may include multiple species of support-bound polymers, each specie designed to bind to a different selected target sequence in polynucleotide strands from different analytes, or the diagnostic reagent may include two species of support-bound polymers, with each specie designed to bind to a different complementary strand of a duplex analyte.
• These multi-specie reagents offer the potential of detecting more than one analyte in a diagnostic test, or of doubling the sensitivity of detection of a single duplex analyte.

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