# Patent

## Title
Precursors for two-step polynucleotide synthesis

## Abstract

Precursors for use in the synthesis of polynucleotides are disclosed. The precursors include a heterocyclic base having an exocyclic amine group and a substituted or unsubstituted triaryl methyl protecting group bound to the exocyclic amine group. In particular embodiments, the precursor has the structure:




wherein:

    
    
        O and H represent oxygen and hydrogen, respectively,
        R1 is hydrido, hydroxyl, protected hydroxyl, lower alkyl, modified lower alkyl, or alkoxy,
        one of R2 or R3 is a hydroxyl protecting group; and the other of R2 or R3 is a reactive group capable of reacting with a reactive site hydroxyl,
        Base is a heterocyclic base having an exocyclic amine group, and
        Tram is a triaryl methyl group having the structure (V)
    
    






wherein the broken line represents a bond to the amino nitrogen of the exocyclic amine group, and R4, R5 and R6 are independently selected from unsubstituted or substituted aryl groups, provided that at least one of R4, R5, and R6 is an aryl group other than phenyl and other than substituted phenyl.

## Background
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
This invention was made with Government support under Agreement No. N39998-01-9-7068. The Government has certain rights in the invention.


RELATED APPLICATIONS 
Related subject matter is disclosed in U.S. patent applications entitled “Method for Polynucleotide Synthesis”, (Ser. No. 10/652,054; “Method of Polynucleotide Synthesis Using Modified Support”, (Ser. No. 10/652,049); “Cleavable Linker for Polynucleotide Synthesis”, (Ser. No. 10/652,063); “Exocyclic Amine Triaryl Methyl Protecting Groups in Two-Step Polynucleotide Synthesis” (Ser. No. 10/652,064); all applications filed in the names of Dellinger et al. on Aug. 30, 2003, the same day as the instant application, all of which are incorporated herein by reference in their entireties, provided that, if a conflict in definition of terms arises, the definitions provided in the present application shall be controlling.
FIELD OF THE INVENTION
The invention relates generally to nucleic acid chemistry and to the chemical synthesis of polynucleotides. More particularly, the invention relates to providing modified starting materials for use in polynucleotide synthesis to provide for reduced incidence of undesired side reactions. The invention is useful in the manufacture of reagents and devices used in the fields of biochemistry, molecular biology and pharmacology, and in medical diagnostic and screening technologies.
BACKGROUND OF THE INVENTION
Solid phase chemical synthesis of DNA fragments is routinely performed using protected nucleoside phosphoramidites. Beaucage et al. (1981) Tetrahedron Lett. 22:1859. In this approach, the 3′-hydroxyl group of an initial 5′-protected nucleoside is first covalently attached to the polymer support. Pless et al. (1975) Nucleic Acids Res. 2:773. Synthesis of the oligonucleotide then proceeds by deprotection of the 5′-hydroxyl group of the attached nucleoside, followed by coupling of an incoming nucleoside-3′-phosphoramidite to the deprotected hydroxyl group. Matteucci et al. (1981) J. Am. Chem. Soc. 103:3185. The resulting phosphite triester is finally oxidized to a phosphorotriester to complete one round of the synthesis cycle. Letsinger et al. (1976) J. Am. Chem. Soc. 98:3655. The steps of deprotection, coupling and oxidation are repeated until an oligonucleotide of the desired length and sequence is obtained. This process is illustrated schematically in FIG. 1 (wherein “B” represents a purine or pyrimidine base, “DMT” represents dimethoxytrityl and “iPR” represents isopropyl). Optionally, after the coupling step, the product may be treated with a capping agent designed to esterify failure sequences and cleave phosphite reaction products on the heterocyclic bases.
The chemical group conventionally used for the protection of nucleoside 5′-hydroxyls is dimethoxytrityl, which is removable with acid. Khorana (1968) Pure Appl. Chem. 17:349; Smith et al. (1962) J. Am. Chem. Soc. 84:430. This acid-labile protecting group provides a number of advantages for working with both nucleosides and oligonucleotides. For example, the DMT group can be introduced onto a nucleoside regioselectively and in high yield. Brown et al. (1979) Methods in Enzymol. 68:109. Also, the lipophilicity of the DMT group greatly increases the solubility of nucleosides in organic solvents, and the carbocation resulting from acidic deprotection gives a strong chromophore, which can be used to indirectly monitor coupling efficiency. Matteucci et al. (1980) Tetrahedron Lett. 21:719. In addition, the hydrophobicity of the group can be used to aid separation on reverse-phase HPLC. Becker et al. (1985) J. Chromatogr. 326:219.
However, the use of DMT as a hydroxyl-protecting group for conventional oligonucleotide synthesis has a number of perceived drawbacks. The N-glycosidic linkages of oligodeoxyribonucleotides are susceptible to acid catalyzed cleavage (Kochetkov et al., Organic Chemistry of Nucleic Acids (New York: Plenum Press, 1972)), and even when the protocol is optimized, recurrent removal of the DMT group with acid during oligonucleotide synthesis results in depurination. Shaller et al. (1963) J. Am. Chem. Soc. 85:3821. The N-6-benzoyl-protected deoxyadenosine nucleotide is especially susceptible to glycosidic cleavage, resulting in a substantially reduced yield of the final oligonucleotide. Efcavitch et al. (1985) Nucleosides & Nucleotides 4:267. Attempts have been made to address the problem of acid-catalyzed depurination utilizing alternative mixtures of acids and various solvents; see, for example, Sonveaux (1986) Bioorganic Chem. 14:274. However, this approach has met with limited success. McBride et al. (1986) J. Am. Chem. Soc. 108:2040. Also, using the conventional synthesis scheme set forth in FIG. 1 requires additional steps per cycle of addition of a nucleotide to the growing polynucleotide chain, including the post-coupling deprotection step in which the DMT group is removed following oxidation of the internucleotide phosphite triester linkage to a phosphorotriester.
The problems associated with the use of DMT are exacerbated in solid phase oligonucleotide synthesis where “microscale” parallel reactions are taking place on a very dense, packed surface. Applications in the field of genomics and high throughput screening have fueled the demand for precise chemistry in such a context. Side-reactions, which are known to occur at detectable but acceptable levels during routine synthesis, can rise to unacceptable levels under the conditions required for these expanded applications. Thus, increasingly stringent demands are placed on the chemical synthesis cycle as it was originally conceived, and the problems associated with conventional methods for synthesizing oligonucleotides are rising to unacceptable levels in these expanded applications.
Recently, alternate schemes for synthesis of polynucleotides have been described. See, e.g. U.S. Pat. No. 6,222,030 to Dellinger et al., U.S. Pat. Appl'n Publ'n No. US2002/0058802 A1 to Dellinger et al., Seio et al. (2001) Tetrahedron Lett. 42 (49):8657-8660. These schemes involve protecting groups other than DMT at the 3′ or 5′ positions and correspondingly different conditions for performing reactions such as deprotection at the 3′ or 5′ positions. These schemes have the additional advantage of reducing the number of steps required per cycle of addition of a nucleotide to the growing polynucleotide chain. FIG. 2 illustrates such a process having a two-step synthesis cycle, represented in FIG. 2 as a coupling step and a simultaneous deprotection and oxidation step.
In previously reported methods such as that shown in FIG. 1, the newly synthesized oligonucleotides containing N-protected nucleobases are typically deprotected using displacement by nucleophiles such as ammonia or methylamine. These reagents can have similar properties to (and thus may not be compatible with) the reagents used for the alternative removal of 3′ or 5′ protecting groups in simplified 2-step DNA synthesis. Also, the anhydrous solvents required for effective coupling reactions may result in lower solubilities of reactive monomers than desired.
Furthermore, the conditions used in the previously reported two-step synthesis (such as shown in FIG. 2) were discovered to result in a low incidence of other, unexpected (and undesired) side reactions. Removal of the 3′ or 5′ protecting group also resulted in a small amount of removal of the N-protecting group from the nucleobase. This premature deprotection frees up reactive sites for phosphoramidite coupling and can result in nucleobase modifications and chain branching.
Thus, what is needed is an improved synthesis of polynucleotides having a reduced incidence of the undesired side reactions, and providing greater solubility for the reactive monomers in anhydrous solvents.
SUMMARY OF THE INVENTION
The invention addresses the aforementioned deficiencies in the art, and provides novel methods and materials for synthesis of polynucleotides. More specifically, the present invention provides precursors having an exocyclic amine triaryl methyl protecting group. Such precursors may be advantageously employed in performing two-step polynucleotide synthesis.
The precursors described in accordance with the current invention comprise a heterocyclic base having an exocyclic amine group and a substituted or unsubstituted triaryl methyl protecting group bound to the exocyclic amine group. The precursors typically have the structure (I):

Rag-Sugar-Base-Tram  (I)

Wherein the groups are defined as follows:

Rag—a reactive group capable of reacting with a reactive site hydroxyl of a nucleoside moiety (e.g. on a nascent polynucleotide molecule in the process of being synthesized) to result in formation of an internucleotide bond,
Sugar—a sugar group such as may be found in a nucleotide or nucleotide analog, typically ribose or 2′-deoxyribose, wherein the sugar group is substituted with one or more substituents,
Base—a heterocyclic base having an exocyclic amine group, typically attached to the sugar group at the 1′ position of the sugar group, and
Tram—a triaryl methyl protecting group, optionally having one or more substituents, the triaryl methyl protecting group bound to the heterocyclic base via the exocyclic amine group. The triaryl methyl protecting group has three aryl groups directly bound to a central methyl carbon, wherein at least one of the three aryl groups is an aromatic group other than phenyl.
The present invention also provides methods of synthesizing polynucleotides using precursors described herein. In an embodiment, the method of synthesizing polynucleotides includes forming an internucleotide bond and then exposing the result of the forming an internucleotide bond step to a composition which concurrently oxidizes the internucleotide bond and removes a hydroxyl protecting group from the sugar group.
Further information about the groups described above, precursors having the structure (I), and use of such precursors in methods for synthesis of polynucleotides is described herein. The use of a triaryl methyl protecting group provides for protection of the exocyclic amines from undesirable side reactions during synthesis. The triaryl methyl protecting groups may then be released from the synthesized polynucleotide under mildly acidic conditions.
Additional objects, advantages, and novel features of this invention shall be set forth in part in the descriptions and examples that follow and in part will become apparent to those skilled in the art upon examination of the following specifications or may be learned by the practice of the invention. The objects and advantages of the invention may be realized and attained by means of the materials and methods particularly pointed out in the appended claims.



BRIEF DESCRIPTION OF THE DRAWINGS
These and other features of the invention will be understood from the description of representative embodiments of the method herein and the disclosure of illustrative materials for carrying out the method, taken together with the Figures, wherein
FIG. 1 schematically illustrates prior art synthesis of polynucleotides.
FIG. 2 depicts a synthesis scheme employing a two step synthesis cycle, including a coupling step and a simultaneous deprotection and oxidation step.
FIG. 3 depicts a method of synthesis of polynucleotides according to the present invention.



To facilitate understanding, identical reference numerals have been used, where practical, to designate corresponding elements that are common to the Figures. Figure components are not drawn to scale.
DETAILED DESCRIPTION
Before the invention is described in detail, it is to be understood that unless otherwise indicated this invention is not limited to particular materials, reagents, reaction materials, manufacturing processes, or the like, as such may vary. It is also to be understood that the terminology used herein is for purposes of describing particular embodiments only, and is not intended to be limiting. It is also possible in the present invention that steps may be executed in different sequence where this is logically possible. However, the sequence described below is preferred.
It must be noted that, as used in the specification and the appended claims, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “an insoluble support” includes a plurality of insoluble supports. In this specification and in the claims that follow, reference will be made to a number of terms that shall be defined to have the following meanings unless a contrary intention is apparent:
A “nucleotide” refers to a sub-unit of a nucleic acid (whether DNA or RNA or analogue thereof) which includes a phosphate group, a sugar group and a heterocyclic base, as well as analogs of such sub-units. A “nucleoside” references a nucleic acid subunit including a sugar group and a heterocyclic base. A “nucleoside moiety” refers to a portion of a molecule having a sugar group and a heterocyclic base (as in a nucleoside); the molecule of which the nucleoside moiety is a portion may be, e.g. a polynucleotide, oligonucleotide, or nucleoside phosphoramidite. A “nucleotide monomer” refers to a molecule which is not incorporated in a larger oligo- or poly-nucleotide chain and which corresponds to a single nucleotide sub-unit; nucleotide monomers may also have activating or protecting groups, if such groups are necessary for the intended use of the nucleotide monomer. A “polynucleotide intermediate” references a molecule occurring between steps in chemical synthesis of a polynucleotide, where the polynucleotide intermediate is subjected to further reactions to get the intended final product, e.g. a phosphite intermediate which is oxidized to a phosphate in a later step in the synthesis, or a protected polynucleotide which is then deprotected. An “oligonucleotide” generally refers to a nucleotide multimer of about 2 to 200 nucleotides in length, while a “polynucleotide” includes a nucleotide multimer having at least two nucleotides and up to several thousand (e.g. 5000, or 10,000) nucleotides in length. It will be appreciated that, as used herein, the terms “nucleoside”, “nucleoside moiety” and “nucleotide” will include those moieties which contain not only the naturally occurring purine and pyrimidine bases, e.g., adenine (A), thymine (T), cytosine (C), guanine (G), or uracil (U), but also modified purine and pyrimidine bases and other heterocyclic bases which have been modified (these moieties are sometimes referred to herein, collectively, as “purine and pyrimidine bases and analogs thereof”). Such modifications include, e.g., methylated purines or pyrimidines, acylated purines or pyrimidines, and the like, or the addition of a protecting group such as acetyl, difluoroacetyl, trifluoroacetyl, isobutyryl, benzoyl, or the like. The purine or pyrimidine base may also be an analog of the foregoing; suitable analogs will be known to those skilled in the art and are described in the pertinent texts and literature. Common analogs include, but are not limited to, 1-methyladenine, 2-methyladenine, N6-methyladenine, N6-isopentyladenine, 2-methylthio-N-6-isopentyladenine, N,N-dimethyladenine, 8-bromoadenine, 2-thiocytosine, 3-methylcytosine, 5-methylcytosine, 5-ethylcytosine, 4-acetylcytosine, 1-methylguanine, 2-methylguanine, 7-methylguanine, 2,2-dimethylguanine, 8-bromoguanine, 8-chloroguanine, 8-aminoguanine, 8-methylguanine, 8-thioguanine, 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, 5-ethyluracil, 5-propyluracil, 5-methoxyuracil, 5-hydroxymethyluracil, 5-(carboxyhydroxymethyl)uracil, 5-(methylaminomethyl)uracil, 5-(carboxymethylaminomethyl)-uracil, 2-thiouracil, 5-methyl-2-thiouracil, 5-(2-bromovinyl)uracil, uracil-5-oxyacetic acid, uracil-5-oxyacetic acid methyl ester, pseudouracil, 1-methylpseudouracil, queosine, inosine, 1-methylinosine, hypoxanthine, xanthine, 2-aminopurine, 6-hydroxyaminopurine, 6-thiopurine and 2,6-diaminopurine.
The term “alkyl” as used herein, unless otherwise specified, refers to a saturated straight chain, branched or cyclic hydrocarbon group of 1 to 24, typically 1-12, carbon atoms, such as methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, t-butyl, pentyl, cyclopentyl, isopentyl, neopentyl, hexyl, isohexyl, cyclohexyl, 3-methylpentyl, 2,2-dimethylbutyl, and 2,3-dimethylbutyl. The term “lower alkyl” intends an alkyl group of one to six carbon atoms, and includes, for example, methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, t-butyl, pentyl, cyclopentyl, isopentyl, neopentyl, hexyl, isohexyl, cyclohexyl, 3-methylpentyl, 2,2-dimethylbutyl, and 2,3-dimethylbutyl. The term “cycloalkyl” refers to cyclic alkyl groups such as cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl and cyclooctyl.
The term “modified alkyl” refers to an alkyl group having from one to twenty-four carbon atoms, and further having additional groups, such as one or more linkages selected from ether-, thio-, amino-, phosphor oxo-, ester-, and amido-, and/or being substituted with one or more additional groups including lower alkyl, aryl, alkoxy, thioalkyl, hydroxyl, amino, sulfonyl, thio, mercapto, imino, halo, cyano, nitro, nitroso, azido, carboxy, sulfide, sulfone, sulfoxy, phosphoryl, silyl, silyloxy, and boronyl. The term “modified lower alkyl” refers to a group having from one to six carbon atoms and further having additional groups, such as one or more linkages selected from ether-, thio-, amino-, phosphor keto-, ester-, and amido-, and/or being substituted with one or more groups including lower alkyl; aryl, alkoxy, thioalkyl, hydroxyl, amino, sulfonyl, thio, mercapto, imino, halo, cyano, nitro, nitroso, azido, carboxy, sulfide, sulfone, sulfoxy, phosphoryl, silyl, silyloxy, and boronyl. The term “alkoxy” as used herein refers to a substituent —O—R wherein R is alkyl as defined above. The term “lower alkoxy” refers to such a group wherein R is lower alkyl. The term “thioalkyl” as used herein refers to a substituent —S—R wherein R is alkyl as defined above.
The term “alkenyl” as used herein, unless otherwise specified, refers to a branched, unbranched or cyclic (e.g. in the case of C5 and C6) hydrocarbon group of 2 to 24, typically 2 to 12, carbon atoms containing at least one double bond, such as ethenyl, vinyl, allyl, octenyl, decenyl, and the like. The term “lower alkenyl” intends an alkenyl group of two to six carbon atoms, and specifically includes vinyl and allyl. The term “cycloalkenyl” refers to cyclic alkenyl groups.
The term “alkynyl” as used herein, unless otherwise specified, refers to a branched or unbranched hydrocarbon group of 2 to 24, typically 2 to 12, carbon atoms containing at least one triple bond, such as acetylenyl, ethynyl, n-propynyl, isopropynyl, n-butynyl, isobutynyl, t-butynyl, octynyl, decynyl and the like. The term “lower alkynyl” intends an alkynyl group of two to six carbon atoms, and includes, for example, acetylenyl and propynyl, and the term “cycloalkynyl” refers to cyclic alkynyl groups.
The term “aryl” as used herein refers to an aromatic species containing 1 to 5 aromatic rings, either fused or linked, and either unsubstituted or substituted with 1 or more substituents typically selected from the group consisting of lower alkyl, aryl, aralkyl, lower alkoxy, thioalkyl, hydroxyl, thio, mercapto, amino, imino, halo, cyano, nitro, nitroso, azido, carboxy, sulfide, sulfone, sulfoxy, phosphoryl, silyl, silyloxy, and boronyl; and lower alkyl substituted with one or more groups selected from lower alkyl, alkoxy, thioalkyl, hydroxyl thio, mercapto, amino, imino, halo, cyano, nitro, nitroso, azido, carboxy, sulfide, sulfone, sulfoxy, phosphoryl, silyl, silyloxy, and boronyl. Typical aryl groups contain 1 to 3 fused aromatic rings, and more typical aryl groups contain 1 aromatic ring or 2 fused aromatic rings. Aromatic groups herein may or may not be heterocyclic. The term “aralkyl” intends a moiety containing both alkyl and aryl species, typically containing less than about 24 carbon atoms, and more typically less than about 12 carbon atoms in the alkyl segment of the moiety, and typically containing 1 to 5 aromatic rings. The term “aralkyl” will usually be used to refer to aryl-substituted alkyl groups. The term “aralkylene” will be used in a similar manner to refer to moieties containing both alkylene and aryl species, typically containing less than about 24 carbon atoms in the alkylene portion and 1 to 5 aromatic rings in the aryl portion, and typically aryl-substituted alkylene. Exemplary aralkyl groups have the structure —(CH2)j—Ar wherein j is an integer in the range of 1 to 24, more typically 1 to 6, and Ar is a monocyclic aryl moiety.
The term “electron withdrawing” denotes the tendency of a substituent to attract valence electrons of the molecule of which it is a part, i.e., an electron-withdrawing substituent is electronegative.
The term “alpha effect,” as in an “alpha effect” nucleophilic deprotection reagent, is used to refer to an enhancement of nucleophilicity that is found when the atom adjacent a nucleophilic site bears a lone pair of electrons. As the term is used herein, a nucleophile is said to exhibit an “alpha effect” if it displays a positive deviation from a Bronsted-type nucleophilicity plot. Hoz et al. (1985) Israel J. Chem. 26:313. See also, Aubort et al. (1970) Chem. Comm. 1378; Brown et al. (1979) J. Chem. Soc. Chem. Comm.171; Buncel et al. (1982) J. Am. Chem. Soc. 104:4896; Edwards et al. (1962) J. Am. Chem. Soc. 84:16; Evanseck et al. (1987) J. Am. Chem Soc. 109:2349. The magnitude of the alpha effect is dependent upon the electrophile which is paired with the specific nucleophile. McIsaac, Jr. et al. (1972), J. Org. Chem. 37:1037. Peroxy anions are example of nucleophiles which exhibit strong alpha effects.
The term “heterocyclic” refers to a five- or six-membered monocyclic structure or to an eight- to eleven-membered bicyclic structure which is either saturated or unsaturated. The heterocyclic groups herein may be aliphatic or aromatic. Each heterocyclic group consists of carbon atoms and from one to four heteroatoms selected from the group consisting of nitrogen, oxygen and sulfur. As used herein, the term “nitrogen heteroatoms” includes any oxidized form of nitrogen, and the quaternized form of nitrogen. The term “sulfur heteroatoms” includes any oxidized form of sulfur. Examples of heterocyclic groups include purine, pyrimidine, piperidinyl, morpholinyl and pyrrolidinyl. “Heterocyclic base” refers to any natural or non-natural heterocyclic moiety that can participate in base pairing or base stacking interaction on an oligonucleotide strand.
“Exocyclic” refers to a group situated outside of the ring of a cyclic chemical structure, e.g. a portion of a substituent of the ring is exocyclic to the ring. As used herein, exocyclic amine refers to an amine group that is a substituent of a ring of a heterocyclic base and includes embodiments in which the nitrogen of the amine group is attached directly to a member of the ring structure and also includes embodiments in which the nitrogen of the amine group may be linked to the ring structure of the heterocyclic base via an intervening group.
An “internucleotide bond” refers to a chemical linkage between two nucleoside moieties, such as a phosphodiester linkage in nucleic acids found in nature, or such as linkages well known from the art of synthesis of nucleic acids and nucleic acid analogues. An internucleotide bond may comprise a phospho or phosphite group, and may include linkages where one or more oxygen atoms of the phospho or phosphite group are either modified with a substituent or replaced with another atom, e.g. a sulfur atom or the nitrogen atom of a mono- or di-alkyl amino group.
“Moiety” and “group” are used to refer to a portion of a molecule, typically having a particular functional or structural feature, e.g. a linking group (a portion of a molecule connecting two other portions of the molecule), or an ethyl moiety (a portion of a molecule with a structure closely related to ethane).
“Linkage” as used herein refers to a first moiety bonded to two other moieties, wherein the two other moieties are linked via the first moiety. Typical linkages include ether (—O—), oxo (—C(O)—), amino (—NH—), amido (—N—C(O)—), thio (—S—), phospho (—P—), ester (—O—C(O)—).
“Bound” may be used herein to indicate direct or indirect attachment. In the context of chemical structures, “bound” (or “bonded”) may refer to the existence of a chemical bond directly joining two moieties or indirectly joining two moieties (e.g. via a linking group). The chemical bond may be a covalent bond, an ionic bond, a coordination complex, hydrogen bonding, van der Waals interactions, or hydrophobic stacking, or may exhibit characteristics of multiple types of chemical bonds. In certain instances, “bound” includes embodiments where the attachment is direct and also embodiments where the attachment is indirect.
“Functionalized” references a process whereby a material is modified to have a specific moiety bound to the material, e.g. a molecule or substrate is modified to have the specific moiety; the material (e.g. molecule or support) that has been so modified is referred to as a functionalized material (e.g. functionalized molecule or functionalized support).
The term “halo” or “halogen” is used in its conventional sense to refer to a chloro, bromo, fluoro or iodo substituent.
By “protecting group” as used herein is meant a species which prevents a portion of a molecule from undergoing a specific chemical reaction, but which is removable from the molecule following completion of that reaction. This is in contrast to a “capping group,” which permanently binds to a segment of a molecule to prevent any further chemical transformation of that segment. As used herein, a “triaryl methyl protecting group” is a substituted or unsubstituted triaryl methyl group used (or intended to be used) as a protecting group as described in greater detail elsewhere herein. An “exocyclic amine protecting group” is a protecting group bonded to an exocyclic amine of a heterocyclic base as provided herein. “Exocyclic amine triaryl methyl protecting group” references a triaryl methyl protecting group bonded to an exocyclic amine of a heterocyclic base as provided herein, i.e. a substituted or unsubstituted triaryl methyl group is bonded to the amino nitrogen of a exocyclic amine group. A “hydroxyl protecting group” refers to a protecting group where the protected group is a hydroxyl. “Reactive site hydroxyl” references a hydroxyl group capable of reacting with a precursor to result in an internucleotide bond being formed. In typical embodiments, the reactive site hydroxyl is the terminal 5′-hydroxyl during 3′-5′ polynucleotide synthesis and is the 3′-hydroxyl during 5′-3′ polynucleotide synthesis. An “acid labile protected hydroxyl” is a hydroxyl group protected by a protecting group that can be removed by acidic conditions. Similarly, an “acid stabile protected hydroxyl” is a hydroxyl group protected by a protecting group that is not removed (is stabile) under acidic conditions. A trityl group is a triphenyl methyl group, in which one or more of the phenyl groups of the triphenyl methyl group is optionally substituted. A “substituted trityl group” or a “substituted triphenyl methyl group” is a triphenyl methyl group on which one of the hydrogens of the phenyl groups of the triphenyl methyl group is replaced by a substituent.
The term “substituted” as used to describe chemical structures, groups, or moieties, refers to the structure, group, or moiety comprising one or more substituents. As used herein, in cases in which a first group is “substituted with” a second group, the second group is attached to the first group whereby a moiety of the first group (typically a hydrogen) is replaced by the second group.
“Substituent” references a group that replaces another group in a chemical structure. Typical substituents include nonhydrogen atoms (e.g. halo groups), functional groups (carbonyl, alkoxy, silyl, silyloxy or), hydrocarbyl groups. Possible substituents are alkyl, lower alkyl, aryl, aralkyl, lower alkoxy, thioalkyl, halo, cyano, azido, sulfide, sulfone, sulfoxy, silyl, silyloxy, and lower alkyl.
A “group” includes both substituted and unsubstituted forms. Typical substituents include one or more lower alkyl, modified alkyl, any halogen, hydroxy, or aryl. Any substituents are typically chosen so as not to substantially adversely affect reaction yield (for example, not lower it by more than 20% (or 10%, or 5% or 1%) of the yield otherwise obtained without a particular substituent or substituent combination).
Hyphens, or dashes, are used at various points throughout this specification to indicate attachment, e.g. where two named groups are immediately adjacent a dash in the text, this indicates the two named groups are attached to each other. Similarly, a series of named groups with dashes between each of the named groups in the text indicates the named groups are attached to each other in the order shown. Also, a single named group adjacent a dash in the text indicates the named group is typically attached to some other, unnamed group. In some embodiments, the attachment indicated by a dash may be, e.g. a covalent bond between the adjacent named groups. In some other embodiments, the dash may indicate indirect attachment, i.e. with intervening groups between the named groups. At various points throughout the specification a group may be set forth in the text with or without an adjacent dash, (e.g. amido or amido-, further e.g. Trl or Trl-, yet further e.g. Lnk, Lnk- or -Lnk-) where the context indicates the group is intended to be (or has the potential to be) bound to another group; in such cases, the identity of the group is denoted by the group name (whether or not there is an adjacent dash in the text). Note that where context indicates, a single group may be attached to more than one other group (e.g. the Sugar group, herein; further e.g. where a linkage is intended, such as linking groups).
“Optional” or “optionally” means that the subsequently described circumstance may or may not occur, so that the description includes instances where the circumstance occurs and instances where it does not. For example, the phrase “optionally substituted” means that a non-hydrogen substituent may or may not be present, and, thus, the description includes structures wherein a non-hydrogen substituent is present and structures wherein a non-hydrogen substituent is not present. At various points herein, a moiety may be described as being present zero or more times: this is equivalent to the moiety being optional and includes embodiments in which the moiety is present and embodiments in which the moiety is not present. If the optional moiety is not present (is present in the structure zero times), adjacent groups described as linked by the optional moiety are linked to each other directly. Similarly, a moiety may be described as being either (1) a group linking two adjacent groups, or (2) a bond linking the two adjacent groups: this is equivalent to the moiety being optional and includes embodiments in which the moiety is present and embodiments in which the moiety is not present. If the optional moiety is not present (is present in the structure zero times), adjacent groups described as linked by the optional moiety are linked to each other directly.
Accordingly, an embodiment in accordance with the invention is directed to methods and materials for synthesizing polynucleotides. An embodiment of a method for synthesizing a polynucleotide includes forming an internucleotide bond by contacting a precursor (described below) with a nucleoside moiety under conditions and for a time sufficient to allow the precursor to react with the nucleoside moiety to result in formation of the internucleotide bond.
The precursors employed in methods according to the current invention comprise a heterocyclic base having an exocyclic amine group and a substituted or unsubstituted triaryl methyl protecting group bound to the exocyclic amine group. The precursors typically have the structure (I):

Rag-Sugar-Base-Tram  (I)

Wherein the groups are defined as follows:

Rag—a reactive group capable of reacting with a reactive site hydroxyl of a nucleoside moiety (e.g. on a nascent polynucleotide molecule in the process of being synthesized) to result in formation of an internucleotide bond; the reactive group is typically a phosphorus derivative as described below in reference to structure (III)
Sugar—a sugar group such as may be found in a nucleotide or nucleotide analog, typically ribose, 2′-deoxyribose, arabinose, xylose, or lyxose, wherein the sugar group is substituted with one or more substituents,
Base—a heterocyclic base having an exocyclic amine group, typically attached to the sugar group at the 1′ position of the sugar group, and
Tram—a triaryl methyl protecting group, optionally modified with one or more substituents, the triaryl methyl protecting group bound to the heterocyclic base via the exocyclic amine group.
The sugar group may be any sugar group (or substituted sugar group) known in the art of nucleotide synthesis and nucleotide analog synthesis. The skilled practitioner will appreciate that polynucleotide analogs may be accomplished using such known sugars. Representative sugar groups may be selected from monosaccharides, ketoses, aldoses, pentoses (five carbon sugars), hexoses (six carbon sugars), including any such groups modified by e.g. oxidation, deoxygenation, introduction of other substituents, alkylation and acylation of hydroxyl groups, and chain branching. The sugar group is typically ribose or 2′-deoxyribose, although other sugars may be used. In an embodiment, the sugar is arabinose. In another embodiment, the sugar is selected from xylose or lyxose. In typical embodiments, the sugar group is a monosaccharide; representative monosaccharides include glycerose, dihydroxyacetone, erythrose, erythrulose, xylose, lyxose, arabinose, ribose, xylulose, ribulose, rhamnose, fucose, glucose, mannose, galactose, fructose, sorbose, glucoheptose, galamannoheptose, sedoheptulose, mannoheptulose, and others.
In certain embodiments, the sugar group is a polyhydroxyketone having the structure (IIa)

H—[CH(OH)]n—C(═O)—[CH(OH)]m—H  (IIa)

in which n is an integer from 1 to about 5 and m is an integer from 1 to about 5; provided that one of the hydrogens or hydroxyls in structure (IIa) is replaced by the reactive group; and provided that the heterocyclic base is directly bound to one of the carbons of structure (IIa) (thereby replacing a hydrogen or hydroxyl of structure (IIa) or adding to the carbonyl carbon of structure (IIa)). It will be readily apparent to the reader skilled in the art that, in embodiments in which the heterocyclic base is added to (i.e. bound directly to) the carbonyl carbon of structure (IIa), the other groups (e.g. the carbonyl oxygen) bound to the carbonyl carbon may be changed to preserve normal valency rules for the groups, e.g. to hydroxyl, hydrido, or other suitable groups. Typically, the polyhydroxyketone has at least three carbon atoms, typically at least four carbon atoms, more typically at least five carbon atoms, and typically has up to about eight carbon atoms, more typically up to about ten carbon atoms. In particular embodiments, the sugar group is based on the given structure in this paragraph but is modified, e.g. by deoxygenation, by introduction of other substituents (e.g. replacement of a hydrogen or hydroxyl by a substituent), by alkylation and/or acylation of hydroxyl groups, by chain branching, and by formation of an intramolecular hemiacetal, and by combinations of the above. Also contemplated are sugar groups in which the given structure (IIa) is modified by intramolecular cyclization reaction, e.g. forming a furanose, pyranose, or other ring structure. As used herein, a sugar group “based on” structure (IIa) references any structure disclosed in this paragraph, also encompassing the modifications to structure (IIa) as described in this paragraph.

In certain embodiments, the sugar group is a polyhydroxyaldehyde having the structure (IIb)

H—[CH(OH)]n—C(═O)H  (IIb)

in which n is an integer from 2 to about 8, typically from 3 to 7, more typically from 4 to 6; provided that one of the hydrogens or hydroxyls in structure (IIb) is replaced by the reactive group; provided that one of the hydrogens or hydroxyls in structure (IIb) is replaced by the reactive group; and provided that the heterocyclic base is directly bound to one of the carbons of structure (IIb) (thereby replacing a hydrogen or hydroxyl of structure (IIb) or adding to the carbonyl carbon of structure (IIb)). It will be readily apparent to the reader skilled in the art that, in embodiments in which the heterocyclic base is added to (i.e. bound directly to) the carbonyl carbon of structure (IIb), the other groups (e.g. the carbonyl oxygen, the aldehydic hydrogen) bound to the carbonyl carbon may be changed to preserve normal valency rules for the groups, e.g. to hydroxyl, hydrido, or other suitable groups. In particular embodiments, the sugar group is based on the given structure in this paragraph but is modified, e.g. by deoxygenation, by introduction of other substituents (e.g. replacement of a hydrogen or hydroxyl by a substituent), by alkylation and/or acylation of hydroxyl groups, by chain branching, and by formation of an intramolecular hemiacetal, and by combinations of the above. Also contemplated are sugar groups in which the given structure (IIb) is modified by intramolecular cyclization reaction, e.g. forming a furanose, pyranose, or other ring structure. As used herein, a sugar group “based on” structure (IIb) references any structure disclosed in this paragraph, also encompassing the modifications to structure (IIb) as described in this paragraph.

The sugar group is substituted with one or more substituents, e.g. the reactive group and the hydroxyl protecting group as described herein. In typical embodiments, the precursor has the structure (III)




Wherein the groups are defined as follows:

O and H represent oxygen and hydrogen, respectively
R1 is typically hydrido or hydroxyl (or hydroxyl protecting group), wherein when R1 is hydrido, the sugar is 2′-deoxyribose, as will be present in DNA synthesis, and when R1 is hydroxyl (or hydroxyl protecting group), the sugar is ribose, as will be present in RNA synthesis. In certain embodiments, R1 is lower alkyl, modified lower alkyl, or alkoxy.
One of R2 or R3 is a hydroxyl protecting group releasable under conditions of simultaneous deprotection and oxidation during the polynucleotide synthesis cycle, as further described herein; and the other of R2 or R3 is a reactive group (Rag-) as referenced above with regard to structure (I). Under appropriate conditions as described herein, the reactive group specifically reacts with a reactive site hydroxyl such that the desired product of the reaction is achieved in acceptable yield. In this regard, “specifically reacts” means that an acceptable amount of precursor reacts as described herein with the nucleoside moiety to result in internucleotide bond formation in acceptable yield. In various embodiments, the acceptable yield is at least about 5%, at least about 10%, at least about 20%, at least about 30%, at least about 50%, or even more, where the percent indicated is the proportion of precursor incorporated (in moles) over the theoretical amount of precursor (in moles) that would be incorporated if the reaction was 100% completed, expressed as a percent. In particular embodiments, the reactive group Rag may comprise a leaving group which is replaced by a portion of the nucleoside moiety as a result of the reaction.
The reactive group typically is a phosphorus derivative capable of coupling to a reactive site hydroxyl of a nucleoside moiety (e.g. on a nascent polynucleotide molecule in the process of being synthesized). A reactive group that is a phosphorus derivative has the structure (IV)




Wherein the groups are defined as follows:

The broken line indicates the bond to the sugar group, typically through either the 3′-O or 5′-O of the sugar group, though other suitable sites on the sugar group may serve to bond to the reactive group, particularly when the sugar group is other than a pentose.
X may be a halogen (particularly Cl or Br) or a secondary amino group, NQ1Q2. Preferred phosphorus derivatives are phosphoramidites, where X is NQ1Q2, and in which Q1 and Q2 may be the same or different and are typically selected from the group consisting of alkyl, aryl, aralkyl, cycloalkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkynyl, modified alkyl, optionally containing one or more nonhydrocarbyl linkages such as ether linkages, thio linkages, oxo linkages, amine, azole, and imine linkages, and optionally substituted on one or more available carbon atoms with a nonhydrocarbyl substituent such as cyano, nitro, halo, or the like. Typically, Q1 and Q2 represent lower alkyl, more preferably sterically hindered lower alkyls such as isopropyl, t-butyl, isobutyl, sec-butyl, neopentyl, tert-pentyl, isopentyl, sec-pentyl, and the like. More typically, Q1 and Q2 both represent isopropyl. Alternatively, Q1 and Q2 may be linked to form a mono- or polyheterocyclic ring having a total of from 1 to 3, usually 1 to 2 heteroatoms and from 1 to 3 rings. In such a case, Q1 and Q2 together with the nitrogen atom to which they are attached represent, for example, pyrrolidone, morpholino or piperidino. Usually, Q1 and Q2 have a total of from 2 to 12 carbon atoms. Examples of specific —NQ1Q2 moieties thus include, but are not limited to, dimethylamine, diethylamine, diisopropylamine, dibutylamine, methylpropylamine, methylhexylamine, methylcyclopropylamine, ethylcyclohexylamine, methylbenzylamine, methylcyclohexylmethylamine, butylcyclohexylamine, morpholine, thiomorpholine, pyrrolidine, piperidine, 2,6-dimethylpiperidine, piperazine, and the like.
Y is typically hydrido or hydrocarbyl (including substituted hydrocarbyl), typically alkyl, alkenyl, aryl, aralkyl, or cycloalkyl. More typically, Y represents: lower alkyl; benzyl; substituted benzyl; electron-withdrawing β-substituted aliphatic, particularly electron-withdrawing β-substituted ethyl such as β-trihalomethyl ethyl, β-cyanoethyl, β-sulfoethyl, β-nitro-substituted ethyl, and the like; electron-withdrawing substituted phenyl, particularly halo-, sulfo-, cyano- or nitro-substituted phenyl; or electron-withdrawing substituted phenylethyl. Still more typically, Y represents methyl, β-cyanoethyl, methyl-β-cyanoethyl, dimethyl-β-cyanoethyl, phenylsulfonylethyl, methyl-sulfonylethyl, p-nitrophenylsulfonylethyl, 2,2,2-trichloro-1,1-dimethylethyl, 2-(4-pyridyl)ethyl, 2-(2-pyridyl)ethyl, allyl, 4-methylene-1-acetylphenol, β-thiobenzoylethyl, 1,1,1,3,3,3-hexafluoro-2-propyl, 2,2,2-trichloroethyl, p-nitrophenylethyl, p-cyanophenyl-ethyl, 9-fluorenylmethyl, 1,3-dithionyl-2-methyl, 2-(trimethylsilyl)ethyl, 2-methylthioethyl, 2-(diphenylphosphino)-ethyl, 1-methyl-1-phenylethyl, 3-buten-1-yl, 4-(trimethylsilyl)-2-buten-1-yl, cinnamyl, α-methylcinnamyl, and 8-quinolyl.
Still referring to structure (III), the hydroxyl protecting group (e.g. on either the 3′-O or 5′-O, that is, designated by one of R2 or R3, respectively) is any suitable protecting group that is known to be releasable under conditions of simultaneous deprotection and oxidation during the polynucleotide synthesis cycle. Exemplary protecting groups that may be released to free the hydroxyl group during the simultaneous deprotection and oxidation step are described in U.S. Pat. No. 6,222,030 to Dellinger et al.; U.S. Pat. Appl'n Publ'n No. US2002/0058802 A1 to Dellinger et al.; and Seio et al. (2001) Tetrahedron Lett. 42 (49):8657-8660. In certain embodiments, the protecting groups may be carbonate protecting groups as described in U.S. Pat. No. 6,222,030. In some embodiments, the protecting groups may be aryl carbonate protecting groups as described in U.S. Pat. No. 6,222,030. In other embodiments, the protecting groups may be non-carbonate protecting groups as described in U.S. Pat. Appl'n Publ'n No. US2002/0058802 A1, such as for example, 3′- or 5′-O-silyl or -siloxyl protecting groups, 3′- or 5′-O-ester protecting groups, and 3′- or 5′-O-carbamate protecting groups. The hydroxyl protecting group may be, for example, a protecting group which is labile under nucleophilic attack under neutral or mildly basic conditions. Examples of protecting groups which are labile under nucleophilic attack under neutral or mildly basic conditions are: ester protecting groups, carbamate protecting groups, siloxane protecting groups, silane protecting groups, and sulfonate protecting groups that β-eliminate. Examples of suitable hydroxyl protecting groups for one of R2 or R3 in structure (III) are described in “Protective Groups in Organic Synthesis” by T. W. Green, Wiley Interscience.
With regard to the description of R2 and R3 of structure (III), it is well known within the art that synthesis of a polynucleotide may typically be performed in a 3′ to 5′ direction, or, alternatively, in the 5′ to 3′ direction. It will be apparent from the description herein given ordinary knowledge in the art that the hydroxyl protecting group and the reactive group designated by R2 and R3 may occupy either the 5′-O or 3′-O positions as described above. The synthesis and use of such alternate embodiments will be readily apparent given the skill in the art and the disclosure herein.
The Base group referenced in both structure (I) and in structure (III) may be any heterocyclic base that has an exocyclic amine group. Typical examples of heterocyclic bases include the naturally occurring purine and pyrimidine bases, e.g., adenine (A), thymine (T), cytosine (C), guanine (G), or uracil (U), as well as modified purine and pyrimidine bases and other heterocyclic bases which have been modified (these moieties are sometimes referred to herein, collectively, as “purine and pyrimidine bases and analogs thereof”). Any heterocyclic base having an exocyclic amine which is known in the literature of nucleotide analogs forms the basis for the Base group referenced in structure (I) or structure (III). Typical examples include adenine, cytosine, guanine, and common analogs as recited earlier herein, provided the analog retains the exocyclic amine group. Certain nucleotide analogs that are contemplated in this context include those described in U.S. patent application Ser. No. 10/324,409 entitled “Method Of Producing Nucleic Acid Molecules With Reduced Secondary Structure”, filed on Dec. 18, 2002, and also those described in U.S. patent application Ser. No. 09/358,141 entitled “Method Of Producing Nucleic Acid Molecules With Reduced Secondary Structure”, filed on Jul. 20, 1999 now abandoned. In particular embodiments, the exocyclic amine group is directly bonded to the ring structure of the heterocyclic base, that is, the nitrogen of the amine group is attached directly to a member of the ring structure of the heterocyclic base. In some embodiments, the amine group may be linked to the ring structure of the heterocyclic base via an intervening group, such as an alkyl group or a modified lower alkyl group, e.g. a lower alkyl group having additional groups, such as one or more linkages selected from ether-, thio-, amino-, phospho-, keto-, ester-, and amido-, and/or being substituted with one or more groups including lower alkyl; aryl, alkoxy, thioalkyl, hydroxyl, amino, sulfonyl, nitro, and halo.
The Base group is typically bound by an N-glycosidic linkage to the 1′ carbon of the sugar group, although other configurations are to be encompassed by the invention. In other embodiments, the Base group is bound by a C-glycosidic linkage to the 1′ carbon of the sugar group. In some embodiments the Base group is bound to a carbon other than the 1′ carbon of the sugar group. Other positions of the Base group on the sugar group and other linkages between the Base group and the sugar group may be practiced by those of skill in the synthesis of nucleotide analogs given the disclosure herein, especially where analogous structures having the given heterocyclic base and sugar group are known in the art.
With reference to structures (I) and (III), the Tram group is a triaryl methyl protecting group, optionally modified with one or more substituents. The triaryl methyl protecting group is bound to the heterocyclic base via the exocyclic amine group. The exocyclic amine group has an amino nitrogen which is typically bound to the central methyl carbon of the triaryl methyl protecting group. The triaryl methyl protecting group may be substituted or unsubstituted. A substituted triaryl methyl group may have one substituent (i.e. a singly substituted triaryl methyl group) on one of the aromatic rings of the triaryl methyl group, or may have multiple substituents (i.e. a multiply substituted triaryl methyl group) on one or more of the aromatic rings of the triaryl methyl group.
The triaryl methyl protecting group is an optionally substituted triaryl methyl group and has the structure (V),




wherein the broken line represents a bond to the amino nitrogen of the exocyclic amine group on which the triaryl methyl group is a protecting group, and R4, R5, and R6 are independently selected from aromatic ring moieties, each aromatic ring moiety comprising 4-, 5-, or 6-membered rings. Each aromatic ring moiety can independently be heterocyclic, non-heterocyclic, polycyclic or part of a fused ring system. Each aromatic ring moiety can be unsubstituted or substituted with one or more groups each independently selected from the group consisting of lower alkyl, aryl, aralkyl, lower alkoxy, thioalkyl, hydroxyl, thio, mercapto, amino, imino, halo, cyano, nitro, nitroso, azido, carboxy, sulfide, sulfone, sulfoxy, phosphoryl, silyl, silyloxy, and boronyl; and lower alkyl substituted with one or more groups selected from lower alkyl, alkoxy, thioalkyl, hydroxylthio, mercapto, amino, imino, halo, cyano, nitro, nitroso, azido, carboxy, sulfide, sulfone, sulfoxy, phosphoryl, silyl, silyloxy, and boronyl. As used herein, an aromatic ring moiety may be referenced as an “aromatic ring structure”. As used herein, the “central methyl carbon” of a triaryl methyl group is the carbon bonded directly to the three aromatic ring structures. Typical triaryl methyl groups that may be employed in embodiments herein are described in U.S. Pat. No. 4,668,777 to Caruthers; use of such groups in accordance with the present invention is within ordinary skill in the art given the disclosure herein.
In certain embodiments, R4, R5, and R6 are each independently selected from substituted or unsubstituted aromatic groups such as phenyl, biphenyl, naphthanyl, indolyl, pyridinyl, pyrrolyl, thiophenyl, furanyl, annulenyl, quinolinyl, anthracenyl, and the like. In some embodiments, at least one of R4, R5 and R6 is selected from substituted or unsubstituted aromatic groups other than phenyl such as naphthanyl, indolyl, pyridinyl, pyrrolyl, furanyl, annulenyl, quinolinyl, anthracenyl, and the like; in such embodiments zero, one, or two of R4, R5, and R6 are selected from substituted or unsubstituted phenyl.
In some embodiments, two of R4, R5, and R6 are independently selected from structure (VI)




and the remaining one of R4, R5, and R6 is selected from an aromatic group other than phenyl. In other embodiments, only one of R4, R5, and R6 has the structure (VI), and the remaining two of R4, R5, and R6 are independently selected from aromatic groups other than phenyl such as naphthanyl, indolyl, pyridinyl, pyrrolyl, furanyl, annulenyl, quinolinyl, anthracenyl, and the like. In structure (VI), the broken line represents the bond to the central methyl carbon of the triaryl methyl group, and R7, R8, R9, R10, and R11 are each independently selected from hydrido; lower alkyl, aryl, aralkyl, lower alkoxy, thioalkyl, hydroxyl, thio, mercapto, amino, imino, halo, cyano, nitro, nitroso, azido, carboxy, sulfide, sulfone, sulfoxy, phosphoryl, silyl, silyloxy, and boronyl; and lower alkyl substituted with one or more groups selected from lower alkyl, alkoxy, thioalkyl, hydroxyl thio, mercapto, amino, imino, halo, cyano, nitro, nitroso, azido, carboxy, sulfide, sulfone, sulfoxy, phosphoryl, silyl, silyloxy, and boronyl.
In particular embodiments, R4, R5, and R6 are each independently selected from phenyl, methoxyphenyl, dimethoxyphenyl and trimethoxyphenyl groups, such that the Tram-group of structure (I) or structure (III) may be an unsubstituted trityl group, a monomethoxytrityl group, a dimethoxytrityl group, a trimethoxytrityl group, a tetramethoxytrityl group, a pentamethoxytrityl group, a hexamethoxytrityl group, and so on.
In particular embodiments, R4, R5, and R6 are each independently selected from phenyl, methoxyphenyl groups, dimethoxyphenyl groups, trimethoxyphenyl groups, tetramethoxyphenyl groups, pentamethoxyphenyl groups, or furyanyl groups such that the Tram group of structure (I) or structure (III) may be an unsubstituted trityl group, a monomethoxytrityl group, a dimethoxytrityl group, a trimethoxyl trityl group, a tetramethoxy trityl group, a pentamethoxytrityl group, an anisylphenylfuranylmethyl group, a dianisylfuranylmethyl group, a phenyldifuranylmethyl group, an anisyldifuranylmethyl group or a trifuranylmethyl group.
In certain embodiments, the precursor may be e.g. a portion of an oligonucleotide or polynucleotide, a portion of a di-, tri-, tetra-, or penta-nucleotide (a small polynucleotide having 2, 3, 4, or 5 nucleotide monomer subunits). In such embodiments, the precursor typically has the structure (I) described above, provided that the Sugar group is attached to a nucleotide moiety, an oligonucleotide moiety, or a polynucleotide moiety, in which the attached nucleotide moiety, oligonucleotide moiety, or polynucleotide moiety may have appropriate protecting groups. For example, the precursor may be a di- or tri-nucleotide in which the 3′ or 5′ hydroxyl bears a hydroxyl protecting group that is removed during the deprotection/oxidation step.
In an embodiment, the method of synthesizing polynucleotides further includes, after the internucleotide bond is formed, exposing the result of the forming an internucleotide bond step to a composition which concurrently oxidizes the internucleotide bond and removes a hydroxyl protecting group from the Sugar group.
In use, a precursor that has the structure (I) is contacted with a reactive site hydroxyl of a nucleoside moiety to result in formation of an internucleotide bond. Such a reaction is generally shown in FIG. 3, as discussed further, below. FIG. 3 schematically illustrates 3′-to-5′ synthesis of a polynucleotide using the method of the present invention. In the figure, the moiety Rhpg represents a hydroxyl protecting group releasable under conditions of simultaneous deprotection and oxidation during the polynucleotide synthesis cycle, as further described herein. In FIG. 3, Beatpg represents a heterocyclic base having an exocyclic amine group, and further having an exocyclic amine triaryl methyl protecting group bonded to the exocyclic amine group. As may be seen, in the second step of the synthesis cycle, deprotection and oxidation occur concurrently. The synthesis may be contrasted with that schematically illustrated in FIG. 1, the prior, conventional method, where the conventional synthesis scheme entails separate oxidation and deprotection steps. The synthesis also may be contrasted with that schematically illustrated in FIG. 2, showing a synthesis with the previously taught starting materials. Such a synthesis scheme is known in the art, such as that taught in, e.g. U.S. Pat. No. 6,222,030 to Dellinger et al.; U.S. Pat. Appl'n Publ'n No. US2002/0058802 A1 to Dellinger et al.; Seio et al. (2001) Tetrahedron Lett. 42 (49):8657-8660. These references describe two-step methods of (1) coupling a hydroxyl-protected nucleoside monomer to a growing oligonucleotide chain, and (2) deprotecting the product using an alpha effect nucleophilic reagent that also oxidizes the internucleotide linkage to give a phosphotriester bond. The coupling and deprotection/oxidation steps are repeated as necessary to give an oligonucleotide having a desired sequence and length.
The invention further provides a method for synthesizing polynucleotides. In an embodiment, the method comprises forming an internucleotide bond by contacting a precursor having the structure (I) as described above with a nucleoside moiety under conditions and for a time sufficient to allow the precursor to react with the nucleoside moiety to result in formation of the internucleotide bond. In particular embodiments, a precursor having the structure (III) as described above is contacted with a nucleoside moiety under conditions and for a time sufficient to allow the precursor to react with the nucleoside moiety to result in formation of the internucleotide bond. The nucleoside moiety typically comprises a reactive site hydroxyl that is capable of reacting with the reactive group of the precursor to result in formation of an internucleotide bond.
In an embodiment, the method of synthesizing polynucleotides further includes, after the internucleotide bond is formed, exposing the result of the forming an internucleotide bond step to a composition which concurrently oxidizes the internucleotide bond and removes a hydroxyl protecting group (the simultaneous deprotection and oxidation step).
In an embodiment of the method for 3′ to 5′ synthesis, a precursor having the structure (III) as described above is contacted with a nucleoside moiety having the structure (VII):




Wherein the groups are defined as follows:

Base' is a heterocyclic base, optionally protected with a protecting group,
◯is a solid support, a growing oligonucleotide attached to a solid support, a growing oligonucleotide not attached to a solid support, a hydroxyl, or a hydroxyl protecting group, and
R1 is as described above.
The nucleoside moiety of structure (VII) has a reactive site hydroxyl that is available to react with the reactive group of a precursor. The coupling reaction is performed under conditions and for a time sufficient to allow the precursor to react with the nucleoside moiety to result in formation of the internucleotide bond. The product of the coupling reaction may be represented as structural formula (VIII), as follows:




Wherein the groups are defined as follows:

Rhpg represents a hydroxyl protecting group releasable under conditions of simultaneous deprotection and oxidation during the polynucleotide synthesis cycle,
Each R1 is independently as described above with regard to structure (III)
◯, Base, Base', Tram, and Y, are each as described above.
In FIG. 3, this step (the “coupling” reaction) is illustrated in context of a full synthesis cycle. The coupling reaction may be conducted under standard conditions used for the synthesis of oligonucleotides and conventionally employed with automated oligonucleotide synthesizers. Such methodology will be known to those skilled in the art and is described in the pertinent texts and literature, e.g., in D. M. Matteuci et al. (1980) Tet. Lett. 521:719 and U.S. Pat. No. 4,500,707.
It will be apparent to the skilled reader that, for polynucleotide synthesis, different bases may be employed each synthesis cycle depending on the desired sequence of the final product. Also, in some cycles, the desired heterocyclic base may not have an exocyclic amine and thus not require an exocyclic amine triaryl methyl protecting group in accordance with the invention. Synthesis of polynucleotides having such desired sequences is within the scope of the invention, as implied by the Base' group in structures (VII) and (VIII).
In the second step of the synthesis cycle shown in FIG. 3, the product is treated with a combined deprotection/oxidation reagent to oxidize the newly formed internucleotide bond and to remove the hydroxyl protecting group at the 5′ terminus, thus converting the moiety —ORhpg to —OH. The resulting —OH is then available to serve as the reactive site hydroxyl for the next round of the synthesis cycle. Advantageously, the combined deprotection/oxidation step may be conducted in connection with fluorescent or other readily detectable hydroxyl protecting groups, enabling monitoring of individual reaction steps. Further, the method is useful in carrying out either 3′-to-5′ synthesis or 5′-to-3′ synthesis. Finally, the method readily lends itself to the highly parallel, microscale synthesis of oligonucleotides.
The deprotection/oxidation reaction essentially may be conducted under the reported conditions used for the synthesis of polynucleotides as described in, e.g. U.S. Pat. No. 6,222,030 to Dellinger et al.; U.S. Pat. Appl'n Publ'n No. US2002/0058802 A1 to Dellinger et al.; Seio et al. (2001) Tetrahedron Lett. 42 (49):8657-8660. As will be appreciated by those of ordinary skill in the art, given the disclosure herein, the conditions for the deprotection/oxidation step may vary depending on the nature of the protecting groups used. In order to be compatible with the exocyclic amine triaryl methyl protecting group provided for by the current invention, the conditions for the simultaneous deprotection and oxidation step (i.e. required conditions for release of the hydroxyl protecting group) should be selected such that the exocyclic amine triaryl methyl protecting groups remain stably attached to the exocyclic amine groups. Typical conditions for the deprotection/oxidation reaction include a pH in the neutral to moderately basic range. In particular embodiments, the pH of the deprotection/oxidation reaction is at least about 6.0, typically at least about 6.5, more typically at least about 7.0, still more typically at least about 7.5, and the pH is typically less than about 12, typically less than about 11, more typically less than about 10.5, still more typically less than about 10.
The combined deprotection/oxidation reagent may be selected to provide particularly advantageous synthesis conditions and characteristics, as are described herein. In an embodiment, the combined deprotection/oxidation reagent provides for contacting of the elongating polynucleotide chain with an alpha effect nucleophile under neutral or mildly basic aqueous conditions to remove reactive site hydroxyl protecting groups where such protecting groups are labile under nucleophilic attack; the alpha effect nucleophile also serves to oxidize the phosphite triester linkage to a phosphotriester linkage.
In an embodiment, the combined deprotection/oxidation reagent provides a nucleophilic deprotection reagent under neutral or mildly basic conditions in aqueous solution. During the second step of the polynucleotide synthesis cycle (the deprotection/oxidation step in FIG. 3), the product is treated with an “alpha effect” nucleophile in order to remove the protecting group at the reactive site hydroxyl (e.g. the 5′ terminus), thus converting the moiety —ORhpg to —OH. The alpha effect nucleophile also oxidizes the newly formed phosphite triester linkage to give the phosphotriester linkage as shown in FIG. 3.
The deprotection/oxidation reagent may be any compound or mixture of compounds that is compatible with the synthesis of polynucleotides and has the properties discussed herein. Typically, the deprotection/oxidation reagent includes a concentration of an oxidant that is high enough to rapidly oxidize the newly formed phosphite internucleotide linkage. This is typically at least 0.1% vol/vol, typically at least 0.5% vol/vol, more typically at least about 1.0% vol/vol, still more typically at least about 3.0% vol/vol. The concentration of the oxidant typically should be low enough to avoid appreciable (e.g. less than 1% per iteration of the synthesis cycle) amounts of oxidative destruction of the nucleobases or protected nucleobases. This concentration is typically less than 10% vol/vol, more typically less than 9% vol/vol, still more typically less than 7% vol/vol.
The deprotection/oxidation reagent in typical embodiments provides a source of a peroxyanion at neutral to mildly basic pH in the reaction mixture during the deprotection/oxidation reaction. The concentration of the peroxyanion will be related to the acid dissociation constant of the hydroperoxide species at equilibrium. The concentration of peroxyanion is typically in the range 0.01% to 99% of the total hydroperoxide concentration (i.e. sum of all hydroperoxide species, e.g. protonated and unprotonated forms), more typically in the range 0.05% to 90% of the total hydroperoxide concentration, yet more typically in the range 0.1% to 50% of the total hydroperoxide concentration, still more typically in a range of 1.0% to 30% of the total hydroperoxide concentration.
In certain embodiments, the nucleophilic deprotection reagent that exhibits an alpha effect is a peroxide or a mixture of peroxides. In typical embodiments, the pH at which the deprotection/oxidation reaction is conducted is generally in the range of about three pH units below the pKa of the nucleophilic deprotection reagent (that is, the pKa for formation of the corresponding peroxy anion) up to about three pH units above the pKa of the nucleophilic deprotection reagent. More typically, the pH of the deprotection/oxidation reaction is in the range of about one pH unit below the pKa of the nucleophilic deprotection reagent up to about pH 11. Preferably the pH will be the range that allows a high enough concentration of the peroxy anion to form, e.g. from about the pKa of the peroxide up to a pH of about 11. The peroxide may be either inorganic or organic. Suitable inorganic peroxides include those of the formula M+OOH—, where M+ is any counter ion, including for example H+, Li+, Na+, K+, Rb+, Cs+, or the like; and lithium peroxide or hydrogen peroxide and alkaline stabilized forms thereof can be particularly suitable. Suitable organic peroxides include those of the formula ROOH, where R is selected from the group consisting of alkyl, aryl, substituted alkyl, substituted aryl, and modified alkyl. More particularly, the organic peroxide will have one of the following three general structures (IX), (X) or (XI)




in which R21 through R27 are generally hydrocarbyl optionally substituted with one or more nonhydrocarbyl substituents and optionally containing one or more nonhydrocarbyl linkages. Generally, R21 through R27 are independently selected from the group consisting of hydrido, alkyl, modified alkyl, aryl, aralkyl, cycloalkyl, cycloalkylalkyl, alkenyl, cycloalkenyl, alkynyl aralkynyl, cycloalkynyl, substituted aralkyl, substituted cycloalkyl, substituted cycloalkylalkyl, substituted alkenyl, substituted cycloalkenyl, substituted alkynyl substituted aralkynyl, substituted cycloalkynyl, hydrocarbyl, and substituted hydrocarbyl. T-butyl-hydroperoxide or metachloroperoxybenzoic acid can be particularly suitable. As a specific example, the m-chloroperoxybenzoic acid (mCPBA) peroxy anion has been found to be useful for removal of protecting groups on the reactive site hydroxyl.

As indicated in FIG. 3, the steps of the synthesis cycle include a coupling step and a simultaneous deprotection/oxidation step. In an embodiment of a method of synthesizing a polynucleotide in accordance with the present invention, these steps of the synthesis cycle may be repeated multiple times to produce a polynucleotide having the desired sequence.
The use of a triaryl methyl protecting group provides for protection of the exocyclic amines from undesirable side reactions during synthesis. The triaryl methyl protecting groups may then be removed from the synthesized polynucleotide under mildly acidic conditions. In particular embodiments, the triaryl methyl protecting groups may be removed by weak acids under conditions that do not result in destruction of the glycosidic linkage, typically glacial acetic acid or glacial acetic acid/water mixtures.
In embodiments employing solid phase synthesis techniques, the synthesized polynucleotide may be released from the solid support to yield the polynucleotide free in solution (not attached to the support).
The nucleoside moiety which is to be contacted with the precursor in a method in accordance with the present invention is typically bound to an insoluble support, e.g. directly or via an intervening polynucleotide strand. The support may comprise any suitable material adapted for its intended use in polynucleotide synthesis. The support should be essentially inert to the conditions of reactions used for the polynucleotide synthesis. Typically the support is a solid material having a surface to which the nucleoside moiety (or a polynucleotide which comprises the nucleoside moiety) is bound, directly or indirectly (i.e. via an intermediate moiety or moieties, e.g. moieties typically referred to in the art variously as linking groups, tethers, or spacers); such that the nucleoside moiety, which has the reactive site hydroxyl, is accessible to the precursor when the support is contacted with a solution containing the precursor.
In certain embodiments, the support comprises a solid substrate and a modification layer disposed on or bound to (directly or indirectly) the substrate, and the nucleoside moiety having the reactive site hydroxyl is bound to (directly or indirectly) the modification layer. Such modification layer may be formed on the substrate by methods known in the art of modifying surface properties of supports used in polynucleotide synthesis, or known in the art of modifying supports to provide desired surface properties. In certain embodiments, the modification layer may be, e.g., a coating, a material deposited by deposition techniques known in the art, a hydrophobic layer, or a hydrophilic layer. In particular embodiments, the support comprises a chemically active group bound to a substrate via a silane group. Particularly contemplated are supports taught in U.S. Pat. No. 6,258,454 to Lefkowitz et al. (2001) as supports having a chemically active moiety bound to a substrate via a linking group attached to a silane group bound to the surface of a substrate.
EXAMPLES
The practice of the present invention will employ, unless otherwise indicated, conventional techniques of synthetic organic chemistry, biochemistry, molecular biology, and the like, which are within the skill of the art. Such techniques are explained fully in the literature.
The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to perform the methods and use the compositions disclosed and claimed herein. Efforts have been made to ensure accuracy with respect to numbers (e.g., amounts, temperature, etc.) but some errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, percents are wt./wt., temperature is in ° C. and pressure is at or near atmospheric. Standard temperature and pressure are defined as 20° C. and 1 atmosphere.
A synthesis of reagents used in certain embodiments of the present invention is now described. It will be readily apparent that the reactions described herein may be altered, e.g. by using modified starting materials to provide correspondingly modified products, and that such alteration is within ordinary skill in the art. Given the disclosure herein, one of ordinary skill will be able to practice variations that are encompassed by the description herein without undue experimentation.
Abbreviations used in the examples include: B is a heterocyclic base having an exocyclic amine group, BProt is a heterocyclic base having an exocyclic amine group with a trityl protecting group on the exocyclic amine group; TiPSCl is 1,3-dichloro-1,1,3,3-tetraisopropyldisiloxane; TEMED is N,N,N′,N′-Tetramethylethylenediamine; Py is pyridine; MeCN is acetonitrile; DMT is dimethoxytrityl; MMT is monomethoxytrityl; TMT is trimethoxytrityl; CytDMT is cytosine which has a dimethoxytrityl protecting group on the exocyclic amine group; CytTMT is cytosine which has a trimethoxytrityl protecting group on the exocyclic amine group (and so on for other bases and protecting groups on the exocyclic amine group of the indicated base); MS is mass spectrometry, MS (ES) is mass spectrometry (electrospray), HRMS (FAB) is high resolution mass spectrometry (fast atom bombardment); DCM is methylene chloride; EtOAc is ethyl acetate; iPr is isopropyl; Et3N is triethylamine; TCA is trichloroacetic acid; TEAB is tetraethylammonium bicarbonate. Trityl refers to a substituted or unsubstituted triphenyl methyl group; context may indicate which is desired or intended.
Preparation of 2-Furanyl-di-(2,4-dimethoxyphenyl)methanol
Methyl-2-furoate (1.58 g, 0.0125 mol) was dissolved in 100 mL of dry THF. A dropping funnel containing 50 mL of a 0.5 M solution of 2,4-dimethoxyphenylmagnesium bromide in THF (Aldrich) was attached to the reaction flask and the system was purged with argon. The reaction flask was submerged in an ice bath for 5 minutes, at which time the Grignard solution was added drop-wise over 15 minutes. After addition was complete, the reaction was allowed to warm to room temperature and was stirred overnight. A brown solution resulted after 14 hours of stirring. This solution was added to 150 g crushed ice and the slush was stirred with  ̃0.5 g sodium bicarbonate during drop-wise addition of conc. HCl. A violet color was observed upon addition of acid, which was continued until effervescence was observed. The resulting neutral suspension was extracted into  ̃400 mL EtOAc and the organic layer was dried over MgSO4. Removal of solvent in a rotary evaporator gave a clear/yellow oil. Upon standing in  ̃30 mL EtOAc (12 h), the oil had turned deep blue and a white crystalline solid had settled out. The solid was collected and gave 1.7 g desired product. The blue solution was chromatographed in 50% EtOAc/50% hexanes and the second product to elute (deep violet upon acid treatment on TLC plate) was collected. Recrystallization of this product gave an additional 1.3 g pure desired alcohol. 3.0 g/4.6 g=65% yield.
Preparation of 2-Furanyl-di-(2-methoxyphenyl)methanol
Methyl-2-furoate (1.58 g, 0.0125 mol) was dissolved in 100 mL of dry THF. A dropping funnel containing 50 mL of a 0.5 M solution of 2-methoxyphenylmagnesium bromide in THF (Aldrich) was attached to the reaction flask and the system was purged with argon. The reaction flask was submerged in an ice bath for 5 minutes, at which time the Grignard solution was added drop-wise over 15 minutes. After addition was complete, the reaction was allowed to warm to room temperature and was stirred overnight. A brown solution resulted. This solution was added to 150 g crushed ice and the slush was stirred with  ̃0.5 g sodium bicarbonate during drop-wise addition of conc. HCl. A lavender color was observed upon addition of acid, which was continued until effervescence was observed. The resulting neutral suspension was extracted into  ̃400 mL EtOAc and the organic layer was dried over MgSO4. Removal of solvent in vacuo gave a clear/yellow oil. The oil was purified by silica gel column chromatography and the product eluted using a 50:50 (vol:vol) mixture of EtOAc:hexanes. The purified product was evaporated to a solid gum yielding 3.1 grams/82% yield. The product was characterized by HPLC, 1H NMR, and FAB mass spectroscopy FAB+311 m/e.
The compounds prepared in the previous two paragraphs are triaryl methyl compounds that are useful in preparing protected heterocyclic bases, e.g. by placing a triaryl methyl protecting group on exocyclic amines present on a desired heterocyclic base. Use of such compounds will be readily apparent to persons of ordinary skill in the art given the disclosure herein.
Trityl Protection of Nucleobases




Synthesis of 5′,3′-O-(Tetraisopropyldisiloxane-1,3-diyl) deoxynucleosides

Deoxynucleoside (10 mmole) was coevaporated 3 times with pyridine. Anhydrous pyridine (35 mL) and 1,3-Dichloro-1,1,3,3-tetraisopropyldisiloxane (3.47 g, 11 mmole) were added, and the mixture was stirred overnight at room temperature. The solution was concentrated and chromatographed on silica gel with 6% methanol in CHCl3.

    B=Cytosine: yield 99.9%; MS (ES) m/z 470(M+H)
    B=Adenine: yield 92%; MS (ES) m/z 494(M+H)
    B=Guanine; yield 98%; MS (ES) m/z 510(M+H)

Synthesis of N-trityl deoxynucleosides 5′,3′-O-(Tetraisopropyldisiloxane-1,3-diyl) deoxynucleoside (10 mmole) was coevaporated 3 times with pyridine, and then dried on vacuum pump for 12 hours. Anhydrous pyridine (30 mL) and trityl chloride (11 mmole) were added, and the mixture was stirred at room temperature until TLC (CHCl3/MeOH 9:1) showed full disappearance of nucleoside substrate (16-24 hours). The reaction was quenched with water/ice. Crude product was extracted with DCM, washed with 5% aqueous solution of NaHCO3, and dried with anhydrous Na2SO4. After filtration the organic layer was concentrated to dryness and left on vacuum pump for 3 hours. Hydrogen fluorideaq (1.4 mL, 35 mmole) was carefully added (with vigorous stirring) to ice-cold solution of TEMED (7.5 mL, 50 mmole) in acetonitrile (20 mL). The TEMED-HF reagent so formed was then transferred via teflon tubing to the flask with 5′,3′-O-(tetraisopropyldisiloxane-1,3-diyl) N-trityl protected deoxynucleoside (10 mmole), and the mixture was stirred for 2.5 hours. The solution was concentrated, the residue coevaporated with each: pyridine, toluene, and EtOH. The crude product was purified by silica gel column chromatography using CHCl3/Py (99.9:0.1) with a gradient of methanol (0-8%).

    B=CytDMT: yield 98%; MS (ES) m/z 530(M+H), 552(M+Na), 568(M+K)
    B=CytTMT: yield 98%; MS (ES) m/z 560(M+H), 566(M+Li), 582(M+Na), 598(M+K), 692(M+Cs)
    B=AdeDMT: yield 91%; MS (ES) m/z 554(M+H)
    B=AdeMMT: yield 99.9%; MS (ES) m/z 524(M+H)
    B=GuaDMT: yield 70.4%; MS (ES) m/z 570(M+H)

5′-Carbonate protection of N-trityl deoxynucleosides







Synthesis of 5′-O-[3-(trifluoromethyl)phenoxy]carbonyl N-trityl deoxynucleosides

N-Trityl protected deoxynucleoside (5 mmole) was coevaporated 3 times with pyridine, dried on vacuum pump for 16 hours, and then dissolved in anhydrous pyridine (50 mL). The solution was cooled in dry ice/EtOH bath, and 3-(trifluoromethyl)phenyl chloroformate (1.19 g, 5.25 mmole) was added. The cooling bath was removed, the reaction mixture was shaken until all the reactant was completely dissolved, and then left overnight with stirring. The reaction was quenched with water. The product was extracted with DCM, washed with 5% aqueous solution of NaHCO3, and dried with anhydrous Na2SO4. The product was purified by silica gel column chromatography with CHCl3/benzene (9:1), followed by slow gradient from 1% to 5% of methanol in CHCl3 containing 0.1% Py.

    B=CytDMT: yield 73%; HRMS (FAB) calc'd for C38H34N3O8F3 (M+) 717.2298, found 717.2321
    B=CytTMT: yield 46%; HRMS (FAB) calc'd for C39H36N3O9F3 (M+) 747.2404, found 747.2378
    B=AdeDMT: yield 61%; HRMS (FAB) calc'd for C39H33N5O7F3 (M−H) 740.2332, found 740.2331
    B=AdeMMT: yield 75%; MS (ES) m/z 712(M+H), 734 (M+Na), 750 (M+K)
    B=GuaDMT: yield 60%; HRMS (FAB) calc'd for C39H35N5O8F3 (M+H) 758.2438, found 758.2473

Phosphitylation of 5′-carbonate protected deoxynucleosides







Synthesis of deoxynucleoside 3′-O-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidites

The protected deoxynucleoside (3 mmole) and tetrazole (210 mg, 3 mmole) were dried separately on a vacuum pump for 16 hours. Deoxynucleoside was dissolved in anhydrous DCM (30 mL), and 2-cyanoethyl-N,N,N′,N′-tetraisopropylphosphane (950 mg, 3.15 mmole) was added in one portion. Tetrazole was added slowly to the reaction mixture over 1 hour. The reaction mixture was then stirred for another 3 hours. A small amount of Et3N (approx. 0.5 mL) was added to neutralize the solution. The solvent was removed in vacuo, and the crude product chromatographed with benzene followed by a gradient of EtOAc (0-40 or 60%) in benzene containing 0.1% Et3N.

    B=CytDMT: yield 61%; 31P NMR (CDCl3) δ 150.21, 150.10; HRMS (FAB) calc'd for C47H51N5O9F3 (M+) 917.3377, found 917.3346
    B=CytTMT: yield 71%; 31P NMR (CDCl3) δ 150.18, 150.09; HRMS (FAB) calc'd for C48H53N5O10F3 (M+) 947.3482, found 947.3503
    B=AdeDMT: yield 74%; 31P NMR (CDCl3) δ 150.13, 150.05; HRMS (FAB) calc'd for C47H51N7O8F3 (M+) 941.3489, found 941.3510
    B=AdeMMT: yield 72%; MS (ES) m/z 912(M+H), 934 (M+Na), 950 (M+K)
    B=GuaDMT: yield 48%; 31P NMR (CDCl3) δ 150.00, 149.88; HRMS (FAB) calc'd for C48H52N7O9F3 (M+H) 958.3516, found 958.3556


It will be apparent to one of skill in the art that the series of syntheses described above may be altered to employ analogous starting materials that react in a similar manner to give analogous products, and that such alteration of the synthesis is within ordinary skill in the art. For example, the base “B” in the synthesis may be selected from nucleobases, modified nucleobases, other heterocyclic bases, and analogues thereof, provided the base “B” has an exocyclic amine group. As another example, the protecting group may be located on the 3′-hydroxyl and the reactive phosphorus moiety may then be located on the 5′-hydroxyl. As further example, the 5′-hydroxyl protecting group may be replaced with a different protecting group, such as phenyloxycarbonyloxy, p-(phenylazo)phenyloxycarbonyl-oxy, o-nitrophenyloxycarbonyloxy, 9-fluorenylmethoxycarbonyloxy, 2,2,2-Trichloro-1,1-dimethylethoxycarbonyloxy, 4-chlorophenyloxycarbonyloxy, bis(trimethylsiloxy)-cyclobenzhydroxysilyloxy, bis(trimethylsiloxy)cyclododecyloxysilyloxy, and the like.
Synthesis on the Solid Support
The deoxynucleoside 3′-O-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidites synthesized above were used for the synthesis of polynucleotides. Synthesis of polynucleotides was conducted on a solid support as described herein with the following specified conditions:
Monomer concentration is 0.1 Molar solution in MeCN
Activator: Tetrazole (0.45 Molar solution in MeCN)
Cycle: 300 sec coupling

    
    
        2.5, 5 or 7 min deprotection (removal of the 5′-hydroxyl protecting group) using a buffered aqueous solution of peroxyanions
    
    
    1. Trityl deprotection (3% TCA/DCM, 15 min to 2 hours, RT)
    2. Cleavage from the support (conc.NH4OH, 2 hours, RT)
    RP-HPLC analysis: ODS-Hypersil (5μ) column, flow 1.5 mL/min
    0-20% MeCN in 50 mM TEAB (linear gradient) in 40 min


Products synthesized according to the method of the present invention included: (AT)5 (SEQ ID NO:1); A9T (SEQ ID NO:2); (CT)5 (SEQ ID NO:3); and C9T (SEQ ID NO:4). Reverse-phase HPLC analysis demonstrated an acceptable product that typically was equivalent or superior to similar products synthesized using the conventional 4-step process.
The triaryl methyl protecting groups can be individually modified to optimize their use for each of the naturally occurring nucleobases or for use with modified nucleobases. The use of triaryl methyl protecting groups that are resistant to strong nucleophiles can prevent or reduce certain undesirable types of nucleobase modifications such as deamination (loss of the amine group) and depurination (loss of the purine base). In addition, the triaryl methyl protecting group typically imparts a great deal of hydrophobicity to the precursor. This hydrophobicity aids in the solubility of the precursor in anhydrous solvents required for effective coupling.
While the foregoing embodiments of the invention have been set forth in considerable detail for the purpose of making a complete disclosure of the invention, it will be apparent to those of skill in the art that numerous changes may be made in such details without departing from the spirit and the principles of the invention. Accordingly, the invention should be limited only by the following claims.
All patents, patent applications, and publications mentioned herein are hereby incorporated by reference in their entireties, provided that, if there is any conflict in definitions, the present specification shall be controlling.

## Claims

1. A compound having the structure (III)




wherein:
O and H represent oxygen and hydrogen, respectively,
R1 is hydrido, hydroxyl, protected hydroxyl, lower alkyl, substituted lower alkyl, or alkoxy,
one of R2 or R3 is a hydroxyl protecting group; and the other of R2 or R3 is a reactive group capable of reacting with a reactive site hydroxyl of a nucleoside moiety to produce either a phosphite diester or a phosphite triester internucleotide linkage,
Base is a heterocyclic base having an exocyclic amine group, and
Tram is an abbreviation representing an exocyclic amine group protected by a triaryl methyl group having the structure (V)




wherein the broken line represents a bond to the amino nitrogen of the exocyclic amine group, and R4, R5 and R6 are independently selected from unsubstituted or substituted aryl groups, provided that at least one of R4, R5, and R6 is an unsubstituted or substituted furanyl group.

2. The compound of claim 1, wherein at least one of R4, R5, and R6 is an optionally substituted aryl group independently selected from naphthanyl, pyridinyl, 2-thienyl, 3-thienyl, furanyl, annulenyl, quinolinyl, and anthracenyl.

3. The compound of claim 1, wherein R4, R5, and R6 are aryl groups independently selected from phenyl, methoxyphenyl, dimethoxyphenyl, trimethoxyphenyl, and furanyl.

4. The compound of claim 1 wherein the phosphorous derivative reactive group has the structure (V): (page 18, line 4)



wherein:
the broken line indicates the bond to the sugar group;
X is selected from a halo group and a secondary amino group; and
Y is selected from hydrido, hydrocarbyl, and substituted hydrocarbyl.

5. The compound of claim 4, wherein X is a secondary amino group having the structure —NQ1Q2; in which Q1 and Q2 are independently selected from the group consisting of alkyl, aryl, aralkyl, cycloalkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkynyl, and substituted alkyl.

6. The compound of claim 4, wherein Y is selected from alkyl, lower alkyl, alkenyl, benzyl, substituted benzyl, aryl, aralkyl, cycloalkyl, β-(electron-withdrawing group) substituted alkyl, β-(electron-withdrawing group) substituted ethyl; electron-withdrawing substituted phenyl; and electron-withdrawing substituted phenylethyl.

7. The compound of claim 4, wherein X is a diisopropyl amino group and Y is selected from methyl, benzyl, substituted benzyl, β-cyanoethyl, methyl-β-cyanoethyl, dimethyl-β-cyanoethyl, phenylsulfonylethyl, methyl-sulfonylethyl, p-nitrophenylsulfonylethyl, 2,2,2-trichloro-1,1-dimethylethyl, 2-(4-pyridyl)ethyl, 2-(2-pyridyl)ethyl, allyl, 4-methylene-1-acetylphenol, β-thiobenzoylethyl, 1,1,1,3,3,3-hexafluoro-2-propyl 2,2,2-trichloroethyl, p-nitrophenylethyl, p-cyanophenyl-ethyl, 9-fluorenylmethyl, 1,3-dithionyl-2-methyl, 2-(trimethylsilyl)ethyl, 2-methylthioethyl, 2-(diphenylphosphino)-ethyl, 1-methyl-1-phenylethyl, 3-buten-1-yl, 4-(trimethylsilyl)-2-buten-1-yl, cinnamyl, α-methylcinnamyl, and 8-quinolyl.

8. The compound of claim 4, wherein X is a diisopropyl amino group and Y is selected from a cyanoethyl, benzyl, and substituted benzyl group.

9. The compound of claim 8, wherein the hydroxyl protecting group is an optionally substituted aryl carbonate protecting group.