Provided a polymerizable compound represented by the following Formula A-1 or Formula A-2: In Formula A-1 or Formula A-2, R.sup.1 represents an electron-donating group; n represents an integer from 1 to 5; R.sup.2 represents a hydrogen atom, a halogen atom, or —OR.sup.O, wherein R.sup.O represents a hydrogen atom, an alkyl group, or a protecting group of a hydroxy group; R.sup.3 represents a hydrogen atom or a protecting group of a hydroxy group; and X represents a structure represented by any one of Formula B-1 to Formula B-5.

Provided a polymerizable compound represented by the following Formula A-1 or Formula A-2: In Formula A-1 or Formula A-2, R.sup.1 represents an electron-donating group; n represents an integer from 1 to 5; R.sup.2 represents a hydrogen atom, a halogen atom, or —OR.sup.O, wherein R.sup.O represents a hydrogen atom, an alkyl group, or a protecting group of a hydroxy group; R.sup.3 represents a hydrogen atom or a protecting group of a hydroxy group; and X represents a structure represented by any one of Formula B-1 to Formula B-5.

The invention relates to a compound having the structure:

##STR00001## or a pharmaceutically acceptable salt thereof, along with pharmaceutical compositions and therapeutic methods thereof.

A compound has the following formula (I) or formula (II), an isomer thereof, a tautomer thereof, a pharmaceutical acceptable solvate thereof, or a pharmaceutical acceptable prodrug thereof. ##STR00001##

Provided herein are reagents and methods for incorporating modified nucleotides into DNA and detecting DNA synthesis. In particular, haloalkyl-modified nucleobases are provided for incorporation into nucleic acids for detection by bioluminescent binding agents.

Embodiments for the synthesis of sensitive oligonucleotides as well as insensitive oligonucleotides are provided. Sulfur-based groups are used for the protection of exo-amino groups of nucleobases, phosphate groups and 2′—OH groups, and as cleavable linker for linking oligonucleotides to a support. Oligonucleotide syntheses are achieved under typical conditions using phosphoramidite chemistry with important modifications. To prevent replacing sulfur-based protecting groups by acyl groups via cap-exchange, special capping agents are used. To retain hydrophobic tag to assist RP HPLC purification, special phosphoramidites are used in the last synthetic cycle. With the sulfur-based groups for protection and linking, oligonucleotide deprotection and cleavage are achieved via oxidation followed by beta-elimination under mild conditions. Therefore, besides for insensitive oligonucleotide synthesis, the embodiments of the invention are capable for the synthesis of oligonucleotide analogs containing sensitive functional groups that cannot survive the harsh conditions used in prior art oligonucleotide synthesis technologies.

Nucleoside or nucleotide analog compounds having the structure shown below, a method for preparing them, and applications in nucleic acid sequencing are disclosed. The compounds have formula (I): ##STR00001## wherein L.sub.1, L.sub.2, and L.sub.3 are each independently a covalent bond or a covalently linked group; B is a base or a base derivative selected from purines, pyrimidines, or analogs thereof; R.sub.1 is —OH, a phosphate group, or a nucleotide; R.sub.2 as H or a cleavable group; R.sub.3 is a detectable group or a targeting group; R.sub.5 is an inhibitory group; R.sub.4 is H, —NH.sub.2, or —OR.sub.6, wherein R.sub.6 is H or a cleavable group; and C is a cleavable group or a cleavable bond.

The present disclosure provides prodrugs of 4′-C-substituted-2-halo-2′-deoxyadenoside nucleosides, and compositions, methods, and kits thereof. Such compounds can be useful for treating viral infections including, but not limited to, human immunodeficiency virus.

Aspects of the present disclosure include compositions that make use of phosphorus and/or nucleobase protecting groups which find use in the synthesis of long polynucleotides. Phosphorus protecting groups are provided that help increase the stepwise coupling yield and/or phosphorous protecting groups that can be removed during the oxidation step. Amidine nucleobase protecting groups are provided that find use in the subject compositions and methods which provides for e.g., increased resistance to depurination during polynucleotide synthesis. In some instances, the methods and compositions disclosed herein utilize a combination of the phosphorus and amidine nucleobase protecting groups in the synthesis of polynucleotides having a sequence of 200 or more monomeric units in length. Also provided are methods for synthesizing a polynucleotide (e.g., a DNA) using one or more compounds disclosed herein.

Aspects of the present disclosure include compositions that make use of phosphorus and/or nucleobase protecting groups which find use in the synthesis of long polynucleotides. Phosphorus protecting groups are provided that help increase the stepwise coupling yield and/or phosphorous protecting groups that can be removed during the oxidation step. Amidine nucleobase protecting groups are provided that find use in the subject compositions and methods which provides for e.g., increased resistance to depurination during polynucleotide synthesis. In some instances, the methods and compositions disclosed herein utilize a combination of the phosphorus and amidine nucleobase protecting groups in the synthesis of polynucleotides having a sequence of 200 or more monomeric units in length. Also provided are methods for synthesizing a polynucleotide (e.g., a DNA) using one or more compounds disclosed herein.