Abstract: Cleavable nucleotide analogs are provided. The nucleotide analog includes a nucleotide molecule attached to a cleavable moiety wherein the cleavable moiety comprises a protective group and/or a linker attached to a fluorophore. The cleavable moiety is linked to the oxygen atom of the 3?-OH of the pentose of the nucleotide molecule. The nucleotide analogs can be used in making polynucleotide molecules using template independent polymerases. The nucleotide analogs can act as reversible terminators during DNA sequencing by synthesis. The cleavage of the cleavable moiety restores a free 3?-OH functional group allowing growth of the polynucleotide molecule. The general structures as well as proposed synthetic schemes for the nucleotide analogs are also provided.

Abstract: A composition for use in extending a molecular chain includes a carrier group and a payload group. The carrier group comprising a signaling group and a blocking group. A first bond bonds the payload group to the carrier group and a second bond bonds the signaling group to the blocking group. The first and second bonds are selectively cleavable such that the first bond is cleavable without cleaving the second bond. The payload group is to be attached to the molecular chain, while the blocking group is to block further attachments to the molecular chain once the payload group has been attached. The signaling group comprises a photon emitter that emits a signature photon in response to interrogation by an interrogatory photon. The carrier group transitions from a loaded state to an empty state upon cleavage of the first covalent bond.

Abstract: A method for making a polynucleotide is provided including (a) delivering one or more reaction reagents including an error prone or template independent DNA polymerase, cations and a selected nucleotide to a reaction site including an initiator sequence having a terminal nucleotide for a time period and under conditions capable of covalently adding one or more of the selected nucleotide to the terminal nucleotide at the 3? end of the initiator such that the selected nucleotide becomes a terminal nucleotide, and (b) determining whether the selected nucleotide has been added to the terminal nucleotide, wherein if the selected nucleotide has not been added to the terminal nucleotide, then repeating step (a) until the selected nucleotide has been added, and (c) repeating steps (a) and (b) until the polynucleotide is formed.

Abstract: Cleavable nucleotide analogs are provided. The nucleotide analog includes a nucleotide molecule attached to a cleavable moiety wherein the cleavable moiety comprises a protective group and/or a linker attached to a fluorophore. The cleavable moiety is linked to the oxygen atom of the 3?-OH of the pentose of the nucleotide molecule. The nucleotide analogs can be used in making polynucleotide molecules using template independent polymerases. The nucleotide analogs can act as reversible terminators during DNA sequencing by synthesis. The cleavage of the cleavable moiety restores a free 3?-OH functional group allowing growth of the polynucleotide molecule. The general structures as well as proposed synthetic schemes for the nucleotide analogs are also provided.

Abstract: An enzymatic method of making a polynucleotide is provided. The method includes combining a selected nucleotide triphosphate, one or more cations, a template-independent polymerase, and an associated processivity factor in an aqueous reaction medium including a target substrate comprising an initiator sequence and having a 3? terminal nucleotide attached to a single stranded portion, such that the template-independent polymerase and the associated processivity factor interact with the target substrate under conditions which covalently add one or more of the selected nucleotide triphosphate to the 3? terminal nucleotide. Also provided are mutant template-independent polymerases having a processivity factor attached thereto.

Abstract: Methods and apparatus of modulating polynucleotide synthesis are provided. The methods include delivering reagents comprising enzymes, nucleotides and ions to oligonucleotide primers wherein the reagents catalyze incorporation of the nucleotides to 3? ends of the oligonucleotide primers, and modulating incorporation of the nucleotides to the 3? ends of the oligonucleotide primers. Polynucleotide synthesis is modulated by modulating presence or absence of catalytic cation cofactors to provide sequence defined synthesis of polynucleotides. In certain embodiments, the polynucleotides encode information.

Abstract: A composition for use in extending a molecular chain includes a carrier group and a payload group. The carrier group comprising a signaling group and a blocking group. A first bond bonds the payload group to the carrier group and a second bond bonds the signaling group to the blocking group. The first and second bonds are selectively cleavable such that the first bond is cleavable without cleaving the second bond. The payload group is to be attached to the molecular chain, while the blocking group is to block further attachments to the molecular chain once the payload group has been attached. The signaling group comprises a photon emitter that emits a signature photon in response to interrogation by an interrogatory photon. The carrier group transitions from a loaded state to an empty state upon cleavage of the first covalent bond.

Abstract: A method for making a polynucleotide is provided including (a) delivering one or more reaction reagents including an error prone or template independent DNA polymerase, cations and a selected nucleotide to a reaction site including an initiator sequence having a terminal nucleotide for a time period and under conditions capable of covalently adding one or more of the selected nucleotide to the terminal nucleotide at the 3? end of the initiator such that the selected nucleotide becomes a terminal nucleotide, and (b) determining whether the selected nucleotide has been added to the terminal nucleotide, wherein if the selected nucleotide has not been added to the terminal nucleotide, then repeating step (a) until the selected nucleotide has been added, and (c) repeating steps (a) and (b) until the polynucleotide is formed.