205 results about "Single stranded oligonucleotides" patented technology

One aspect of the present invention relates to a double-stranded oligonucleotide comprising at least one aralkyl ligand. In certain embodiments, an aralkyl ligand is bound to only one of the two oligonucleotide strands comprising the double-stranded oligonucleotide. In certain embodiments, an aralkyl ligand is bound to both of the oligonucleotide strands comprising the double-stranded oligonucleotide. In certain embodiments, the oligonucleotide strands comprise at least one modified sugar moiety. In certain embodiments, at least one phosphate linkage in the oligonucleotide has been replaced with a phosphorothioate linkage. In a preferred embodiment, the aralkyl ligand is naproxen or ibuprofen. Another aspect of the present invention relates to a single-stranded oligonucleotide comprising at least one aralkyl ligand. In certain embodiments, the oligonucleotide comprises at least one modified sugar moiety. In certain embodiments, at least one phosphate linkage in the oligonucleotide has been replaced with a phosphorothioate linkage. In a preferred embodiment, the aralkyl ligand is naproxen or ibuprofen. The aralkyl ligand improves the pharmacokinetic properties of the oligonucleotide.

The invention provides pharmaceutical compositions comprising short single stranded oligonucleotides, of length of between 8 and 17 nucleobases which are complementary to human microRNAs. The short oligonucleotides are particularly effective at alleviating miRNA repression in vivo. It is found that the incorporation of high affinity nucleotide analogues into the oligonucleotides results in highly effective anti-microRNA molecules which appear to function via the formation of almost irreversible duplexes with the miRNA target, rather than RNA cleavage based mechanisms, such as mechanisms associated with RNaseH or RISC.

One aspect of the present invention relates to a ribonucleoside substituted with a phosphonamidite group at the 3′-position. In certain embodiments, the phosphonamidite is an alkyl phosphonamidite. Another aspect of the present invention relates to a double-stranded oligonucleotide comprising at least one non-phosphate linkage. Representative non-phosphate linkages include phosphonate, hydroxylamine, hydroxylhydrazinyl, amide, and carbamate linkages. In certain embodiments, the non-phosphate linkage is a phosphonate linkage. In certain embodiments, a non-phosphate linkage occurs in only one strand. In certain embodiments, a non-phosphate linkage occurs in both strands. In certain embodiments, a ligand is bound to one of the oligonucleotide strands comprising the double-stranded oligonucleotide. In certain embodiments, a ligand is bound to both of the oligonucleotide strands comprising the double-stranded oligonucleotide. In certain embodiments, the oligonucleotide strands comprise at least one modified sugar moiety. Another aspect of the present invention relates to a single-stranded oligonucleotide comprising at least one non-phosphate linkage. Representative non-phosphate linkages include phosphonate, hydroxylamine, hydroxylhydrazinyl, amide, and carbamate linkages. In certain embodiments, the non-phosphate linkage is a phosphonate linkage. In certain embodiments, a ligand is bound to the oligonucleotide strand. In certain embodiments, the oligonucleotide comprises at least one modified sugar moiety.

This invention relates to a method of modulating the expression of a target gene in an organism comprising administering an iRNA agent, wherein the iRNA comprises at least one 2′-deoxy-2′-fluoro (2′-F) nucleotide in the antisense strand and at least one modified nucleotide in the sense strand. The invention also relates to compositions comprising a single-stranded oligonucleotide that contains at least one 2′-deoxy-2′-fluoro (2′-F) nucleotide. siRNA molecule containing these oligonucleotides have decreased immunogenicity.

One aspect of the present invention relates to a double-stranded oligonucleotide comprising at least one non-natural nucleobase. In certain embodiments, the non-natural nucleobase is difluorotolyl, nitroindolyl, nitropyrrolyl, or nitroimidazolyl. In a preferred embodiment, the non-natural nucleobase is difluorotolyl. In certain embodiments, only one of the two oligonucleotide strands comprising the double-stranded oligonucleotide contains a non-natural nucleobase. In certain embodiments, both of the oligonucleotide strands comprising the double-stranded oligonucleotide independently contain a non-natural nucleobase. In certain embodiments, the oligonucleotide strands comprise at least one modified sugar moiety. Another aspect of the present invention relates to a single-stranded oligonucleotide comprising at least one non-natural nucleobase. In a preferred embodiment, the non-natural nucleobase is difluorotolyl. In certain embodiments, the ribose sugar moiety that occurs naturally in nucleosides is replaced with a hexose sugar, polycyclic heteroalkyl ring, or cyclohexenyl group. In certain embodiments, at least one phosphate linkage in the oligonucleotide has been replaced with a phosphorothioate linkage.

One aspect of the present invention relates to a double-stranded oligonucleotide comprising at least one ligand. In certain embodiments, a ligand is bound to only one of the two oligonucleotide strands comprising the double-stranded oligonucleotide. In certain embodiments, both of the oligonucleotide strands of the double-stranded oligonucleotide independently comprise a bound ligand. In certain embodiments, the oligonucleotide strands comprise at least one modified sugar moiety. In certain embodiments, a phosphate linkage in one or both of the strands of the oligonucleotide has been replaced with a phosphorothioate or phosphorodithioate linkage. In a preferred embodiment, the ligand is cholesterol or 5β-cholanic acid. Another aspect of the present invention relates to a single-stranded oligonucleotide comprising at least one ligand. In certain embodiments, the oligonucleotide comprises at least one modified sugar moiety. In certain embodiments, a phosphate linkage of the oligonucleotide has been replaced with a phosphorothioate or phosphorodithioate linkage. In a preferred embodiment, the ligand is cholesterol or 5β-cholanic acid. The ligand improves the pharmacokinetic properties of the oligonucleotide.

The invention provides pharmaceutical compositions comprising short single stranded oligonucleotides, of length of between 8 and 26 nucleobases which are complementary to human microRNAs selected from the group consisting of miR19b, miR21, miR122a, miR155 and miR375. The short oligonucleotides are particularly effective at alleviating miRNA repression in vivo. It is found that the incorporation of high affinity nucleotide analogues into the oligonucleotides results in highly effective anti-microRNA molecules which appear to function via the formation of almost irreversible duplexes with the miRNA target, rather than RNA cleavage based mechanisms, such as mechanisms associated with RNaseH or RISC.

Aspects of the invention provide single stranded oligonucleotides for activating or enhancing expression of a target gene. Further aspects provide compositions and kits comprising single stranded oligonucleotides for activating or enhancing expression of a target gene. Methods for modulating expression of a target gene using the single stranded oligonucleotides are also provided. Further aspects of the invention provide methods for selecting a candidate oligonucleotide for activating or enhancing expression of a target gene.

Devices, systems, and methods for detecting nucleic acid hybridization, including single nucleic base mutations at low concentrations, are disclosed, using capture units having nanoparticles with attached single-stranded oligonucleotides that are capable of hybridizing target oligonucleotides and reporter molecules having nanoparticles with attached single-stranded oligonucleotides, without the use of labeling or target modification.

Aspects of the invention provide single stranded oligonucleotides for activating or enhancing expression of MECP2. Further aspects provide compositions and kits comprising single stranded oligonucleotides for activating or enhancing expression of MECP2. Methods for modulating expression of MECP2 using the single stranded oligonucleotides are also provided. Further aspects of the invention provide methods for selecting a candidate oligonucleotide for activating or enhancing expression of MECP2.

Nucleic acid probes are provided, each of which is formed of a single-stranded oligonucleotide which can hybridize to a target nucleic acid and is labeled with a fluorescent dye or with a fluorescent dye and a quencher substance. The nucleic acid probes can be easily designed, permit determination, polymorphous analysis or real-time quantitative PCR of nucleic acids in short time, and are not dissociated during reactions. Nucleic acid determination methods, polymorphous analysis methods and real-time quantitative PCR methods, which make use of the nucleic acid probes, are also provided.

The present invention relates to processes and reagents for oligonucleotide synthesis and purification. One aspect of the present invention relates to compounds useful for activating phosphoramidites in oligonucleotide synthesis. Another aspect of the present invention relates to a method of preparing oligonucleotides via the phosphoramidite method using an activator of the invention. Another aspect of the present invention relates to sulfur-transfer agents. In a preferred embodiment, the sulfur-transfer agent is a 3-amino-1,2,4-dithiazolidine-5-one. Another aspect of the present invention relates to a method of preparing a phosphorothioate by treating a phosphite with a sulfur-transfer reagent of the invention. In a preferred embodiment, the sulfur-transfer agent is a 3-amino-1,2,4-dithiazolidine-5-one. Another aspect of the present invention relates to compounds that scavenge acrylonitrile produced during the deprotection of phosphate groups bearing ethylnitrile protecting groups. In a preferred embodiment, the acrylonitrile scavenger is a polymer-bound thiol. Another aspect of the present invention relates to agents used to oxidize a phosphite to a phosphate. In a preferred embodiment, the oxidizing agent is sodium chlorite, chloroamine, or pyridine-N-oxide. Another aspect of the present invention relates to methods of purifying an oligonucleotide by annealing a first single-stranded oligonucleotide and second single-stranded oligonucleotide to form a double-stranded oligonucleotide; and subjecting the double-stranded oligonucleotide to chromatographic purification. In a preferred embodiment, the chromatographic purification is high-performance liquid chromatography.

Provided herein are biomolecular hybridization devices comprising a substrate with a permanently and covalently attached surface of functional groups and an adsorbed monolayer of unmodified, single-stranded oligonucleotides all of which are 10 to about 24 bases in length as a saturated film of constrained oligonucleotides on the surface via direct non-covalent phosphate-surface adsorptive contact of substantially all phosphate groups of each oligonucleotide. The constrained oligonucleotides are effective to dissociably hybridize to a complementary single-stranded nucleic acid with asymmetric, non-helical base pairing and without oligonucleotide dissociation from the surface of the device. Also, provided are methods for hybridizing solution-state target nucleic acids to probe nucleic acids and for identifying a nucleotide sequence to which a nucleotide-binding protein binds using the biomolecular hybridization devices.

The invention relates to biological technical field, and provides a high affinity adapter body capable of specifically binding with saxitoxin acetate, and the sequence of single-stranded DNA adapter body as SEQ ID NO: 2. By mutation and truncation of an in vitro screened adapter body, a high affinity single-stranded oligonucleotide adapter body capable of specifically identifying the saxitoxin acetate can be obtained. The adapter body has a broad application prospect, and can be used for separation and enrichment of trace concentrations of STX (saxitoxin) in a sample, rapid detection of saxitoxin, and preparation of a drug for neutralization of saxitoxin sodium ion channel inhibition effect, and removal of toxins in water.

The invention relates to a nucleic acid aptamer for specifically identifying ochratoxin A and a preparation method thereof. The sequence of the single-chain DNA (deoxyribonucleic acid) aptamer is a sequence I. The nucleic acid aptamer for specifically identifying the ochratoxin A is characterized in that by adopting the index enrichment ligand system advancing technology based on graphene oxide separation, and in-vitro screening, the single-chain oligonucleotide aptamer with high affinity and ability of specifically identifying the OTA toxin is obtained; the specificity is good, the stability is high, the cost is low, the synthesizing and modifying are easy, the convenience in use is realized, the toxicity is avoided, and the like; the nucleic acid aptamer can be applied to studying of biological sensors and solid-phase affinity purifying columns based on the nucleic acid aptamer, and analyzing methods for quick detection on agricultural products, and the like.

Aspects of the invention provide single stranded oligonucleotides for activating or enhancing expression of PTEN. Further aspects provide compositions and kits comprising single stranded oligonucleotides for activating or enhancing expression of PTEN. Methods for modulating expression of PTEN using the single stranded oligonucleotides are also provided. Further aspects of the invention provide methods for selecting a candidate oligonucleotide for activating or enhancing expression of PTEN.

The present invention relates to construction of hepatitis B virus siRNA expression vector and its antiviral therapeutic application. According to the design principle said construction includes the following steps: respectively selecting nucleotide sequence of HBV envelope protein (MS) coding region 69nt-87nt, polymerase(p) coding region 708nt-726nt and core protein (c) coding region 2052 nt-2070nt, designing correspondent siRNA sequence, using BLAST software to analyze homogenously to confirm that it is HBV highly conservative sequence, then chemically synthesizing single-stranded oligonucleotide, external annearing to form double-stranded DNA, connecting it with eukaryotic expression vector pTZU6+1, enzyme excision identification and sequence determination and analysis show that siRNA extression vectors of three target hepatitis B virus (HBV) gene sequences are constructed. The tests show that HBV siRNA has the strong action of inhibiting virus replication and expression.

The invention belongs to the field of marine fish mitochondrial genome research, and particularly relates to a marine fish mitochondrion 12S rRNA (ribosomal ribonucleic acid) gene amplification primer. The primer is composed of two single-chain oligonucleotide chains, wherein a light chain primer is a nucleotide sequence shown as SEQ ID NO.1, and a heavy chain primer is a nucleotide sequence shown as SEQ ID NO.2. The invention also provides a design method of the amplification primer and a method for amplifying a marine fish DNA (deoxyribonucleic acid) solution by using the amplification primer. The invention can efficiently and specifically amplify multiple marine fish mitochondrion 12S rRNA genes and can be used for the analytical study on the system evolution of different taxonomic categories of fishes, thereby providing a powerful tool for fish species identification, germplasm resource survey and system evolution research.

The invention relates to a method for the electrochemical detection of sequence-specific nucleic acid oligomer hybridization events. To this end single DNA/RNA/PNA oligomer strands which at one end are covalently joined to a support surface and at the other, free end, covalently linked to a redox pair, are used as hybridization matrix (probe). As a result of treatment with the oligonucleotide solution (target) to be examined, the electric communication between the conductive support surface and the redox pair bridged by the single-strand oligonucleotide, which communication initially is either absent or very weak, is modified. In case of hybridization, the electric communication between the support surface and the redox pair, which is now bridged by a hybridized double-strand oligonucleotide, is increased. This permits the detection of a hybridization event by electrochemical methods such as cyclic voltametry, amperometry or conductivity measurement.

The present invention relates to one pair of PCR primers named as G-dloop, and provides one pair of amplification primers capable of amplifying the high variation zone of rockfish mitochondrial genome in high efficiency and its design method. The amplification primers consist of two single strand oligonucleotides. Through logging-on Genebank to search vertebrate mitochondrion DNA cytochrome b gene and the high conservation area of 16S rRNA gene sequence and homologous comparison, one pair of amplification primers is obtained. Through long PCR amplification, the target segments of 32 varieties of rockfish are obtained and sequenced. The obtained sequences are compared by means of using homologous comparison software Clustal X 1.83 to fine the conservation sequences in the cytochrome b5' ends and the 12S rRNA 3' ends of the mitochondrial genomes of the 32 varieties of rockfish, and the said amplification primers are designed based on the degeneracy principle.

The present invention relates to chimeric RNA oligonucleotides that are single-stranded oligonucleotides. These compounds are capable of targeting particular genes and reducing DNA methyltransferase activity. Accordingly, these compounds are particularly useful in the treatment of disease associated with aberrant DNA methyltransferase activity, such as cancer or a genetic disorder.

The invention discloses a nucleic acid aptamer capable of specifically recognizing shigella, a screening method and application thereof. In the technical scheme, the single-stranded DNA oligonucleotide aptamer capable of specifically recognizing shigella is obtained through the SELEX (Systematic Evolution of Ligands by Exponential enrich-m ent) technology, and the aptamer can be converted to a report aptamer for detecting shigella through marking a marker such as fluorescein, so that the invention has wide application prospects of quick and accurate detection of shigella in food.