Methods and kits for depleting amplicons that correspond to undesired RNA species present in a sample are provided. The disclosed methods and kits employ a blocker that anneals with at least a portion of the undesired RNA, resulting in a duplex that is not a suitable substrate for ligating an adapter to the end of the undesired RNA.

High-fidelity, high-throughput nucleic acid sequencing enables healthcare practitioners and patients to gain insight into genetic variants and potential health risks. However, previous methods of nucleic acid sequencing often introduces sequencing errors (for example, mutations that arise during the preparation of a nucleic acid library, during amplification, or sequencing). Provided herein are sequencing adapters comprising a nondegenerate or variable length molecular barcode and compositions comprising a plurality of sequencing adapters, which can be useful for sequencing nucleic acids. Further provided are methods of using the sequencing adapters, including methods of sequencing nucleic acids, methods of identifying an error in a nucleic acid sequence, and methods of determining the number of nucleic acid molecules in a library.

High-fidelity, high-throughput nucleic acid sequencing enables healthcare practitioners and patients to gain insight into genetic variants and potential health risks. However, previous methods of nucleic acid sequencing often introduces sequencing errors (for example, mutations that arise during the preparation of a nucleic acid library, during amplification, or sequencing). Provided herein are sequencing adapters comprising a nondegenerate or variable length molecular barcode and compositions comprising a plurality of sequencing adapters, which can be useful for sequencing nucleic acids. Further provided are methods of using the sequencing adapters, including methods of sequencing nucleic acids, methods of identifying an error in a nucleic acid sequence, and methods of determining the number of nucleic acid molecules in a library.

A nucleic acid complex includes a single-stranded nucleic acid and a cross-linked double-stranded nucleic acid including the first nucleic acid strand linked to at least one of the 5′ end and the 3′ end of the single-stranded nucleic acid and the second nucleic acid strand including a base sequence that is completely or sufficiently complementary to the first nucleic acid strand.

Disclosed herein are oligonucleotides and methods for detecting a target nucleic acid, as well as methods of diagnosing a subject with a disease or a disorder by detecting a target nucleic acid using the oligonucleotides and methods disclosed herein. The oligonucleotides include a quadruplex-forming sequence. Prior to binding the target nucleic acid, the quadruplex-forming sequence is in a non-quadruplex conformation. Upon binding the target nucleic acid, the sequence transforms to the quadruplex conformation, which can be detected, for example, using optical methods. The methods are based on thermodynamic properties and do not require the use of enzymes. The methods can be used to diagnose a subject with a disease or a disorder, prognose the outcome of a disease or disorder, or predict the development of a future disease or disorder.

Disclosed herein are oligonucleotides and methods for detecting a target nucleic acid, as well as methods of diagnosing a subject with a disease or a disorder by detecting a target nucleic acid using the oligonucleotides and methods disclosed herein. The oligonucleotides include a quadruplex-forming sequence. Prior to binding the target nucleic acid, the quadruplex-forming sequence is in a non-quadruplex conformation. Upon binding the target nucleic acid, the sequence transforms to the quadruplex conformation, which can be detected, for example, using optical methods. The methods are based on thermodynamic properties and do not require the use of enzymes. The methods can be used to diagnose a subject with a disease or a disorder, prognose the outcome of a disease or disorder, or predict the development of a future disease or disorder.

A generic point of care based portable device and method thereof as a platform technology for detecting pathogenic infection via nucleic acid based testing achieving sample-to-result integration, comprising the following interconnected stand-alone modules: a thermal unit for executing piece-wise isothermal reactions in a pre-programmable concomitant fashion without necessitating in-between operative intervention; a colorimetric detection unit seamlessly interfaced with smartphone-app based analytics for detecting the target analyte. The said platform technology is thus capable of detecting targeted pathogen-associated RNA by coupling additional complementary DNA probe hybridization combined with isothermal reaction purposed for reverse transcription of RNA followed by amplification of the resulting c-DNA as well as subsequent specific binding of the same in a single user-step in a concomitant fashion and its smartphone-enabled interpretation, in a generic modular format that renders operative suitability outside controlled laboratory environment in a user-friendly manner, with predictive accuracy favorably comparable with gold standard RT-PCR tests.

A generic point of care based portable device and method thereof as a platform technology for detecting pathogenic infection via nucleic acid based testing achieving sample-to-result integration, comprising the following interconnected stand-alone modules: a thermal unit for executing piece-wise isothermal reactions in a pre-programmable concomitant fashion without necessitating in-between operative intervention; a colorimetric detection unit seamlessly interfaced with smartphone-app based analytics for detecting the target analyte. The said platform technology is thus capable of detecting targeted pathogen-associated RNA by coupling additional complementary DNA probe hybridization combined with isothermal reaction purposed for reverse transcription of RNA followed by amplification of the resulting c-DNA as well as subsequent specific binding of the same in a single user-step in a concomitant fashion and its smartphone-enabled interpretation, in a generic modular format that renders operative suitability outside controlled laboratory environment in a user-friendly manner, with predictive accuracy favorably comparable with gold standard RT-PCR tests.

The method for predicting the anti-tumor response in a human or animal having a tumor to multiple kinase inhibitors, using any multiple kinase inhibitor, comprises selection of genes encoding for protein kinases targeted by the said tyrosine kinase inhibitor, for each one of these genes, providing at least one nucleic acid probe which hybridizes to said gene under stringent conditions, thus providing an array of nucleic acid probes, having a biological sample containing cancer cells from said human or animal, extracting DNA from the sample, fragmenting into DNA fragments, optionally labeling the DNA fragments, submitting the optionally labeled DNA fragments to hybridization with the array of nucleic acid probes, recovering and quantifying for all the genes the gains or losses in gene copy numbers, wherein gains and losses of gene copy numbers of each selected gene are used to determine whether the tumor is sensitive or not to said kinase inhibitor.

Described herein are methods and compositions that make use of pseudo-complementary bases to reduce unwanted hybridization in assays to detect and/or quantify particular nucleotide sequences, as well as in nucleic acid sequencing protocols.