This invention relates to the preparation of nucleic acid samples for analysis. The invention may be particularly useful for single stranded samples. Embodiments of the invention involve the attachment of double stranded or hairpin oligonucleotides using template independent polymerase enzymes in the preparation of nucleic acid sequencing libraries.

This invention relates to the preparation of nucleic acid samples for analysis. The invention may be particularly useful for single stranded samples. Embodiments of the invention involve the attachment of double stranded or hairpin oligonucleotides using template independent polymerase enzymes in the preparation of nucleic acid sequencing libraries.

In a method of deducing the number of repeat units in a selected short tandem repeat (STR) in a genomic sample, at least a single stranded target DNA generated from a genomic sample comprising a selected STR, an STR probe (P1,P1′), a reference probe (P2), and two blockers (B1,B2) are provided, and at least three differential hybridization experiments are carried out, based on which the number of STR probe oligonucleotides (P1,P1′) bound per target DNA strand in each differential hybridization experiment is determined. The method further comprises the step of comparing these numbers of STR probe oligonucleotides (P1,P1′) bound per target DNA strand in the differential hybridization experiments for deducing the number of repeat units in the selected STR on the single stranded target DNA strand. Also disclosed are kits for carrying out STR genotyping by differential hybridization.

An object of the present invention is to provide methods for amplifying and detecting a nucleic acid that allow efficient hybridization, and devices and kits for use in the methods. The present invention includes amplifying a target nucleic acid into a double-stranded nucleic acid having a single-stranded region at each end, and detecting this nucleic acid. The present invention also provides detection devices and kits that make use of these methods.

An object of the present invention is to provide methods for amplifying and detecting a nucleic acid that allow efficient hybridization, and devices and kits for use in the methods. The present invention includes amplifying a target nucleic acid into a double-stranded nucleic acid having a single-stranded region at each end, and detecting this nucleic acid. The present invention also provides detection devices and kits that make use of these methods.

A method of tagged-base DNA sequencing readout on waveguide surfaces includes immobilizing, a surface of a waveguide, a nucleotide fragment, exposing the nucleotide fragment to a first plurality of capped nucleotides, wherein the first plurality of capped nucleotides include a first plurality of nucleotide types, each distinct nucleotide type has a distinct capping agent, and each distinct capping agent has a distinct optical signature, severing base pair connections between the at least a nucleotide fragment and the first plurality of capped nucleotides, wherein the nucleotide fragment remains attached and a first single nucleotide, of the first plurality of capped nucleotides, remains immobilized on a nucleotide binding locus adjacent to the first nucleotide sequence, and detecting a first distinct optical signature of a first distinct capping agent of the first single nucleotide using the waveguide.

A method of tagged-base DNA sequencing readout on waveguide surfaces includes immobilizing, a surface of a waveguide, a nucleotide fragment, exposing the nucleotide fragment to a first plurality of capped nucleotides, wherein the first plurality of capped nucleotides include a first plurality of nucleotide types, each distinct nucleotide type has a distinct capping agent, and each distinct capping agent has a distinct optical signature, severing base pair connections between the at least a nucleotide fragment and the first plurality of capped nucleotides, wherein the nucleotide fragment remains attached and a first single nucleotide, of the first plurality of capped nucleotides, remains immobilized on a nucleotide binding locus adjacent to the first nucleotide sequence, and detecting a first distinct optical signature of a first distinct capping agent of the first single nucleotide using the waveguide.

Provided are an isolated oligonucleotide and a use thereof in nucleic acid sequencing, wherein the isolated oligonucleotide comprises a first strand, wherein the 5′-end nucleotide of the first strand has a phosphate group, and the 3′-end nucleotide of the first strand is a dideoxynucleotide, and a second strand, wherein the 5′-end nucleotide of the second strand does not have a phosphate group, and the 3′-end nucleotide of the second strand is a dideoxynucleotide, wherein the first strand is longer than the second strand in length, and a double-stranded structure is formed between the first strand and the second strand.

Provided are an isolated oligonucleotide and a use thereof in nucleic acid sequencing, wherein the isolated oligonucleotide comprises a first strand, wherein the 5′-end nucleotide of the first strand has a phosphate group, and the 3′-end nucleotide of the first strand is a dideoxynucleotide, and a second strand, wherein the 5′-end nucleotide of the second strand does not have a phosphate group, and the 3′-end nucleotide of the second strand is a dideoxynucleotide, wherein the first strand is longer than the second strand in length, and a double-stranded structure is formed between the first strand and the second strand.

The present invention provides a primer for nucleic acid random fragmentation and a nucleic acid random fragmentation method. The primer consists of a plurality of upstream random primers and downstream random primers. The sequence composition of the upstream random primers is 5′-X-Y-3′, and the sequence composition of the downstream random primers is 5′-P-Y′-X′-close-3′, wherein Y and Y′ are random sequences, X is all or part of sequences of a sequencing platform 5′ end adaptor, X′ is all or part of sequences of a sequencing platform 3′ end adaptor, P is phosphorylation modification, and close is close modification. The primer of the present invention adopts double random anchoring of both the upstream random primers and the downstream random primers, and a DNA sample can be randomly broken.