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US 2020/0399691 A1Published application
Sample preparation methods, systems and compositions
AssigneeKarius, Inc.
InventorsTimothy A. BLAUWKAMP, Rene SIT, Igor D. VILFAN
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Abstract
The disclosure provides methods, compositions, systems, and kits for the concurrent detection and analysis of different structural and chemical forms of nucleic acids in a sample.
Claims17
1-114. (canceled)
A method of performing an amplification reaction on a first RNA and a first DNA, comprising:
- a) providing a sample comprising a mixture of said first DNA and said first RNA, wherein said first DNA does not comprise a sequence complementary to said first RNA;
- b) tagging said first DNA with a first tag without using a transposase;
- c) tagging said first RNA with a second tag;
- d) performing an amplification or primer extension reaction on said first DNA with a polymerase that is selective for DNA templates;
- and
- e) synthesizing a complementary cDNA strand from said first RNA with a reverse transcriptase.
3 more elements
A method of sequencing nucleic acids comprising:
- a) providing a sample comprising double-stranded nucleic acids and single-stranded nucleic acids;
- and
- b) attaching a first adapter to an end of said double-stranded nucleic acids;
- c) denaturing said double-stranded nucleic acids into single-stranded nucleic acids;
- d) sequencing nucleic acids ligated to said first adapter and identifying sequences
- e) associated with said first adapter as being double-stranded.
3 more elements
A method for concurrent processing of different nucleic acid forms in a sample comprising:
- a) denaturing said nucleic acid forms in a sample;
- b) attaching a first adapter to one end of a first nucleic acid form and attaching a second adapter to one end of a second nucleic acid form;
- c) primer extending said first and said second attached nucleic acid forms;
- d) attaching a third adapter comprising a priming element;
- and
- e) amplifying said first and second nucleic forms.
3 more elements
A reaction mixture composition comprising:
- a) an adapter;
- b) a first ligase that has a preference for a first nucleic acid form;
- c) a second ligase that has a preference for a second nucleic acid form;
- and
- d) a buffer.
2 more elements
A reaction mixture comprising:
- a) a ligase;
- b) a DNA-dependent polymerase that has non-templated activity, wherein said non-templated base is N1;
- and
- c) a RT polymerase that has non-templated activity, wherein said non-templated base is N2, wherein N1 and N2 are different nucleic acid bases.
1 more element
A method for processing different nucleic acid forms in a sample comprising:
- a) denaturing said different nucleic acid forms in a sample, wherein said different nucleic acid forms comprise a first nucleic acid form and a second nucleic acid form;
- b) attaching a first adapter to said first nucleic acid form and a second adapter to said second nucleic acid form;
- c) amplifying said first nucleic acid form using a DNA-dependent polymerase that has non-templated activity, wherein said non-templated activity comprises adding at least one N1 nucleotide or a first sequence to amplified products of said amplification of said first nucleic acid form;
- and
- d) amplifying said second nucleic acid form using a reverse transcriptase polymerase that has non-templated activity, wherein said non-templated activity comprises adding at least one N2 nucleotide or a second sequence to amplified products of said amplification of said second nucleic acid form, wherein said N1 nucleotide and said N2 nucleotide are different nucleotides or said first sequence is different from said second sequence.
2 more elements
Dependencies are inferred from the claim text.