A method of preparing nucleic acids for analysis, the method comprising: (a) contacting a nucleic acid molecule comprising a target nucleotide sequence with a first target-specific primer that specifically anneals to the target nucleotide sequence under conditions to generate a primer-hybridized nucleic acid molecule; (b) contacting the primer-hybridized nucleic acid molecule with a plurality of types of nucleotides for incorporation into a first strand that is complementary to the nucleic acid molecule, wherein at least one of the plurality of types of nucleotides comprises a capture moiety; (c) conducting a first strand synthesis reaction that is primed by the first target-specific primer of the primer-hybridized nucleic acid molecule and that uses the nucleic acid molecule of the primer-hybridized nucleic acid molecule as a template, wherein a product of the first strand synthesis reaction comprises at least one capture moiety; (d) conducting a second strand synthesis reaction that is primed by a fragment of the nucleic acid molecule and that uses the product of the first strand synthesis reaction as a template to generate a double-stranded nucleic acid comprising the at least one capture moiety; (e) ligating an adapter nucleic acid to the double-stranded nucleic acid to produce a ligation product comprising the at least one capture moiety; (f) capturing the ligation product by contacting the ligation product with an immobilized binding partner of the capture moiety; and (g) amplifying the ligation product by polymerase chain reaction using a second target-specific primer that comprises a 3' portion that specifically anneals to the target nucleotide sequence and a first adapter primer that specifically anneals to a complementary sequence of the adapter nucleic acid, wherein the second target-specific primer comprises a 5' tail portion that does not specifically anneal to the target nucleotide sequence. (a) contacting a nucleic acid molecule comprising a target nucleotide sequence with a first target-specific primer that specifically anneals to the target nucleotide sequence under conditions to generate a primer-hybridized nucleic acid molecule; (b) contacting the primer-hybridized nucleic acid molecule with a plurality of types of nucleotides for incorporation into a first strand that is complementary to the nucleic acid molecule, wherein at least one of the plurality of types of nucleotides comprises a capture moiety; (c) conducting a first strand synthesis reaction that is primed by the first target-specific primer of the primer-hybridized nucleic acid molecule and that uses the nucleic acid molecule of the primer-hybridized nucleic acid molecule as a template, wherein a product of the first strand synthesis reaction comprises at least one capture moiety; (d) conducting a second strand synthesis reaction that is primed by a fragment of the nucleic acid molecule and that uses the product of the first strand synthesis reaction as a template to generate a double-stranded nucleic acid comprising the at least one capture moiety; (e) ligating an adapter nucleic acid to the double-stranded nucleic acid to produce a ligation product comprising the at least one capture moiety; (f) capturing the ligation product by contacting the ligation product with an immobilized binding partner of the capture moiety; and (g) amplifying the ligation product by polymerase chain reaction using a second target-specific primer that comprises a 3' portion that specifically anneals to the target nucleotide sequence and a first adapter primer that specifically anneals to a complementary sequence of the adapter nucleic acid, wherein the second target-specific primer comprises a 5' tail portion that does not specifically anneal to the target nucleotide sequence.