Selective terminal tagging of nucleic acids

A method for adding a terminal sequence tag to a target DNA molecule, the method comprising:

• a) providing:
• 1) a sample containing at least one target DNA molecule;
• 2) a first oligonucleotide comprising:
• a) a 5′ overhanging portion that exhibits a user-defined first sequence tag, wherein the 5′ overhanging portion comprises deoxyribonucleotides;
• b) a 3′ hybridizing portion that exhibits a sequence that is capable of hybridizing to the 3′-end of the target DNA molecule, wherein said 3′ hybridizing portion comprises a ribonucleic acid section;
• and
• c) a blocked 3′-end;
• and
• 3) a DNA polymerase;
• b) contacting the target DNA molecule with the first oligonucleotide under conditions allowing hybridization of the 3′ hybridizing portion of the first oligonucleotide to the target DNA molecule;
• c) incubating the target DNA molecule to which the first oligonucleotide is hybridized with the DNA polymerase under conditions wherein the 3′ end of the target DNA molecule is extended using the 5′ overhanging portion of the first oligonucleotide as a template to generate a first DNA template that exhibits a terminal sequence tag that is complementary to the first sequence tag of the first oligonucleotide;
• d) removing the ribonucleic acid section of the first oligonucleotide that is hybridized to the target DNA molecule to generate a cleaved first oligonucleotide that has a 3′ end that is capable of being extended by a DNA polymerase;
• and
• e) extending the 3′-end of the cleaved first oligonucleotide using the first DNA template as a template to generate a double-stranded DNA molecule comprising the first DNA template that exhibits the terminal sequence tag and a second DNA template that has the first sequence tag of the first oligonucleotide.