Methods and kits for joining fragmented nucleic acids together

A homogeneous method for joining fragmented nucleic acids together to produce a full-length target nucleic acid, comprising the steps of:

• a) performing an amplifying step comprising contacting a sample suspected of comprising fragmented target nucleic acids with:
• a pair of external primers comprising a first nucleic acid sequence and a second nucleic acid sequence to produce a first amplification product comprising a first sense strand and a first anti-sense strand if any fragmented target nucleic acids are present in the sample;
• and
• a pair of internal primers complementary to each other comprising a third nucleic acid sequence and a fourth nucleic acid sequence, the third nucleic acid sequence configured to hybridize to the first antisense strand of the first amplification product to produce a second sense strand of a second amplification product and the fourth nucleic acid sequence configured to hybridize to the first sense strand of the first amplification product to produce a second anti-sense strand of the second amplification product;
• and
• b) generating the full-length target nucleic acid by:
• i) annealing a first 3′ end region of the first sense strand with a second 3′ end region of the first anti-sense strand, wherein the first 3′ end region of the first sense strand primes the extension of the first sense strand over the first anti-sense strand, and the second 3′ end region of the first anti-sense strand primes the extension of the first anti-sense strand over the first sense strand;
• and
• ii) annealing a third 3′ end region of the second sense strand with a fourth 3′ end region of the second anti-sense strand, wherein the third 3′ end region of the second sense strand primes the extension of the second sense strand over the second anti-sense strand, and the fourth 3′ end region of the second anti-sense strand primes the extension of the second anti-sense strand over the second sense strand;
• wherein steps a) and b) and substeps i) and ii) are performed in a homogeneous manner;
• and
• wherein the sample suspected of comprising the fragmented target nucleic acids is a biological sample or a clinical sample, wherein the biological sample is selected from respiratory specimens, fecal specimens, blood specimens, dermal swabs, nasal swabs, wound swabs, blood cultures, skin, or soft tissue infections.