An abnormally long HIV-1 env DNA PCR product due to altered sequences of primer binding sites.
To investigate the generation of an abnormally long HIV-1 env PCR DNA product the latter was cloned and sequenced followed by sequence analysis of HIV-1 primer binding sites. We found that the formation of an abnormally long PCR product was due to HIV-1 env sequence alteration (a) in the reverse primer binding site resulting in faulty primer binding and (b) downstream from the forward primer sequence resulting in a new binding site with reverse complementary sequence with respect to the forward primer at the opposite end of the PCR product. Both changes led to amplification of a longer PCR product with forward primer alone. Our results indicate that the HIV-1 genetic diversity in the env gene can lead to amplification of a specific PCR product of unexpected size which can be disregarded in the absence of its cross-validation.
Boriskin
Y S
YS
Department of Medical Microbiology, St. George's Hospital Medical School, London, UK.
Sharland
M
M
Booth
J C
JC
D000293:Adolescent; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D002648:Child; D002675:Child, Preschool; D015686:Gene Products, env / Q000235:genetics*; D005814:Genes, Viral; D014644:Genetic Variation; D015497:HIV-1 / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D016133:Polymerase Chain Reaction / Q000379:methods; D012680:Sensitivity and Specificity
D015686:Gene Products, env