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PubMed2005

Evaluation of an oligonucleotide ligation assay for detection of mutations in HIV-1 subtype C individuals who have high level resistance to nucleoside reverse transcriptase inhibitors and non-nucleoside reverse transcriptase inhibitors.

The oligonucleotide ligation assay (OLA) has been proposed as an affordable alternative to sequence-based HIV-1 drug resistance testing in resource poor settings. The aim was to evaluate OLA for detecting mutations K103N, Y181C, K65R, Q151M, M184V and T215Y/F in subtype C. Forty-four subtype C and 8 subtype B HIV-1 positive individuals were analysed using the ViroSeqtrade mark HIV-1 genotyping assay (Applied Biosystems, Foster City, CA). A one-step RT-PCR and nested PCR were performed using subtype B specific primers from the OLA kit (NIH AIDS Research and Reference Reagent Program). Seventy-eight subtype C sequences were used to design subtype C specific primers. Ligation and detection steps were followed according to OLA kit protocol. For codons, K103N, Y181C, K65R, Q151M, M184V and T215Y/F, four or more mismatches compared to the probe or mismatches less than four bases from the ligation site were not tolerated. Results revealed accurate identification of mutations in 2/10, 4/9 3/9, 6/7, 2/7 and 6/7 VQA samples and 5/20, 4/17 0/20, 18/24, 5/24 and 13/24 subtype C positive individuals, respectively. It was concluded that the probes and primers in the NIH reference kit would need modification to optimize detection of mutations in subtype C individuals.

Anti-HIV Agents↗
PubMed1980

A method for determining the positional isotope exchange in a nucleoside triphosphate: cyclization of nucleoside triphosphate by dicyclohexylcarbodiimide.

The preparations of [beta gamma-18O,gamma-18O3]ATP and [beta gamma-18O,beta-18O2]ATP and a procedure for studying the positional isotopic exchange method of Midelfort and Rose [Midelfort, C.F., & Rose, I.A. (1976) J. Biol. Chem. 251, 5881-5887] are described for detection of transient ATP cleavage to ADP in enzyme active sites. ATP is cyclized by reaction with dicyclohexylcarbodiimide in anhydrous pyridine to give adenosine 5'-trimetaphosphate. This rapidly undergoes ring opening on adding water to re-form ATP. This results in the randomization of the beta- and gamma-phosphates. The new gamma-phosphate is hydrolyzed to Pi by using glycerokinase and D-glyceraldehyde. Mass spectral analysis of the 18O distribution in this Pi allows the extent of positional isotopic exchange to be determined. Procedures suitable for use with GTP are also described.

Adenosine Triphosphate↗