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Table 3 Overview of the IPDA at different annealing temperatures

From: Development of a highly sensitive and specific intact proviral DNA assay for HIV-1 subtype B and C

 

Number of detected copies

Gblock (input 1000 copies)

Annealing temperature

Sequence at probe region

Description

60 °C

58 °C

55 °C

53 °C

CCTTGGGTTCTTGGGAGC

Env intact matching probe

1293.6

1238.6

1001.0

1273.1

CCTTAGGTTCTTGGGAGC

Env G-A mutation 5th nucleotide

2.0

2.8

1021.4

1372.1

CCTTGGGTTCTTAGGAGC

Env G-A mutation 13th nucleotide

0.6

0.0

840.4

1177.7

CCTTAGGTTCTTAGGAGC

Env G-A mutation 5th and 13th nucleotide

0.0

0.9

0.4

2.3

  1. Gblock copies containing none, one or two mutations in the env probe were used to test the specificity of detecting only intact env copies. The Gblock containing the intact sequence does match the probe sequence. The Gblock with two mutations matches the unlabeled hypermutation probe
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Virology Journal

ISSN: 1743-422X