Biphasic decay kinetics suggest progressive slowing in turnover of latently HIV-1 infected cells during antiretroviral therapy

Table 3 Patient matched PCR primers

		Position ^C
Primer-ID^a	Function^b	5'	3'	Sequence ^D	Analysis of patient no^E
Ts5'gag	Sense-primer UsRNA/vRNA-ex	1372	1397	CAAGCAGCCATGCAAATGTTAAAAGA	103, 104, 110⁵, 111
				CAAGCAGCTATGCAAATGTTAAAAGA	112
Boe3tq	Antisense-probe UsRNA/vRNA-ex	1430	1405	f-CTATCCCATTCTGCAGCTTCCTCATT-q	104, 110^E, 111, 112
				f-TCTATCCCATTCTGCAGCTTCTTCATT-q	103
Boe2	Antisense-primer UsRNA/vRNA-ex	1488	1467	TCCCCTTGGTTCTCTCATCTGG	104, 110^E, 111, 112
				TCCCCTTGGTTCCCTTATCTGG	103
Skcc1b	cDNA-primer, UsRNA/vRNA-ex	1513	1486	TACTAGTAGTTCCTGCTATGTCACTTCC	103, 110^E, 111, 112
				TCCCCTTGGTTCCCTTATCTGG	104
Mf1	Sense-primer MsRNA-tatrev	5956	5979	CTTAGGCATCTCCTATGGCAGGAA	103, 104, 111, 112
				ATTAGGCATCTCCTATGGCAGGAA	110^E
Ts5'allspl	Sense-primer MsRNA-total	5978	6001	AAGAAGCGGAGACAGCGACGAAGA	103, 104
Mf84	Sense-primer MsRNA-total	6012	6045	ACAGTCAGACTCATCAAGTTTCTCTATCAAAGCA	111
				ACAGTAAGACTCaTCAAGCTTCTCTATCAAAGCA	110^E
				CAGTCAGACTCATCAAGCTTCTCTATCAAAGCA	112
mf2tq	Antisense-probe MsRNA-total MsRNA-tatrev	8421	8399	f-TTCCTTCGGGCCTGTCGGGTCCC-q	104
				f-TTCCTTCGGGCCTGTCTGGTCCC-q	103
Mf226tq	Sense-Probe MsRNA-total MsRNA-tatrev	8397	8414	f-AGGGGACCCGACAGGCCC-q	110^E, 112
				f-AGGGGACGACCCGACAGG-q	111
Mf83	Antisense/cDNA-primer MsRNA-total MsRNA-tatrev	8459	8433	GGATCTGTCTCTGTCTCTCTCTCCACC	111
				TGATCTGCCTCTGTCTTGCTCTCCACC	103
				GGATGTGTCTCTGTCTCTGTCTCCACC	104
				TGATGTGTCTCTGTCTCTCTCTCCACC	110^E
				GGATCTGTCTCTGTCTCTGTCCCCACC	112

^A ID denominates identification of primers according to internal nomenclature in the authors laboratory[22].
^B Oligonucleotide function; Sense/antisense-primer: oligonucleotide of the respective polarity used for amplification, sense/antisense probe: fluorogenic probe of the respective polarity used for detection of genuine amplification products, cDNA-primer: oligonucleotide of negative polarity used for reverse transcription prior to amplification. In assays for UsRNA/vRNA-ex separate cDNA and antisense primers were used except for patient 112 (skkcc1b was used for cDNA synthesis and PCR). In assays for MsRNAs, the same primer was used for reverse transcription and amplification.
^C Numbering on the Hxb2 genome according to the software provided by the Los Alamos HIV database; (SEQUENCE LOCATOR, http://www.hiv.lanl.gov).
^D Sequences are indicated 5' to 3' from left to right. Underlined positions show deviation from the standard sequence (HXB2 or clade B consensus) (indicated in bold letters). f = Fluorescein-moiety attached to the DNA-probe, q= Fluorescence quenching moiety attached to the DNA-probe.
^E Note that PCR primers of patient 110 have been previously reported [22]. In this earlier study, in which patient 110 has been referred as "patient 08", different time points and specimens have been analyzed with a focus on the cellular origin of HIV-1 transcription.

ISSN: 1742-4690