. 2009 Apr 21;10(4):1788–1807. doi: 10.3390/ijms10041788

Table 1.

Nucleotide sequences of products of HIV-RNA and M2-RNA recombination in the regions between H_for and M_rev primer binding sites.

Amplicon		Sequences of amplified regions of recombinant RNA molecules²⁾	Number of detected clones³⁾		Comments
Name¹⁾	Length		Bact. colony PCR	Sequencing	Comments
P1	55	[H_FOR] CUAGACGGUGAGUGCUGUG [M_REV]⁴⁾	4	4	Ligation in butt-to-butt manner^*
P2	56	[H_FOR] CUAGACGGUAGAGUGCUGUG [M_REV]	1	1	1 nt RNA bulge loop^*
P3	58	[H_FOR] CUAGACGGUGUAGAGUGCUGUG [M_REV]	86	8	3 nts RNA bulge loop^*
P4	54	[H_FOR] CUAGACGGUGUUGCUGUG [M_REV]	1	1	Asymmetric 3 nts internal loop ^*
P5	108	[H_FOR] CUAGACGGUGUAAAAAUCUCUAGC AGUGGCGCCAUGAGGGAAGAAUAUCGAAAGGAA CAGCAGAGUGCUGUG [M_REV]	1	1	Template-independent recombination
P6	38	[H_FOR]AU[M_REV]	1	1
P7	39	[H_FOR] CUA[M_REV]	1	1
P8	107	[H_FOR] CUAGACGGUGUAAAAAUCUCUAGC AGUGGCGCAUGAGGGAAGAAUAUCGAAAGGAAC AGCAGAGUGCUGUG [M_REV]	2	2
P9	73	[H_FOR] CUAGACGGUGUAUCGAAAGGAACA GCAGAGUGCUGUG [M_REV]	2	2
P10	42	[H_FOR] CUAGAU[M_REV]	2	2
P11	76	[H_FOR] [H_FOR] CUAGACGGUGUAGAGUGCU GUG [M_REV]	3	3	3 nts RNA bulge loop, double forward primer
P12	119	[H_FOR] UAGACGGUGUAAAAAUCUCUAGCA GUGGCGCCCGAACAGGGACAUGAGGGAAGAAUA UCGAAAGGAACAGCAGAGUGCUGUG [M_REV]	1	1	Template-independent recombination
P13	55	[H_FOR] CUAGACGGAGAGUGCUGUG [M_REV]	1	1	Symmetric 2 nts internal loop^*
P14	105	[H_FOR] CUAGACGGUGUAAAAAUCUCUAGC AGUGGCGCGAGGGAAGAAUAUCGAAAGGAACAG CAGAGUGCUGUG [M_REV]	1	1	Template-independent recombination
P15	109	[H_FOR] UAGACGGUGUAAAAAUCUCUAGCA GUGGCGCCCGAACAGGGACUUUAUCGGGAGGAA CAGCAGAGUGCUGUG [M_REV]	1	1	Replacement of AA by GG (template-independent recombination)

See Figure 6 for structures.

^¹⁾

Amplicon names correspond to those in Figure 5.

^²⁾

Only RNA sequences between regions corresponding to primers H_for and M_rev are shown.

^³⁾

Number of colonies, detected by bacterial colony PCR and via nucleotide sequencing of plasmids.

^⁴⁾

RNA regions originating from HIV-RNA are shown in red, from M2-RNA—in blue. Template-binding regions are underlined; sequences corresponding to primers are shown as [H_FOR] and [M_REV]. RNA nucleotides within bulge loops are not underlined, nucleotides in internal loops and mismatches are shown in italic. External insertions are highlighted with yellow.