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. 2006 Jun;80(12):6182–6187. doi: 10.1128/JVI.02447-05

TABLE 1.

Characterization of cDNA clones representing recombinant and parental (nonrecombined substrate) BMV RNA3 (−) sequences within the sgp region after in vitro copying of RW1 (−) RNA3 and RW2 (−) RNA3 templates either with BMV replicase or with protein 2a

Enzyme prepn and type of RNA producta Clone no. Crossover regionb Crossover typec Length (nt) (SD) of poly(A) tractd
BMV replicase
    Recombinant sequence 1 II 1 18 (0.43)
2 II 1 18 (0.43)
3 II 2 19 (0.43)
4 II 2 19 (0.43)
5 II 1 18 (0.43)
6 II 1 18 (0.43)
7 II 2 17 (0.43)
    Parental sequence RW1 (−) RNA3 NA NA 18 (0.25)
RW1 (−) RNA3 NA NA 18 (0.25)
RW2 (−) RNA3 NA NA 18 (0.25)
RW2 (−) RNA3 NA NA 19 (0.25)
2a
    Recombinant sequence 1 I 1 16 (2)
2 I 2 20 (2)
3 I 2 18 (2)
4 I 2 19 (2)
5 II 2 19 (2)
6 II 2 17 (2)
7 II 1 19 (2)
8 II 1 19 (2)
9 II 1 22 (2)
10 II 2 16 (2)
11 II 2 17 (2)
12 II 1 21 (2)
13 II 1 25 (2)
    Parental sequence RW1 (−) RNA3 NA NA 17 (1.8)
RW1 (−) RNA3 NA NA 20 (1.8)
RW1 (−) RNA3 NA NA 16 (1.8)
RW2 (−) RNA3 NA NA 15 (1.8)
RW2 (−) RNA3 NA NA 19 (1.8)
a

Types of RNA products were determined by sequencing of RT-PCR-generated cDNAs from copying reaction products of a 1:1 mixture of RW1 (−) and RW2(−) RNA3 templates (reaction time, 90 min). The sequenced sgp regions carried flanking markers derived from either parental [RW1 (−) or RW2 (−)] or recombined (between two RNA templates) (−) RNA3 sequences (see Fig. 1 for more details).

b

Region of crossovers within the tested sgp sequence (see Fig. 1), as follows: region I, 116-nt sequence between C-4/5 and XhoI-1320; and region II, 34-nt sequence between EcoRI-1169 and C-4/5. NA, not applicable.

c

Direction of crossovers, as follows: type 1, RW1 (−) RNA3 (donor)→RW2 (−) RNA3 (acceptor); and type 2, RW2 (−) RNA3 (donor)→RW1 (−) RNA3 (acceptor).

d

Standard deviations for the lengths of poly(A) tracts were calculated based on the 18-adenine wild-type length.