TABLE 3

DNA sequences captured at chromosomal breaks

CloneaUpstream change (nt)bDownstream change (nt)cLength of captured DNA sequence (nt)Source of captured DNA
2-1C−29−72342UId/TK
2-1D−3−64318pCMV-I-SceI (CW)e
2-2A−30353IAP
2-2I−3−423351E. coli genome
2-2J−10487pCMV-I-SecI (CW)
2-3G−6+2 (AA)350IAP
2-5L−50487pCMV-I-SecI (CW)
3-1C+2 (AA)0482pCMV-I-SceI (CW)
3-3D−40468pCMV-I-SceI (CW)
4-1E+6 (ATATAA)0489pCMV-I-SceI (CCW)
4-2C+3 (TAA)0490pCMV-I-SceI (CCW)
4-3F−3−19159pCMV-I-SceI (CW)
5-1D−50487pCMV-I-SceI (CCW)
5-1E−190309UI
5-2A−17−221644UI/TK
5-2F−50488pCMV-I-SceI (CW)
5-5H−60144IAP
5-8E−70140TK
6-1J−80321UI/B2 repeat
6-2D−1−1167UI
6-5H00422UI/IAP
  • a The first character of each clone name refers to the cell line (2 through 6) from which the TFTR clone was recovered.

  • b Number of nucleotides deleted (−) or gained (+) upstream from position of the I-SceI cut site on the top strand of the integrated pYL1 substrate (see Figure 3A). These changes are in addition to the captured DNA sequence. In the three cases involving the gain of several nucleotides (clones 3-1C, 4-1E, and 4-2C), the actual sequences added are indicated in parentheses. The added sequences may be derivatives of the 3′ overhang sequence ATAA produced upon staggered cleavage of the integrated substrate with I-SceI.

  • c Number of nucleotides deleted or gained downstream from the I-SecI cut site on the top strand of the integrated pYL1 substrate (Figure 3A). The changes are in addition to the captured DNA sequence.

  • d UI: sequences of unidentified origin. These sequences are not present in GenBank or EMBL.

  • e Refers to orientation of captured fragment of pCMV-I-SceI. CW: clockwise, meaning that the SV40 origin sequence is positioned to the left of the ColE1 origin as drawn in Figure 1. CCW: counterclockwise, opposite orientation.