Table 1.
MtDNA Deletion Breakpoints from Substantia Nigra Neurons with Primers within the Major Arc
| Deletion | Break Points | Repeat | 5′ Sequence | 3′ Sequence | Class of Deletion | Size (bp) |
|---|---|---|---|---|---|---|
| PD | ||||||
| 1 | 9729–15338 | no repeat | 5′-TCTCTATTTTACCC-3′ | 5′-CTATTCTTGCACG-3′ | Class III | 5608 |
| 2 | 7805–13844 | 5′-CCTAG-3′ | 5′-CCGCCATCAT(CCTAG)-3′ | 5′-ACCTCAACTACCTAA-3′ | Class I | 6038 |
| 3 | 8280–13782 | 5′-CCCCCTCTAC-3′ | 5′-CACCCCCTCTA(CCCCCTCTAG)-3′ | 5′-(CCCCCTCTAC)CTAAAACTC-3′ | Class II | 5501 |
| 4 | 6423–14344 | 5′-ACCCC-3′ | 5′-TCAATATAAA(ACCCC)-3′ | 5′-ATCATACTCTTTC-3′ | I | 7920 |
| 5 | 8482–13460 | 5′-ACCTCCCTCACCA-3′ | 5′-AAACTACCACCT(ACCTCCCTCACCA)-3′ | 5′-TTGGCAGCCTAGCATT-3′ | I | 4977 |
| 6 | 8566–13991 | 5′-TCCTAGACCT-3′ | 5′-TGCCCCCACAA(TCCTAGGCCT)-3′ | 5′-(TCCTAGACCT)AACCTGACTA-3′ | II | 5424 |
| 7 | 7114–13992 | 5′-CCTAGACCTAACCT-3′ | 5′-TCAGGCTACAC(CCTAGACCAAACCT)-3′ | 5′-(CCTAGACCTAACCT)GACTAGAAAA-3′ | II | 6877 |
| 8 | 7114–13992 | 5′-CCTAGACCTAACCT-3′ | 5′-TCAGGCTACAC(CCTAGACCAAACCT)-3′ | 5′-(CCTAGACCTAACCT)GACTAGAAAA-3′ | II | 6877 |
| 9 | 6423–14344 | 5′-ACCCC-3′ | 5′-TCAATATAAA(ACCCC)-3′ | 5′-ATCATACTCTTTC-3′ | I | 7920 |
| 10 | 9659–11536 | 5′-CATAGTCTA-3′ | 5′-AATCACCTGAGCTCAC(CATAGTCTA)-3′ | 5′-(CATAGCCTA)CCCCTTCC-3′ | II | 1876 |
| 11 | 8034–11434 | 5′-GAAGCCCCCAT-3′ | 5′-TACTCCCGATT(GAAGCCCCCAT)-3′ | 5′-CGCTGGGTCAATAGTAC-3′ | I | 3399 |
| 12 | 6423–14344 | 5′-ACCCC-3′ | 5′-TCAATATAAA(ACCCC)-3′ | 5′-ATCATACTCTTTC-3′ | I | 7920 |
| 13 | 10104–11868 | 5′-GCCTTAC-3′ | 5′-AACACCCTCCTA(GCCTTAC)-3′ | 5′-CCCCCACTATTAACCT-3′ | I | 1763 |
| 14 | 8482–13460 | 5′-ACCTCCCTCACCA-3′ | 5′-AAACTACCACCT(ACCTCC>CTCACCA)-3′ | 5′-TTGGCAGCCTAGCATT-3′ | I | 4977 |
| 15 | 8049–14115 | no repeat | 5′-TTCGTATAATAATTAC-3′ | 5′-CCCACTCATCCTAACCC-3′ | III | 6065 |
| 16 | 7677–15013 | no repeat | 5′-CCCTCATAATCAT-3′ | 5′-ATTCTTTATCTGCCTCTT-3′ | III | 7335 |
| 17 | 8482–13460 | 5′-ACCTCCCTCACCA-3′ | 5′-AAACTACCACCT(ACCTCCCTCACCA)-3′ | 5′-TTGGCAGCCTAGCATT-3′ | I | 4977 |
| 18 | 8428–15482 | 5′-ACACTATTC-3′ | 5′-CCCCCATACTCCTT(ACACTATTC)-3′ | 5′-TCACCAGACCTCCTAGG-3′ | I | 7054 |
| 19 | 7409–13688 | 5′-CCCCACCCTAC-3′ | 5′-TATATGGATGCC(CCCCACCCTAC)-3′ | 5′-TAAACCCCATTAACG-3′ | I | 6278 |
| 20 | 7409–13688 | 5′-CCCCACCCTAC-3′ | 5′-TATATGGATGCC(CCCCACCCTAC)-3′ | 5′-TAAACCCCATTAACG-3′ | I | 6278 |
| 21 | 7635–15310 | 5′-TCAT-3′ | 5′-GACGCTACTTCCCCTA(TCAT)-3′ | 5′-TATTGCAGCCCTAGCAAC-3′ | I | 7674 |
| 22 | 8482–13460 | 5′-ACCTCCCTCACCA-3′ | 5′-AAACTACCACCT(ACCTCCCTCACCA)-3′ | 5′-TTGGCAGCCTAGCATT-3′ | I | 4977 |
| Aged | ||||||
| 1 | 7805–13844 | 5′-CCTAG-3′ | 5′-CCGCCATCAT(CCTAG)-3′ | 5′-ACCTCAACTACCTAA-3′ | I | 6038 |
| 2 | 6555–14345 | 5′-CCA-3′ | 5′-GCAACCTCAACA(CCA)-3′ | 5′-TCATACTCTTTCACCC-3′ | I | 7789 |
| 3 | 6437–14077 | 5′-CCATAACCCAA-3′ | 5′-CCCCCTG(CCATAACCCAA)-3′ | 5′-(CCTCAACCCAA)AAAGGCATA-3′ | II | 7639 |
| 4 | 6427–15269 | no repeat | 5′-AAACCCCCTGC-3′ | 5′-CTCACACGATTCTTT-3′ | III | 8841 |
| 5 | 8418–14127 | 5′-TCCT-3′ | 5′-TTACCCCCATAC(TCCT)-3′ | 5′-AACCCTACTCCTAAT-3′ | I | 5708 |
| 6 | 9924–15194 | no repeat | 5′-GAAGCCGCCGCCT-3′ | 5′-CTATCCGCCATCCC-3′ | III | 5269 |
| 7 | 6453–14288 | 5′-CCCCTCT-3′ | 5′-TACCAAACG(CCCCTCT)-3′ | 5′-CCTTCATAAATTATTC-3′ | I | 7834 |
| 8 | 8408–14118 | 5′-CCC-3′ | 5′-ACCATAATTA(CCC)-3′ | 5′-ACTCATCCTAACCC-3′ | I | 5709 |
| 9 | 8482–13460 | 5′-ACCTCCCTCACCA-3′ | 5′-AAACTACCACCT(ACCTCCCTCACCA)-3′ | 5′-TTGGCAGCCTAGCATT-3′ | I | 4977 |
| 10 | 6423–14344 | 5′-ACCCC-3′ | 5′-TCAATATAAA(ACCCC)-3′ | 5′-ATCATACTCTTTC-3′ | I | 7920 |
| 11 | 6416–14182 | 5′-CAATTATCAATATA-3′ | 5′-CACAA(CAATTATCAATATA)-3′ | 5′-(CAATTA_CAATATA)TACACCAACAAA-3′ | II | 7765 |
| 12 | 8049–14115 | no repeat | 5′-TTCGTATAATAATTAC-3′ | 5′-CCCACTCATCCTAACCC-3′ | III | 6065 |
| 13 | 6476–14146 | 5′-TCCTAATCACA-3′ | 5′-CTGATCCG(TCCTAATCACA)-3′ | 5′-TAACCTATTCCCCCG-3′ | I | 7669 |
| 14 | 7815–13581 | 5′-CTCATCGC-3′ | 5′-CATCCTAGTC(CTCATCGC)-3′ | 5′-TACCTCCCTGACAA-3′ | I | 5765 |
| 15 | 7658–15548 | 5′-ATCAAGCCC-3′ | 5′-ATCACCTTTCATG(ATCACGCCC)-3′ | 5′-(ATCAAGCCC)GAATGATATTT-3′ | II | 7889 |
| 16 | 6585–15144 | 5′-GACC-3′ | 5′-CCGGAGGAGGA(GACC)-3′ | 5′-(GTCC)TCCCGTGAGGCCAAA-3′ | II | 8558 |
| 17 | 6585–15144 | 5′-GACC-3′ | 5′-CCGGAGGAGGA(GACC)-3′ | 5′-(GTCC)TCCCGTGAGGCCAAA-3′ | II | 8558 |
| 18 | 6585–15144 | 5′-GACC-3′ | 5′-CCGGAGGAGGA(GACC)-3′ | 5′-(GTCC)TCCCGTGAGGCCAAA-3′ | II | 8558 |
| Multiple-Deletion Patient | ||||||
| 1 | 6577–15154 | 5′-GAGG-3′ | 5′-TTCTTCGACCCCGCCG(GAGG)-3′ | 5′-CCAAATATCATTCTGAG-3′ | I | 8576 |
| 2 | 6587–14285 | 5′-GACCCC-3′ | 5′-CGCCGGAGGAGGA(GACCCC)-3′ | 5′-TCTCCTTCATAAA-3′ | I | 7697 |
| 3 | 9417–13684 | 5′-CCACC-3′ | 5′-CATACCAAGG(CCACC)-3′ | 5′-CTACTAAACCCC-3′ | I | 4266 |
| 4 | 7406–12395 | 5′-CCCCCCACCCTTACCAC-3′ | 5′-TATGGATG(CCCCCCACCCT_ACCAC)-3′ | 5′-(CCCCCCATCCTTACCAC)CCTCGT-3′ | II | 4988 |
| 5 | 6457–14867 | 5′-CTGATCCTCC-3′ | 5′-CCCCTCTTCGT(CTGATCCGTCC)-3′ | 5′-(CTGATCCTCC)AAATCACCACAGG-3′ | II | 8409 |
| 6 | 6587–14285 | 5′-GACCCC-3′ | 5′-CGCCGGAGGAGGA(GACCCC)-3′ | 5′-TCTCCTTCATAAA-3′ | I | 7697 |
| 7 | 6572–12304 | 5′-GCC-3′ | 5′-TTCTTCGACCCC(GCC)-3′ | 5′-CCAAAAATTTTGGT-3′ | I | 5731 |
| 8 | 6585–15144 | 5′-GACC-3′ | 5′-CCGGAGGAGGA(GACC)-3′ | 5′-(GTCC)TCCCGTGAGGCCAAA-3′ | II | 8558 |
| 9 | 8482–13460 | 5′-ACCTCCCTCACCA-3′ | 5′-AAACTACCACCT(ACCTCCCTCACCA)-3′ | 5′-TTGGCAGCCTAGCATT-3′ | I | 4977 |
| 10 | 7367–12063 | no repeat | 5′-TCCTAATAGTAGAAGAACCC-3′ | 5′-CCCTCATGTTCATACACCT-3′ | III | 4694 |
| 11 | 6422–15208 | 5′-AACCC-3′ | 5′-TTATCAATATAA(AACCC)-3′ | 5′-(ATCCC)ATACATTGGG-3′ | II | 8785 |
| 12 | 6551–13852 | 5′-ACCTCAAC-3′ | 5′-CTAACAGACCGCA(ACCTCAAC)-3′ | 5′-TACCTAACCAACAAA-3′ | I | 7300 |
| 13 | 7114–13992 | 5′-CCTAGACCTAACCT-3′ | 5′-TCAGGCTACAC(CCTAGACCAAACCT)-3′ | 5′-(CCTAGACCTAACCT)GACTAGAAAA-3′ | II | 6877 |
| 14 | 8482–13460 | 5′-ACCTCCCTCACCA-3′ | 5′-AAACTACCACCT(ACCTCCCTCACCA)-3′ | 5′-TTGGCAGCCTAGCATT-3′ | I | 4977 |
| 15 | 7409–3688 | 5′-CCCCACCCTAC-3′ | 5′-TATATGGATGCC(CCCCACCCTAC)-3′ | 5′-TAAACCCCATTAACG-3′ | I | 6278 |
| 16 | 7204–13903 | 5′-TATC-3′ | 5′-TTTCTCGGCC(TATC)-3′ | 5′-(TTTC)TCCAACATAC-3′ | II | 6698 |
| 17 | 10071–14622 | no repeat | 5′-AAACTTCGCCT-3′ | 5′-CCACAAACCCCATT-3′ | III | 4550 |
| 18 | 7998–12300 | no repeat | 5′-GACTCCTTGACGT-3′ | 5′-GGCCCCAAAAATTTT-3′ | III | 4301 |
| 19 | 7201–14809 | 5′-TCGGCCTCCCC-3′ | 5′-CACTTTC(TCGGCCTATCC) -3′ | 5′-(TCGACCTCCCC)ACCCCAT-3′ | II | 7607 |
This table displays all 59 mtDNA deletions detected in single substantia nigra neurons between primers at nt 15896–15877 and nt 5855–5875. Repeat sequences are shown in brackets and, where known, the deleted repeat shown in italics, imperfect bases within repeats are underlined, and missing bases are indicated by an underscore.