Here the DNA sequences are displayed to indicate the intended DX secondary structure. This makes it easy to examine the sticky ends presented by each DX molecule. (Note: As this paper was being prepared, we noticed a two base mismatch in unit C of ABCD-hat.) 5' and 3' ends are marked (where possible), and the following punctuation is used:
/ indicates a hairpin
\
TAC\/AGT indicates a half-turn of strands TACTCA and TGAGTA
ATG/\TCA
- and | indicate continuation of a strand
: indicates continuation from the opposite side of the helix
DAO-E AB lattice, Fig. 3a
unit A
3 3
5 GATGGCGT-CCGTTTAC\/AGTCGAGG-ACGGATCG 5
TCACTCTACCGCA GGCAAATG/\TCAGCTCC TGCCTAGCTCACT
| | | |
TAGAGGTAAGACC TGCGGTAT\/AGATAGCA GGCTACTGGAGAT
3 CATTCTGG-ACGCCATA/\TCTATCGT-CCGATGAC 3
5 5
unit B
5 5
3 GCGGTTGT-CCAACTTA\/GGTCTAGG-ACATCTCG 3
CTCTACGCCAACA GGTTGAAT/\CCAGATCC TGTAGAGCATCTC
| | | |
AGTGAGGCAATCC TGTAACGT\/GCCGAACA GGCAAGCGAGTGA
5 CCGTTAGG-ACATTGCA/\CGGCTTGT-CCGTTCGC 5
3 3
DAO-E AB-hat lattice, Figs. 3b and 3c
unit A
3 3
5 GATGGCGT-CCGTTTAC\/AGTCGAGG-ACGGATCG 5
TCACTCTACCGCA GGCAAATG/\TCAGCTCC TGCCTAGCCATAC
| | | |
TAGAGGTAAGACC TGCGGTAT\/AGATAGCA GGCTACTGTCTTG
3 CATTCTGG-ACGCCATA/\TCTATCGT-CCGATGAC 3
5 5
unit B-hat
/TTTCGCTAGGTT TTGCATCGTCTT\
\TTAGCGATCC | | CGTAGCAGTT/
5 | | | | 5
3 GCGGTTGT-CCAACT TA\/GG TCTAGG-ACATCTCG 3
CTCTACGCCAACA GGTTGA-AT/\CC-AGATCC TGTAGAGCCAAGA
| | | |
AGTGAGGCAATCC TGTAAC-GT\/GC-CGAACA GGCAAGCGGTATG
5 CCGTTAGG-ACATTG-CA/\CG-GCTTGT-CCGTTCGC 5
3 3
DAO-E AB-hat lattice, Figs. 4a, 4b, 4c
unit A
3 3
5 GATGGCGT-CCGTTTAC\/AGTCGAGG-ACGGATCG 5
TCACTCTACCGCA GGCAAATG/\TCAGCTCC TGCCTAGCTCACT
| | | |
TAGAGGTAAGACC TGCGGTAT\/AGATAGCA GGCTACTGGAGAT
3 CATTCTGG-ACGCCATA/\TCTATCGT-CCGATGAC 3
5 5
unit B-hat
/TTTCGCTAGGTT TTGCATCGTCTT\
\TTAGCGATCC | | CGTAGCAGTT/
5 | | | | 5
3 GCGGTTGT-CCAACT TA\/GG TCTAGG-ACATCTCG 3
CTCTACGCCAACA GGTTGA-AT/\CC-AGATCC TGTAGAGCATCTC
| | | |
AGTGAGGCAATCC TGTAAC-GT\/GC-CGAACA GGCAAGCGAGTGA
5 CCGTTAGG-ACATTG-CA/\CG-GCTTGT-CCGTTCGC 5
3 3
DAE-O AB lattice, Figs. 2 and 3d
unit A
5 3
GATGGCGACATCC-TGCCGCT-ATGATTACACAGCC-TGAGCATTGACC 5
CTGTAGG ACGGCGA-TACTAATGTGTCGG ACTCGTAACTGGCGTCAGC
| | | |
GTAGCGCCGTTAGT CCAACTG GCATGTAGTATCGT CCGATCAACCAG
5 GGCAATCA-GGTTGAC-CGTACATCATAGCA-GGCTAGTTGGTCGCAGTC
3 5
unit B
3 5
5 CGACGACA-GGCTACG-CCAGTGACCAATCA-GGTACTACGTGCCATCGC
CGTCAGGCTGCTGT CCGATGC GGTCACTGGTTAGT CCATGATGCACG
| | | |
GTGCTGG ACCGCAA-CATGATGCGTTAGG ACGGCATAGCTGCCTACCG
GCAGTCGCACGACC-TGGCGTT-GTACTACGCAATCC-TGCCGTATCGACG 5
5 3
DAE-O AB-hat lattice, Fig. 3e
unit A
5 3
GATGGCGACATCC-TGCCGCT-ATGATTACACAGCC-TGAGCATTGACAC 5
CTGTAGG ACGGCGA-TACTAATGTGTCGG ACTCGTAACTGTGCGTCAG
| | | |
GTAGCGCCGTTAGT CCAACTG GCATGTAGTATCGT CCGATCAACCAG
5 GGCAATCA-GGTTGAC-CGTACATCATAGCA-GGCTAGTTGGTCGCAGTC
3 5
unit B-hat
3 5
5 CGACGACA-GGCTACGCCAG--TGACCAATCA-GGTACTACGTGCCATCGC
CGTCAGGCTGCTGT CCGATGCGGTC ACTGGTTAGT CCATGATGCACG
| | | |
CGTGCTGG ACCGCA-ACAT GATGCGTTAGG ACGGCATAGCTGCCTACCG
GCAGTCGCACGACC-TGGCGT TGTA-CTACGCAATCC-TGCCGTATCGACG 5
5 | | : : 3
/TTCGGTTGTC | : GCGAGTAGTT\
\TTGCCAACAGTT TTCGCTCATCTT/
DAE-O AB-hat lattice, Fig. 3f
unit A
5 3
GATGGCGACATCC-TGCCGCT-ATGATTACACAGCC-TGAGCATTGACAC 5
CTGTAGG ACGGCGA-TACTAATGTGTCGG ACTCGTAACTGTGCGTCAG
| | | |
GTAGCGCCGTTAGT CCAACTG GCATGTAGTATCGT CCGATCAACCAG
5 GGCAATCA-GGTTGAC-CGTACATCATAGCA-GGCTAGTTGGTCGCAGTC
3 5
unit B-hat
TTGAGCGACTTT\
| CTCGCTGATT/
3 | | 5
5 CGACGACA-GGCTACGCCA GT-GACCAATCA-GGTACTACGTGCCATCGC
CGTCAGGCTGCTGT CCGATGCGGT-CA-CTGGTTAGT CCATGATGCACG
| | | |
CGTGCTGG ACCGCA-ACATGA TGCGTTAGG ACGGCATAGCTGCCTACCG
GCAGTCGCACGACC-TGGCGT TGTACT-ACGCAATCC-TGCCGTATCGACG 5
5 | | 3
/TTCGGTTGTC |
\TTGCCAACAGTT
DAE-O ABCD-hat lattice, Figs 4e and 4f.
unit A
5 3
ACTATGCTAGTCC-TGTATGTCAT-GCCGTTGTGCC-TGAGCACCAGTCG 5
GATCAGG ACATACAGTA-CGGCAACACGG ACTCGTGGTCAGCCGTCAG
| | | |
CACAGCGGTAGCGT CCGATACGAT GCAGTACGTGT CCGTAGTTGCTG
5 CCATCGCA-GGCTATGCTA-CGTCATGCACA-GGCATCAACGACGCAGTC
3 5
unit B
3 5
5 CGTTAGCA-GGCTACGCCA-TGTATGCGTCA-GGTCAACATAGCGTGTCG
CAACGAGCAATCGT CCGATGCGGT ACATACGCAGT CCAGTTGTATCG
| | | |
GCCGTCGG ACATTGCCAA-CCAGCGATAGG ACTACTGTGATGCTGATAC
TGAACTCGGCAGCC-TGTAACGGTT-GGTCGCTATCC-TGATGACACTACG 5
5 3
unit C
5 3
GATGGCGACATCC-TGCCGCT-ATGATTACACAGCC-TGAGCATTGACAC 5
CTGTAGG ACGGCGA-TACTAATGTGTCGG ACTCGTAACTGGCACTTGA
| | | |
GTAGCGCCGTTAGT CCAACTGGCA TGTAGTATCGT CCGATCAACCAG
5 GGCAATCA-GGTTGACCGT-ACATCATAGCA-GGCTAGTTGGTCGTTGCT
3 5
unit D-hat
TTGAGCGACTTT\
| CTCGCTGATT/
3 | | 5
5 CGACGACA-GGCTACGCCA GT-GACCAATCA-GGTACTACGTGCCATCGC
CGTCAGGCTGCTGT CCGATGCGGT-CA-CTGGTTAGT CCATGATGCACG
| | | |
CGTGCTGG ACCGCA-ACATGA TGCGTTAGG ACGGCATAGCTGCCTACCG
GCAGTCGCACGACC-TGGCGT TGTACT-ACGCAATCC-TGCCGTATCGACG 5
5 | | 3
/TTCGGTTGTC |
\TTGCCAACAGTT