DNA Melting: DNA Sequences

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Single-stranded DNA sequences:

Name Sequence MW GC %
20bp ATC AAG CAG CCA TCG AAA CT 6079 45
20bp-comp AGT TTC GAT GGC TGC TTG AT 6154 45
20bp-single mismatch AGT TTC GAT TGC TGC TTG AT 6129 40
20bp-double mismatch AGT TTC GAT TGA TGC TTG AT 6153 35
20bp-complete mismatch CAC CGA CGT ACT ATT CCT AA 6021 45
30bp ATC AAG CAG CCA TCG AAA CTT AGG CTT ACA 9168 43.3
30bp-comp TGT AAG CCT AAG TTT CGA TGG CTG CTT GAT 9243 43.3
40bp ATC AAG CAG CCA TCG AAA CTT AGG CTT ACA ACC AGT GAC T 12242 45
40bp-comp AGT CAC TGG TTG TAA GCC TAA GTT TCG ATG GCT GCT TGA T 12348 45

For double-stranded DNA solutions, one of the 20bp, 30bp, or 40bp sequences is mixed in equal concentration with its respective complement, e.g., 30bp and 30bp-comp, in a desired saline solution. For 20bp mismatch solutions, the 20bp sequence is mixed in equal concentration with one of the mismatch sequences. Unless otherwise stated, the DNA concentration is 30 μM, and [KCl] = 100 mM.

Sample naming key:

Name Sample Salt concentration number of mismatches
A 20bp 100mM NaCl none
B 20bp 200mM NaCl none
C 20bp 50mM NaCl none
D 30bp 100mM NaCl none
E 40bp 100mM NaCl none
F 20bp-single mismatch 100mM NaCl one
G 20bp-double mismatch 100mM NaCl two