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. Author manuscript; available in PMC: 2010 Oct 29.
Published in final edited form as: J Phys Chem B. 2009 Oct 29;113(43):14329–14335. doi: 10.1021/jp904830m

Table 1.

DNA hairpins with different loops used in SPR experiments.

loop Tm
5′-biotin-CGAATTCGTCTCCGAATTCG-3′ TCTC 66.0
5′-biotin-CGAATTCGTCTCTCCGAATTCG-3′ TCTCTC 64.2
5′-biotin-CGAATTCGPO3-(C2H4O)6CGAATTCG-3′ 6-EG 73.5
5′-biotin-CGAATTCG(PO3-C3H6O)3CGAATTCG-3′ 3-P 67.3
5′-biotin-CGAATTCG(PO3-C3H6O)4CGAATTCG-3′ 4-P 66.5
5′-biotin-CGAATTCG(PO3-C3H6O)5CGAATTCG-3′ 5-P 63.2
5′-biotin-CGAATTCG(PO3-C3H6O)6CGAATTCG-3′ 6-P 61.1
5′-biotin-CGAATTCG(PO3-C3H6O)7CGAATTCG-3′ 7-P 59.3
5′-biotin-GCGAATTCGCTCTCGCGAATTCGC-3′ TCTC 79.8
5′-biotin-GCGAATTCGCPO3-(C2H4O)6GCGAATTCGC-3′ 6-EG 83.6

Nucleotide and non-nucleotide loops are indicated in bold. At the same length (8 or 10 base pairs), the hairpin with a 6-EG loop has the highest melting temperature. The data were collected in MES buffer containing 92 mM NaCl. The thermal melting temperatures have an error of ±0.5 °C.