Table 2. UV thermal denaturation data with templates having alternative sections.

Entry	Template	Sequences a	Template/sequence ratio	T m b [°C]
				pH 7.5	pH 9.5
1	3′-CC (ACACAT)2 AGTAGT (ACACAT)2 CC	5′-TGTGTA	1/4	25.0	22.9
		5′-TbnGTGTA	1/4	31.1	39.3
2	3′-CC (ACACAT)2 AGTAGT (ACACAT)2 CC	5′-TCATCA	1/1	<5	<5
		5′-TbnCATCA	1/1	<5	<5
3	3′-CC (ACACAT)2 AGTAGT (ACACAT)2 CC	5′-TGTGTA + 5′-TCATCA	1/4/1	25.0	24.3
		5′-TbnGTGTA + 5′-TbnCATCA	1/4/1	35.2	41.1
4	3′-CC AGTAGT (ACACAT AGTAGT)2 CC	5′-TGTGTA	1/2	<5	<5
		5′-TbnGTGTA	1/2	<5	<5
5	3′-CC AGTAGT (ACACAT AGTAGT)2 CC	5′-TCATCA	1/3	<5	<5
		5′-TbnCATCA	1/3	<5	<5
6	3′-CC AGTAGT (ACACAT AGTAGT)2 CC	5′-TGTGTA + 5′-TCATCA	1/2/3	17.5	14
		5′-TbnGTGTA + 5′-TbnCATCA	1/2/3	31.2	35.4
7	3′-CC AGTAGT ACACAT AAAAAAA CC	5′-TCATCA	1/1	<5	<5
		5′-TbnCATCA	1/1	<5	<5
8	3′-CC AGTAGT ACACAT AAAAAAA CC	5′-TGTGTA	1/1	<5	<5
		5′-TbnGTGTA	1/1	<5	<5
9	3′-CC AGTAGT ACACAT AAAAAAA CC	5′-TTTTTTT	1/1	13.9	12.7
		5′-TbnTTTTTT	1/1	12.0	9.8
10	3′-CC AGTAGT ACACAT AAAAAAA CC	5′-TGTGTA + 5′-TCATCA	1/1/1	13.9	13.8
		5′-TbnGTGTA + 5′-TbnCATCA	1/1/1	22.8	25.7
11	3′-CC AGTAGT ACACAT AAAAAAA CC	5′-TCATCA + 5′-TTTTTTT	1/1/1	13.8	12.6
		5′-TbnCATCA + 5′-TbnTTTTTT	1/1/1	12.7	23.6
12	3′-CC AGTAGT ACACAT AAAAAAA CC	5′-TGTGTA + 5′-TTTTTTT	1/1/1	17.9	17.8
		5′-TbnGTGTA + 5′-TbnTTTTTT	1/1/1	22.0	27.7
13	3′-CC AGTAGT ACACAT AAAAAAA CC	5′-TGTGTA + 5′-TCATCA + 5′-TTTTTTT	1/1/1/1	17.9	16.9
		5′-TbnGTGTA + 5′-TbnCATCA + 5′-TbnTTTTTT	1/1/1/1	26.7	30.9

^aT^bn refers to boronothymidine and bold letters represent RNA residues.

^bMelting temperatures are obtained from the maxima of the first derivatives of the melting curve (A260 vs. temperature) recorded in a buffer containing 1 M NaCl and 10 mM of sodium cacodylate, template concentration 3 μM; complementary units concentrations were adjusted according to stoichiometry. Curve fits data were averaged from fits of three denaturation curves.