. Author manuscript; available in PMC: 2013 Jan 10.

Published in final edited form as: Biochemistry. 2011 Dec 20;51(1):63–73. doi: 10.1021/bi201570a

Table 1.

Thermodynamic data for binding of PNA and GPNA to RNA and DNA hairpins.^a

Ent ry		Sequence	K_a × 10⁶ M⁻¹	−ΔH kcal/mol	−ΔS eu	−ΔG kcal/mol	Binding order
1^b	PNA3	NH₂-CTCCTC	84 ± 80	29.4 ± 5.3	63 ± 17	10.6 ± 0.5	1.1 ± 0.2
Symmetric sequence, optimal for both parallel triple helix and anti-parallel duplex (strand invasion)
2	D-GPNA1	NH₂-CT^D-ArgCCT^D-ArgC	4.6 ± 1.6	27.3 ± 2.5	61 ± 9	9.1 ± 0.2	1.8 ± 0.1
3	L-GPNA1	NH₂-CT^L-ArgCCT^L-ArgC	2.2 ± 1.6	24.2 ± 9.6	53 ± 34	8.6 ± 0.5	2.0 ± 0.1
4^c	D-GPNA1	NH₂-CT^D-ArgCCT^D-ArgC	0.4	29.1	72	7.7	2.1
5^c	L-GPNA1	NH₂-CT^L-ArgCCT^L-ArgC	2.5	21.0	41	8.7	2.2

6^b	PNA4	NH₂-CTCTTC	47 ± 22	26.4 ± 3.2	54 ± 12	10.4 ± 0.3	1.3 ± 0.1
Sequence optimal for parallel triple helix
7	D-GPNA2	NH₂-CTCT^D-ArgTC	0.5	70.0	209	7.8	0.5
8	D-GPNA3	NH₂-CT^D-ArgCTT^D-ArgC	0.5	41.8	114	7.8	0.8
9	D-GPNA4	NH₂-CT^D-ArgCT^D-ArgT^D-ArgC	0.6	22.9	50	7.9	1.2
10	L-GPNA2	NH₂-CTCT^L-ArgTC	1.8	39.6	104	8.5	0.7
11	L-GPNA3	NH₂-CT^L-ArgCTT^L-ArgC	0.8	58.8	170	8.0	0.5
12	L-GPNA4	NH₂-CT^L-ArgCT^L-ArgT^L-ArgC	0.5	61.6	181	7.8	0.4

Sequence optimal for anti-parallel duplex (strand invasion)
13^d	D-GPNA5	NH₂-CTT^D-ArgCTC	10.5	19.8	34	9.6	1.4
14^d	D-GPNA6	NH₂-CT^D-ArgTCT^D-ArgC	5.0	13.4	14	9.1	2.0
15^d	D-GPNA7	NH₂-CT^D-ArgT^D-ArgCT^D-ArgC	0.4 ±0.01	25.8 ± 3.7	61 ± 13	7.6 ± 0.0	2.3 ± 0.0
16^d	L-GPNA7	NH²-CT^L-ArgT^L-ArgCT^L-ArgC	3.8 ± 0.1	13.0 ± 7.3	14 ± 25	8.9 ± 0.3	2.1 ± 0.1

Average association constants K_a (± standard deviation) in 100 mM sodium acetate, 1.0 mM EDTA, pH 5.5. Entries 1–3 binding to HRP1, entries 4 and 5 binding to DNA version of HRP1 and entries 6–16 binding to HRP2.

From our previous study, reference 10.

Binding to DNA version of HRP1.

PNA is anti-parallel to purine tract of HRP2 (Figure 4B).