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Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes
N Sugimoto, S Nakano, M Yoneyama, and K Honda

Table S1. Thermodynamic values for DNA duplex formation in 1 M NaCl phosphate buffera obtained with Tm^-1 versus log Ct plot

DNA sequence^b

Tm^-1 versus log Ct plot

[Delta]H°

[Delta]S°

[Delta]^G°37

Tm^-1

kcal/mol

cal/mol/K

kcal/mol

°C

AGCCG

-37.6

-103

-5.8

31.2

ACCGCA

-42.0

-113

-7.0

40.4

ATGCGC

-49.5

-136

-7.2

41.3

CGGTGC

-55.4

-156

-7.1

40.1

CGTGCC

-46.5

-127

-7.0

40.5

TGCGCA

-42.1

-113

-7.0

46.8

AATACCG

-44.5

-125

-5.7

31.7

AGCCGTG

-50.7

-136

-8.5

49.9

AGCTTCA

-43.1

-119

-6.2

34.8

GGACTTA

-50.0

-144

-5.3

30.0

AAAAAAAA

-47.3

-137

-5.0

27.3

AAGCGTAG

-57.4

-159

-8.2

46.1

AATCCAGT

-52.4

-147

-6.8

38.8

ACATATGT

-50.4

-145

-5.6

36.1

ACCTAGTC

-65.6

-190

-6.8

38.1

ACGACCTC

-60.7

-168

-8.6

48.1

AGAGAGAG

-48.2

-131

-7.5

43.2

AGCGTAAG

-62.6

-177

-7.8

43.6

AGTCCTGA

-55.5

-154

-7.8

44.2

ATGCGCAT

-64.0

-177

-9.1

54.9

CACGGCTC

-67.0

-183

-10.3

55.5

CCATATGG

-67.5

-195

-7.1

43.5

CGATATCG

-63.2

-181

-7.1

44.0

CGCGTATA

-56.3

-155

-8.2

46.5

CGCTGTAA

-62.0

-173

-8.2

45.4

CTAGTGGA

-60.3

-170

-7.6

42.5

CTCACGGC

-69.6

-192

-10.2

54.1

CTGAGTCC

-57.8

-161

-8.0

45.0

GAATATTC

-60.1

-180

-4.3

30.1

GACTAGTC

-56.9

-162

-6.6

41.9

GAGTACTC

-57.1

-166

-5.8

37.5

GATTAATC

-58.8

-176

-4.3

29.8

GCATATGC

-55.7

-155

-7.6

48.3

GCCAGTTA

-58.4

-162

-8.4

47.1

GGTGCCAA

-63.7

-176

-9.1

50.3

GTCGAACA

-60.6

-168

-8.6

47.9

GTCTAGAC

-57.0

-163

-6.4

41.2

TAGGCCTA

-55.1

-152

-8.0

50.6

TATGCATA

-48.3

-136

-6.1

39.5

AAAAAAAAA

-62.3

-180

-6.3

36.0

ATAACTGGC

-58.3

-159

-9.0

50.8

ATCTATCCG

-69.0

-194

-8.9

47.8

CGCTGTTAC

-79.9

-225

-10.2

51.9

GCCAGTTAA

-69.8

-197

-8.7

47.1

AAAAAAAAAA

-80.9

-239

-6.7

41.8

CGGCAAGCGC

-85.0

-231

-13.4

62.2

TAGGTTATAA

-65.7

-189

-7.1

39.8

ACGTATTATGC

-76.8

-214

-10.4

53.8

ATTGGATACAAA

-74.6

-207

-10.4

54.1

ACATTATTATTACA

-87.4

-246

-11.1

54.3

^aAll experiments were conducted in a buffer containing 1 M NaCl, 10 mM Na2HPO4, 1 mM Na2EDTA, pH 7.0.
^bThe DNA duplex consists of the denoted DNA strand and its complementary DNA strand.
^cMelting temperatures are calculated at the total oligomer strand concentration of 100 mM.

Table S2. Thermodynamic values for DNA duplex formation in 1 M NaCl phosphate buffera obtained with the curve fitting procedure

DNA sequence^b

Average of curve fits

[Delta]H°

[Delta]S°

^[Delta]G°37

Tm^c

kcal/mol

cal/mol/K

kcal/mol

°C

AGCCG

-40.3

-113

-5.3

27.5

ACCGCA

-44.1

-122

-6.4

35.1

ATGCGC

-47.8

-135

-7.4

33.7

CGGTGC

-57.9

-163

-7.3

41.4

CGTGCC

-46.1

-127

-6.8

38.2

TGCGCA

-42.8

-116

-6.8

45.5

AATACCG

-46.3

-130

-6.1

33.4

AGCCGTG

-52.6

-143

-8.4

47.5

AGCTTCA

-45.3

-127

-5.9

32.8

GGACTTA

-51.4

-147

-5.8

32.7

AAAAAAAA

-45.3

-130

-5.1

26.7

AAGCGTAG

-53.4

-147

-7.8

44.6

AATCCAGT

-52.3

-145

-6.7

41.8

ACATATGT

-50.0

-143

-5.7

36.8

ACCTAGTC

-65.6

-191

-6.2

36.2

ACGACCTC

-58.8

-161

-8.8

49.8

AGAGAGAG

-46.1

-125

-7.3

42.5

AGCGTAAG

-58.8

-165

-7.8

42.9

AGTCCTGA

-53.7

-150

-7.1

40.8

ATGCGCAT

-59.9

-164

-8.8

55.4

CACGGCTC

-62.4

-170

-9.7

53.5

CCATATGG

-64.7

-188

-6.4

40.5

CGATATCG

-62.2

-177

-7.4

46.0

CGCGTATA

-61.3

-170

-8.6

47.7

CGCTGTAA

-58.5

-164

-7.6

43.0

CTAGTGGA

-62.5

-178

-7.3

40.8

CTCACGGC

-65.7

-182

-9.3

50.4

CTGAGTCC

-62.8

-177

-7.9

43.9

GAATATTC

-55.2

-164

-4.3

29.6

GACTAGTC

-54.2

-153

-6.6

43.3

GAGTACTC

-58.1

-169

-5.7

37.0

GATTAATC

-56.1

-167

-4.3

29.6

GCATATGC

-55.8

-154

-8.0

50.7

GCCAGTTA

-59.3

-166

-8.0

43.9

GGTGCCAA

-67.4

-189

-8.8

47.7

GTCGAACA

-64.6

-182

-8.0

45.0

GTCTAGAC

-57.7

-165

-6.5

41.6

TAGGCCTA

-54.2

-148

-8.3

52.8

TATGCATA

-48.9

-139

-5.6

37.7

AAAAAAAAA

-57.2

-165

-6.1

34.3

ATAACTGGC

-62.2

-172

-8.9

49.0

ATCTATCCG

-64.8

-182

-8.4

46.0

CGCTGTTAC

-73.5

-206

-9.5

50.6

GCCAGTTAA

-65.1

-181

-8.9

49.0

AAAAAAAAAA

-75.6

-222

-6.7

37.9

CGGCAAGCGC

-86.1

-235

-13.2

63.1

TAGGTTATAA

-64.5

-186

-6.8

38.4

ACGTATTATGC

-80.9

-227

-10.4

53.0

ATTGGATACAAA

-77.8

-218

-10.2

52.3

ACATTATTATTACA

-92.3

-262

-11.4

52.9

^aAll experiments were conducted in a buffer containing 1 M NaCl, 10 mM Na2HPO4 , 1 mM Na2EDTA, pH 7.0.
^bThe DNA duplex consists of the denoted DNA strand and its complementary DNA strand.
^cMelting temperatures are calculated at the total oligomer strand concentration of 100 mM.

Table S3. Measured and predicted thermodynamic values for DNA/DNA duplex formation in 1 M NaCl phosphate buffera

DNA sequence^b

[Delta]H°

[Delta]S°

^[Delta]G°37

Tm^c

kcal/mol

cal/mol/K

kcal/mol

°C

AGCCG

-39.0

(-39.2)

-108

(-109)

-5.6

(-5.3)

29.3

(27.8)

ACCGCA

-43.1

(-50.2)

-118

(-139)

-6.7

(-7.0)

37.8

(39.9)

ATGCGC

-48.7

(-46.0)

-135

(-127)

-7.3

(-6.6)

37.5

(37.5)

CGGTGC

-56.7

(-50.2)

-160

(-139)

-7.2

(-7.0)

40.8

(39.9)

CGTGCC

-46.3

(-50.2)

-127

(-139)

-6.9

(-7.0)

39.4

(39.9)

TGCGCA

-42.5

(-48.6)

-115

(-134)

-6.9

(-7.0)

46.2

(45.5)

AATACCG

-45.4

(-51.7)

-128

(-147)

-5.9

(-6.0)

32.5

(33.8)

AGCCGTG

-51.7

(-56.8)

-140

(-156)

-8.5

(-8.5)

48.7

(48.2)

AGCTTCA

-44.2

(-48.1)

-123

(-135)

-6.1

(-6.3)

33.8

(35.9)

GGACTTA

-50.7

(-49.7)

-146

(-143)

-5.6

(-5.3)

31.4

(29.6)

AAAAAAAA

-46.3

(-55.4)

-134

(-162)

-5.1

(-5.0)

27.0

(29.0)

AAGCGTAG

-55.4

(-58.9)

-153

(-163)

-8.0

(-8.3)

45.4

(46.9)

AATCCAGT

-52.4

(-56.9)

-146

(-161)

-6.8

(-7.0)

40.3

(39.6)

ACATATGT

-50.2

(-52.4)

-144

(-152)

-5.7

(-5.3)

36.5

(34.2)

ACCTAGTC

-65.6

(-57.7)

-191

(-163)

-6.5

(-7.1)

37.2

(40.2)

ACGACCTC

-59.8

(-65.1)

-165

(-181)

-8.7

(-9.0)

49.0

(49.4)

AGAGAGAG

-47.2

(-52.2)

-128

(-145)

-7.4

(-7.1)

42.8

(41.0)

AGCGTAAG

-60.7

(-58.9)

-171

(-163)

-7.8

(-8.3)

43.2

(46.9)

AGTCCTGA

-54.6

(-58.7)

-152

(-164)

-7.5

(-7.9)

42.5

(44.6)

ATGCGCAT

-62.0

(-59.8)

-171

(-165)

-9.0

(-8.8)

55.2

(53.8)

CACGGCTC

-64.7

(-65.6)

-177

(-179)

-10.0

(-10.0)

54.5

(54.4)

CCATATGG

-66.1

(-55.4)

-192

(-158)

-6.8

(-6.5)

42.0

(41.1)

CGATATCG

-62.7

(-58.4)

-179

(-164)

-7.3

(-7.5)

45.0

(46.8)

CGCGTATA

-58.8

(-61.7)

-163

(-171)

-8.4

(-8.7)

47.1

(48.3)

CGCTGTAA

-60.3

(-60.5)

-169

(-168)

-7.9

(-8.5)

44.2

(47.5)

CTAGTGGA

-61.4

(-56.5)

-174

(-159)

-7.5

(-7.3)

41.7

(41.3)

CTCACGGC

-67.7

(-65.6)

-187

(-179)

-9.8

(-10.0)

52.3

(54.4)

CTGAGTCC

-60.3

(-58.7)

-169

(-164)

-8.0

(-7.9)

44.5

(44.6)

GAATATTC

-57.7

(-50.8)

-172

(-150)

-4.3

(-4.3)

29.9

(28.7)

GACTAGTC

-55.6

(-55.6)

-158

(-160)

-6.6

(-6.1)

42.6

(39.4)

GAGTACTC

-57.6

(-55.6)

-168

(-160)

-5.8

(-6.1)

37.3

(39.4)

GATTAATC

-57.5

(-50.8)

-172

(-150)

-4.3

(-4.3)

29.7

(28.7)

GCATATGC

-55.8

(-54.6)

-155

(-154)

-7.8

(-6.9)

49.5

(43.7)

GCCAGTTA

-58.9

(-59.6)

-164

(-167)

-8.2

(-7.8)

45.5

(43.8)

GGTGCCAA

-65.6

(-65.5)

-183

(-182)

-9.0

(-9.2)

49.0

(50.1)

GTCGAACA

-62.6

(-63.8)

-175

(-179)

-8.3

(-8.3)

46.4

(45.9)

GTCTAGAC

-57.4

(-55.6)

-164

(-160)

-6.5

(-6.1)

41.4

(39.4)

TAGGCCTA

-54.7

(-58.1)

-150

(-163)

-8.2

(-7.5)

51.7

(47.0)

TATGCATA

-48.6

(-50.7)

-138

(-146)

-5.9

(-5.5)

38.6

(35.4)

AAAAAAAAA

-59.8

(-63.4)

-173

(-184)

-6.2

(-6.2)

35.1

(35.7)

ATAACTGGC

-60.3

(-65.2)

-166

(-182)

-9.0

(-8.7)

49.9

(47.6)

ATCTATCCG

-66.9

(-64.1)

-188

(-179)

-8.7

(-8.7)

46.9

(47.9)

CGCTGTTAC

-76.7

(-69.9)

-216

(-193)

-9.9

(-10.0)

51.2

(53.2)

GCCAGTTAA

-67.5

(-67.6)

-189

(-189)

-8.8

(-9.0)

48.1

(48.8)

AAAAAAAAAA

-78.3

(-71.4)

-231

(-206)

-6.7

(-7.4)

39.9

(41.2)

CGGCAAGCGC

-85.6

(-88.2)

-233

(-234)

-13.3

(-15.6)

62.7

(72.8)

TAGGTTATAA

-65.1

(-67.7)

-188

(-194)

-7.0

(-7.7)

39.1

(42.4)

ACGTATTATGC

-78.9

(-81.1)

-221

(-226)

-10.4

(-11.2)

53.4

(55.8)

ATTGGATACAAA

-76.2

(-86.7)

-213

(-243)

-10.3

(-11.4)

53.2

(55.3)

ACATTATTATTACA

-89.9

(-95.2)

-254

(-269)

-11.3

(-12.0)

53.6

(55.6)

GCGCGCd

-59.6

(-54.5)

-163

(-148)

-9.2

(-8.7)

56.2

(55.4)

CAAAAAGd

-49.0

(-46.2)

-144

(-134)

-4.4

(-4.6)

23.9

(24.8)

CGTCGACGd

-64.1

(-71.2)

-175

(-195)

-9.8

(-10.6)

58.3

(60.0)

GAAGCTTCd

-57.4

(-56.7)

-163

(-160)

-6.7

(-6.9)

42.9

(44.1)

GGAATTCCd

-58.3

(-60.4)

-164

(-173)

-7.4

(-6.7)

46.6

(42.3)

GGATATCCd

-54.5

(-58.5)

-158

(-170)

-5.5

(-6.1)

36.2

(38.8)

CAAAAAAAGd

-68.0

(-62.2)

-196

(-178)

-7.3

(-7.0)

40.3

(39.6)

CAAACAAAGd

-64.5

(-63.8)

-182

(-181)

-7.9

(-7.8)

43.8

(43.4)

CAAAGAAAGd

-62.8

(-61.6)

-179

(-174)

-7.3

(-7.6)

40.8

(42.8)

CAAATAAAGd

-58.6

(-58.4)

-168

(-168)

-6.5

(-6.4)

36.8

(36.4)

GCGAATTCGCd

-80.0

(-83.2)

-216

(-227)

-12.9

(-12.7)

67.8

(65.7)

CGCGTACGCGTACGCGd

-158.0

(-152.5)

-416

(-402)

-29.1

(-27.7)

91.0

(89.3)

CACAGe

-33.7

(-31.8)

-97

(-93)

-3.6

(-3.0)

12.1

(5.9)

CAACCAACCAACf

-104.0

(-98.0)

-291

(-271)

-14.1

(-14.0)

61.2

(62.4)

CTTCCTTCCTTCf

-92.3

(-91.4)

-252

(-251)

-14.1

(-13.4)

65.0

(62.6)

^aAll experiments were conducted in a buffer containing 1 M NaCl, 10 mM Na2HPO4 , 1 mM Na2EDTA, pH 7.0. Estimated errors in DH5, DS5, DG537, and Tm are +4%, +4%, +8% and +2%, respectively. The values in parentheses are predicted with our parameters. These predicted values agree with the measured ones within average errors of 6.1% for DH5, 6.8% for DS5, 4.8% for DG537 and 5.7% for Tm.
^bThe DNA duplex consists of the denoted DNA strand and its complementary DNA strand.
^cMelting temperatures are calculated at the total oligomer strand concentration of 100 mM.
^dData from Breslauer et al. (1).
^eData from Hall et al. (10).
^fData from Ratmeyer et al. (17).

This Article

Abstract

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DNA sequence^b	Tm^-1 versus log Ct plot
	[Delta]H°	[Delta]S°	[Delta]^G°37	Tm^-1
	kcal/mol	cal/mol/K	kcal/mol	°C
AGCCG	-37.6	-103	-5.8	31.2
ACCGCA	-42.0	-113	-7.0	40.4
ATGCGC	-49.5	-136	-7.2	41.3
CGGTGC	-55.4	-156	-7.1	40.1
CGTGCC	-46.5	-127	-7.0	40.5
TGCGCA	-42.1	-113	-7.0	46.8
AATACCG	-44.5	-125	-5.7	31.7
AGCCGTG	-50.7	-136	-8.5	49.9
AGCTTCA	-43.1	-119	-6.2	34.8
GGACTTA	-50.0	-144	-5.3	30.0
AAAAAAAA	-47.3	-137	-5.0	27.3
AAGCGTAG	-57.4	-159	-8.2	46.1
AATCCAGT	-52.4	-147	-6.8	38.8
ACATATGT	-50.4	-145	-5.6	36.1
ACCTAGTC	-65.6	-190	-6.8	38.1
ACGACCTC	-60.7	-168	-8.6	48.1
AGAGAGAG	-48.2	-131	-7.5	43.2
AGCGTAAG	-62.6	-177	-7.8	43.6
AGTCCTGA	-55.5	-154	-7.8	44.2
ATGCGCAT	-64.0	-177	-9.1	54.9
CACGGCTC	-67.0	-183	-10.3	55.5
CCATATGG	-67.5	-195	-7.1	43.5
CGATATCG	-63.2	-181	-7.1	44.0
CGCGTATA	-56.3	-155	-8.2	46.5
CGCTGTAA	-62.0	-173	-8.2	45.4
CTAGTGGA	-60.3	-170	-7.6	42.5
CTCACGGC	-69.6	-192	-10.2	54.1
CTGAGTCC	-57.8	-161	-8.0	45.0
GAATATTC	-60.1	-180	-4.3	30.1
GACTAGTC	-56.9	-162	-6.6	41.9
GAGTACTC	-57.1	-166	-5.8	37.5
GATTAATC	-58.8	-176	-4.3	29.8
GCATATGC	-55.7	-155	-7.6	48.3
GCCAGTTA	-58.4	-162	-8.4	47.1
GGTGCCAA	-63.7	-176	-9.1	50.3
GTCGAACA	-60.6	-168	-8.6	47.9
GTCTAGAC	-57.0	-163	-6.4	41.2
TAGGCCTA	-55.1	-152	-8.0	50.6
TATGCATA	-48.3	-136	-6.1	39.5
AAAAAAAAA	-62.3	-180	-6.3	36.0
ATAACTGGC	-58.3	-159	-9.0	50.8
ATCTATCCG	-69.0	-194	-8.9	47.8
CGCTGTTAC	-79.9	-225	-10.2	51.9
GCCAGTTAA	-69.8	-197	-8.7	47.1
AAAAAAAAAA	-80.9	-239	-6.7	41.8
CGGCAAGCGC	-85.0	-231	-13.4	62.2
TAGGTTATAA	-65.7	-189	-7.1	39.8
ACGTATTATGC	-76.8	-214	-10.4	53.8
ATTGGATACAAA	-74.6	-207	-10.4	54.1
ACATTATTATTACA	-87.4	-246	-11.1	54.3

DNA sequence^b	Average of curve fits
	[Delta]H°	[Delta]S°	^[Delta]G°37	Tm^c
	kcal/mol	cal/mol/K	kcal/mol	°C
AGCCG	-40.3	-113	-5.3	27.5
ACCGCA	-44.1	-122	-6.4	35.1
ATGCGC	-47.8	-135	-7.4	33.7
CGGTGC	-57.9	-163	-7.3	41.4
CGTGCC	-46.1	-127	-6.8	38.2
TGCGCA	-42.8	-116	-6.8	45.5
AATACCG	-46.3	-130	-6.1	33.4
AGCCGTG	-52.6	-143	-8.4	47.5
AGCTTCA	-45.3	-127	-5.9	32.8
GGACTTA	-51.4	-147	-5.8	32.7
AAAAAAAA	-45.3	-130	-5.1	26.7
AAGCGTAG	-53.4	-147	-7.8	44.6
AATCCAGT	-52.3	-145	-6.7	41.8
ACATATGT	-50.0	-143	-5.7	36.8
ACCTAGTC	-65.6	-191	-6.2	36.2
ACGACCTC	-58.8	-161	-8.8	49.8
AGAGAGAG	-46.1	-125	-7.3	42.5
AGCGTAAG	-58.8	-165	-7.8	42.9
AGTCCTGA	-53.7	-150	-7.1	40.8
ATGCGCAT	-59.9	-164	-8.8	55.4
CACGGCTC	-62.4	-170	-9.7	53.5
CCATATGG	-64.7	-188	-6.4	40.5
CGATATCG	-62.2	-177	-7.4	46.0
CGCGTATA	-61.3	-170	-8.6	47.7
CGCTGTAA	-58.5	-164	-7.6	43.0
CTAGTGGA	-62.5	-178	-7.3	40.8
CTCACGGC	-65.7	-182	-9.3	50.4
CTGAGTCC	-62.8	-177	-7.9	43.9
GAATATTC	-55.2	-164	-4.3	29.6
GACTAGTC	-54.2	-153	-6.6	43.3
GAGTACTC	-58.1	-169	-5.7	37.0
GATTAATC	-56.1	-167	-4.3	29.6
GCATATGC	-55.8	-154	-8.0	50.7
GCCAGTTA	-59.3	-166	-8.0	43.9
GGTGCCAA	-67.4	-189	-8.8	47.7
GTCGAACA	-64.6	-182	-8.0	45.0
GTCTAGAC	-57.7	-165	-6.5	41.6
TAGGCCTA	-54.2	-148	-8.3	52.8
TATGCATA	-48.9	-139	-5.6	37.7
AAAAAAAAA	-57.2	-165	-6.1	34.3
ATAACTGGC	-62.2	-172	-8.9	49.0
ATCTATCCG	-64.8	-182	-8.4	46.0
CGCTGTTAC	-73.5	-206	-9.5	50.6
GCCAGTTAA	-65.1	-181	-8.9	49.0
AAAAAAAAAA	-75.6	-222	-6.7	37.9
CGGCAAGCGC	-86.1	-235	-13.2	63.1
TAGGTTATAA	-64.5	-186	-6.8	38.4
ACGTATTATGC	-80.9	-227	-10.4	53.0
ATTGGATACAAA	-77.8	-218	-10.2	52.3
ACATTATTATTACA	-92.3	-262	-11.4	52.9

Nucleic Acids Research