Table 1 Biophysical properties and structural-thermodynamic parameters of the top 5 shortlisted SiRNA candidates via sidirect targeting GPR10 mRNA. Abbreviations: Tm — melting temperature; Cp — constant pressure; Conc — concentration; ΔG — Gibbs free energy; GC — guanine-cytosine content.

From: Molecular dynamics simulations based siRNA design against GPR10 reveals stable RNAi therapeutics for hormone-dependent uterine fibroids

siRNA name

mRNA target position

mRNA target sequence (5’→3’)

siRNA guide strand (5’→3’)

siRNA passenger strand (5’→3’)

Seed-Duplex Stability

GC % content

Tm

(Conc)

Tm(Cp)

Thermodynamic Constant ΔG (kcal/mol)

Free Energy of Binding (kcal/mol)

Free Energy of Folding (kcal/mol)

siRNA Efficacy (%)

Guide Tm (°C)

Passenger Tm(°C)

siRNA3

1514–1536

GCCCTTGAAGGACAAACAAAACT

UUUUGUUUGUCCUUCAAGGGC

CCUUGAAGGACAAACAAAACU

5.6

16.6

43%

88.6 °C

89.8 °C

−26.1

−35.2

2

93.2486

siRNA6

1861–1883

CACCTACAAGCTCCCTTTAGAAA

UCUAAAGGGAGCUUGUAGGUG

CCUACAAGCUCCCUUUAGAAA

15.8

16.4

48%

90.9 °C

92.1 °C

−25.9

−38.7

1.7

91.0699

siRNA8

2031–2053

CTGTGTATGTGTGTTTGTGTATG

UACACAAACACACAUACACAG

GUGUAUGUGUGUUUGUGUAUG

19.3

20.4

38%

84.9 °C

86.1 °C

−24

−33.7

1.9

93.4435

siRNA10

2308–2330

CCCACATGATGTGTAGATCAAAC

UUGAUCUACACAUCAUGUGGG

CACAUGAUGUGUAGAUCAAAC

21.4

20.5

43%

86.7 °C

87.8 °C

−24.7

−36.8

1.8

95.2393

siRNA12

3722–3744

CCGAATGAAGCTTTAGTTGTACC

UACAACUAAAGCUUCAUUCGG

GAAUGAAGCUUUAGUUGUACC

19

12

38%

82.9 °C

84.2 °C

−24.8

−32.9

1.8

96.1845

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