Team:SUSTC-Shenzhen-B/algorithm.3

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Algorithm 3

Scoring System 3 is based on the model created by Elena A Lesnik. The score is totally energy based，which includes the free energy change to form stemloop and the energy change to form RNA-DNA duplex. Here the energy of the two parts are both based on Nearest Neighborhood Rules. The minimization of the free energy change of stemloop formation will also give the secondary structure of the stemloop. Compared to d’Aubenton Carafa’s model , the model here considered the free energy of the duplex within the Transcription Elongation Complex[4]. The poly T tail is divided into three parts, including proximal part, distal part and extra part. If there are spacer, it will also be taken into account. [4]

1.Calculation of the Minimum Free Energy Change of Stemloop Formation

The calculation is the same as Scoring System2.

2.Calculation of the Energy Change to Form RNA-DNA duplex

i. Nearest Neighborhood Rules

The energy change of base pair formation is related to its neighborhood. So when calculating energy , the neighborhood should be taken into account.

ii.RNA/DNA Duplex

According to the model created by E.A Lesnik, we divide T tail into three regions, proximal region（5 nt）, distal region（4 nt） and extra region（3 nt）. If the length of T tail ( n ) is less than 12, we will just consider n nucleotides.

We will calculate the free energy change of RNA:DNA hybrid formation of the spacer (if it exists; 0 to 2 nt ) and proximal T region. We also take distal T region and extra T region into account.[4]

iii.Calculation of the Energy Change to Form RNA/DNA duplex

Now there are thermodynamic parameters (based on nearest neighborhood energy rules) [5]for us to calculate the free energy change of RNA:DNA formation. For example, if the sequence is 5’ TTTTCATTGTTA 3’, then the energy change is :

rUUUUCAUUGUUA = initiation energy + rUU +rUU + rUU + rUC + rCA +rAU + rUU + rUG + rGU + rUU + rUA

3.Calculation of Score[4]

Score = deltaG( stemloop ) – [deltaG( spacer ) + deltaG(proximal part)] – 0.5 * deltaG( distal part ) – 0.01 * deltaG( extra part )

Here the 2 to 5 terms are calculated according to RNA/DNA duplex thermodynamic parameters.

[1] J. Mol. Biol. (1990) 216, 835-858 “Prediction of Rho-independent Escherichia coli Transcription Terminators A Statistical Analysis of their RNA Stem-Loop Structures”

[2] Manual of Mfold Version 3.5

[3] http://unafold.math.rpi.edu/lectures/old_RNAfold/node2.html

[4]Nucl. Acids Res.-2001-Lesnik-3583-94 “Prediction of Rho-independent Escherichia coli ”

[5] Biochemistry 1995,34, 1121 1-1 1216 “Thermodynamic Parameters To Predict Stability of RNA-DNA Hybrid Duplexes”