Spreadsheet: 4b577294-8686-4e03-b150-5411df647c4a
Sheet: Sheet1

Table S1 List of dinucleotide/trinucleotide DNA structural scales and their corresponding parameters | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5
Property Name | Reference | PubMedID | Type | Dimension | Comments
DNA denaturation | Statistical mechanical simulation of polymeric DNA melting with MELTSIM | 10366657 | thermodynamic | cal/mol | Dinucleotides with a low value are more likely to denaturate than dinucleotides with a higher value
Duplex Disrupt Energy | Predicting DNA duplex stability from the base sequence | 3459152 | thermodynamic | kcal | Dinucleotides with a high disrupt energy value will be more stable than dinucleotides with a lower energy value
Duplex Free Energy | Improved Thermodynamic Parameters and Helix Initiation Factor to Predict Stability of DNA Duplexes | 8948641 | thermodynamic | kcal/mol | Dinucleotides with a low free energy content will be more stable than dinucleotides with high free energy content
Stacking Energy | An optimized potential function for the calculation of nucleic acid interaction energies: base stacking | DOI: 10.1002/bip.1978.360171005 | thermodynamic | kcal | High values in base stacking reflect dinucleotides of the helix that de-stack or melt more easily; conversely a minimal value would represent more stable dinucleotides
Enthalpy | Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes.   Nucleic Acids Research (1996) 24 Nr. 22, 4501-4505 | 8948641 | thermodynamic | kcal/mol | Values given in the paper (delta H). Low values correspond to strong DNA stability.
Entropy | Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes.   Nucleic Acids Research (1996) 24 Nr. 22, 4501-4505 | 8948641 | thermodynamic | cal/mol/K | Values are given in the paper (delta S).Low values correspond to strong DNA stability.
Melting Temperature | From the sequence to the superstructural properties of DNAs.  Biophysical Chemistry (2002) 95, 23-47 | 11880171 | thermodynamic | others | Normalized melting temperatures of O. Gotoh and [NAME] (1981), Biopolymers, 20, 1033-1042
Twist (free DNA) | The relative flexibility of B-DNA and A-RNA duplexes: database analysis.   Nucleic Acids Research (2004) 32 No. 20 | 15562006 | conformational | degree | Values are given in the supplementary. See figure 1 in Satoshi Fujii et al.(2007) Nucleic Acids Research, 35, 6063–6074 for definition
Tilt (free DNA) | The relative flexibility of B-DNA and A-RNA duplexes: database analysis.   Nucleic Acids Research (2004) 32 No. 20 | 15562006 | conformational | degree | Values are given in the supplementary. See figure 1 in Satoshi Fujii et al.(2007) Nucleic Acids Research, 35, 6063–6075 for definition
Roll (free DNA) | The relative flexibility of B-DNA and A-RNA duplexes: database analysis.   Nucleic Acids Research (2004) 32 No. 20 | 15562006 | conformational | degree | Values are given in the supplementary. See figure 1 in Satoshi Fujii et al.(2007) Nucleic Acids Research, 35, 6063–6076 for definition
Shift (free DNA) | The relative flexibility of B-DNA and A-RNA duplexes: database analysis.   Nucleic Acids Research (2004) 32 No. 20 | 15562006 | conformational | angstroem | Values are given in the supplementary. See figure 1 in Satoshi Fujii et al.(2007) Nucleic Acids Research, 35, 6063–6077 for definition
Slide (free DNA) | The relative flexibility of B-DNA and A-RNA duplexes: database analysis.   Nucleic Acids Research (2004) 32 No. 20 | 15562006 | conformational | angstroem | Values are given in the supplementary. See figure 1 in Satoshi Fujii et al.(2007) Nucleic Acids Research, 35, 6063–6078 for definition
Rise (free DNA) | The relative flexibility of B-DNA and A-RNA duplexes: database analysis.   Nucleic Acids Research (2004) 32 No. 20 | 15562006 | conformational | angstroem | Values are given in the supplementary. See figure 1 in Satoshi Fujii et al.(2007) Nucleic Acids Research, 35, 6063–6079 for definition
Roll (DNA-protein complex) | Role of base-backbone and base-base interactions in alternating DNA conformations   FEBS Letters (1996) 379, 148-152 | 8635581 | conformational | degree | Values are in the Paper under COMPLEX. See figure 1 in Satoshi Fujii et al.(2007) Nucleic Acids Research, 35, 6063–6074 for definition
Twist (DNA-protein complex) | Role of base-backbone and base-base interactions in alternating DNA conformations   FEBS Letters (1996) 379, 148-152 | 8635581 | conformational | degree | Values are in the Paper under COMPLEX. See figure 1 in Satoshi Fujii et al.(2007) Nucleic Acids Research, 35, 6063–6075 for definition
Tilt (DNA-protein complex) | Role of base-backbone and base-base interactions in alternating DNA conformations   FEBS Letters (1996) 379, 148-152 | 8635581 | conformational | degree | Values are in the Paper under COMPLEX. See figure 1 in Satoshi Fujii et al.(2007) Nucleic Acids Research, 35, 6063–6076 for definition
Slide (DNA-protein complex) | Role of base-backbone and base-base interactions in alternating DNA conformations   FEBS Letters (1996) 379, 148-152 | 8635581 | conformational | angstroem | Values are in the Paper under COMPLEX. See figure 1 in Satoshi Fujii et al.(2007) Nucleic Acids Research, 35, 6063–6077 for definition
Shift (DNA-protein complex) | Role of base-backbone and base-base interactions in alternating DNA conformations   FEBS Letters (1996) 379, 148-152 | 8635581 | conformational | angstroem | Values are in the Paper under COMPLEX. See figure 1 in Satoshi Fujii et al.(2007) Nucleic Acids Research, 35, 6063–6078 for definition
Rise (DNA-protein complex) | Role of base-backbone and base-base interactions in alternating DNA conformations   FEBS Letters (1996) 379, 148-152 | 8635581 | conformational | angstroem | Values are in the Paper under COMPLEX. See figure 1 in Satoshi Fujii et al.(2007) Nucleic Acids Research, 35, 6063–6079 for definition
Wedge | CURVATURE: software for the analysis of curved DNA   Bioinformatics (1993) 9 Nr. 4, 435-440 | 8402210 | conformational | degree | Data taken from Bolshoy et al.: PNAS (1991) 88, 2312-2316
Tip | Combining structural analysis of DNA with search routines for the detection of transcription regulatory elements.   Comput. Appl. Biosci. (1996)12 Nr. 5, 441-446 | 8996793 | conformational | degree | Values are not listed in the article but referenced to a file that cant be accessed any more. Values taken from PROPERTY DB.  Calculated by [NAME], and averaged by Ponomarenko
DNA Bending stiffness | Translational Positioning of Nucleosomes on DNA The Role of Sequence-dependent Isotropic DNA Bending Stiffness | 7723041 | conformational | nm | High values correspond to dinucleotides that will bend more easily , while low values correspond to dinucleotides that are more rigid
Propeller twist | B-DNA Twisting Correlates with Base-pair Morphology | 7897660 | conformational | degree | Dinucleotides with a large negative propeller-twist angle tend to be more rigid than dinucleotides with low negative propeller-twist angle.
Protein Induced Deformability | DNA sequence-dependent deformability deduced from protein–DNA crystal complexes | 9736707 | conformational | others | a larger value reflects a more deformable sequence while a smaller value indicates a region where the DNA helix is less likely to be changed dramatically by proteins
Bendability | Trinucleotide models for DNA bending propensity: comparison of models based on DNaseI digestion and nucleosome packaging data | 8579790 | conformational |  | The trinucleotide bendability model is based on Dnase I cutting frequencies. The enzyme Dnase I preferably binds to the minor groove and cuts DNA that is bent, or bendable toward the major groove. Thus Dnase I cutting frequencies on naked DNA can be interpreted as a quantitative measure of major groove compressibility or bendability. DNA regions with a high peak correspond to regions that are more flexible than regions with a low peak value
Nucleosome Position Preference | Sequence periodicities in chicken nucleosome core DNA | 3806678 | conformational |  | NPP is a trinucleotide model based on the preferential location of sequences within a nucleosomal core. The study was performed on sequences wrapped around nucleosome cores and in closed circles of DNA. They calculated the fractional preference of each base pair triplet for a position facing out. High value peaks represent regions where nucleosomes are more likely to appear.
Major [NAME] | Combining structural analysis of DNA with search routines for the detection of transcription regulatory elements.   Comput. Appl. Biosci. (1996)12 Nr. 5, 441-446 | 8996793 | conformational | angstroem | Values are not listed in the article but referenced to a file that cant be accessed any more. Values taken from PROPERTY DB.
Major Groove Depth | Combining structural analysis of DNA with search routines for the detection of transcription regulatory elements.   Comput. Appl. Biosci. (1996)12 Nr. 5, 441-446 | 8996793 | conformational | angstroem | Values are not listed in the article but referenced to a file that cant be accessed any more. Values taken from PROPERTY DB.
Minor Groove Width | Combining structural analysis of DNA with search routines for the detection of transcription regulatory elements.   Comput. Appl. Biosci. (1996)12 Nr. 5, 441-446 | 8996793 | conformational | angstroem | Values are not listed in the article but referenced to a file that cant be accessed any more. Values taken from PROPERTY DB.
Minor Groove Depth | Combining structural analysis of DNA with search routines for the detection of transcription regulatory elements.   Comput. Appl. Biosci. (1996)12 Nr. 5, 441-446 | 8996793 | conformational | angstroem | Values are not listed in the article but referenced to a file that cant be accessed any more. Values taken from PROPERTY DB.
Major Groove Size | B-DNA Twisting Correlates with Base-pair Morphology   [NAME]. Biol. (1995) 247, 34-48 | 7897660 | conformational | angstroem
Major Groove Distance | B-DNA Twisting Correlates with Base-pair Morphology   [NAME]. Biol. (1995) 247, 34-48 | 7897660 | conformational | angstroem
Minor Groove Size | B-DNA Twisting Correlates with Base-pair Morphology   [NAME]. Biol. (1995) 247, 34-48 | 7897660 | conformational | angstroem
Minor Groove Distance | B-DNA Twisting Correlates with Base-pair Morphology   [NAME]. Biol. (1995) 247, 34-48 | 7897660 | conformational | angstroem
hydroxyl radical cleavage pattern | Construction of a genome-scale structural map at single-nucleotide resolution | 17568010 | conformational |  | The hydroxyl radical cleavage pattern is a measure of the local variation in solvent-accessible surface area of duplex DNA, and thus provides information on the local shape and structure of DNA.It is a reflection of an important structural parameter, the solvent-accessible surface area of the DNA backbone. The cleavage pattern thus provides an image of the shape of the DNA backbone and how it varies with respect to nucleotide sequence.