plot.it® Server: References
List of references, with brief explanations
1. An ab initio molecular orbital study on the sequence dependency of DNA conformation: an evalution of intra and inter strand stacking interaction energy. M.Aida J. Theor. Biol. 130, 327-335 (1988) Free energy (delta G) of B->A transition, determined by ab initio molecular orbital calculations, expressed as dinucleotide parameters [kcal/mol].
2. NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures. M.Bansal, D.Bhattacharyya, B.Ravi. Comp. Appl. Biosci., V.11, 281-287, 1995 Roll angle of DNA obtained from all the B-form crystal structures in nucleic acid data base (July 1993) expressed as dinucleotide parameters [degrees].
3. NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures. M.Bansal, D.Bhattacharyya, B.Ravi. Comp. Appl. Biosci., V.11, 281-287, 1995 Tilt of DNA obtained from all the B-form crystal structures in nucleic acid data base (July 1993) expressed as dinucleotide parameters [degrees].
4. NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures. M.Bansal, D.Bhattacharyya, B.Ravi. Comp. Appl. Biosci., V.11, 281-287, 1995 Twist of DNA obtained from all the B-form crystal structures in nucleic acid data base (July 1993) expressed as dinucleotide parameters [degrees].
5. Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. A. Bolshoy, P.McNamara, R.Harrington, E.Trifonov. PNAS USA, V.88, 2312-2316, 1991 Roll angle of DNA obtained from gel migration data on synthetic DNA fragments expressed as dinucleotide parameters [degrees]
6. Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. A. Bolshoy, P.McNamara, R.Harrington, E.Trifonov. PNAS USA, V.88, 2312-2316, 1991 Tilt of DNA obtained from gel migration data on synthetic DNA fragments expressed as dinucleotide parameters [degrees]
7. Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. A. Bolshoy, P.McNamara, R.Harrington, E.Trifonov. PNAS USA, V.88, 2312-2316, 1991 Twist of DNA obtained from gel migration data on synthetic DNA fragments expressed as dinucleotide parameters [degrees].
8. Predicting DNA duplex stability from the base sequence. K.Breslauer, R.Frank, H.Bloecker, L.Marky. PNAS USA, V.83, 3746-3750, 1986 Free energy change (delta G) of DNA melting determined from calorimetric studies on DNA expressed as dinucleotide parameters [kcal/mol].
9. Predicting DNA duplex stability from the base sequence. K.Breslauer, R.Frank, H.Bloecker, L.Marky. PNAS USA, V.83, 3746-3750, 1986 Enthalpy change (delta H) of DNA determined from calorimetric studies on DNA expressed as dinucleotide parameters [kcal/mol].
10. Predicting DNA duplex stability from the base sequence. K.Breslauer, R.Frank, H.Bloecker, L.Marky. PNAS USA, V.83, 3746-3750, 1986 Entropy change (delta S) of DNA melting determined from calorimetric studies on DNA expressed as dinucleotide parameters [cal/mol/K].
11. Roll angle (Calladine)
12. Analysis of compositionally biased regions in sequence databases. Wootton JC, Methods Enzymol 266, 554-571 (1996) Sequence complexity calculated for a window, according to J.C. Wootton. [AU]
13. Molecular weight in Daltons
14. Molecular weight in kilograms
15. DNA rigidity (Young's modulus) values based on a sequence dependent anisotropic bending model of DNA and calculated from a consensus of DNAse I digestion and nucleosome positioning, expressed as trinucleotide parameters (Nm*10-8]
16. Correlation of intrinsic DNA curvature with DNA property periodicity A.Gabrielian and S.Pongor. FEBS Letters, 393, 65-68, (1996). Consensus bendability scale designed for detection of AT and GC type curvature propensity, expressed as trinucleotide parameters [arbitrary scale].
17. Anisotropic elastic bending models of DNA M Gromiha, M.Munteanu, A.Gabrielian, and S.Pongor, J. Biol. Phys.22, 227-243 (1996) DNA rigidity (Young's modulus) values based on a sequence dependent anisotropic bending model of DNA and calculated from DNAse I digestion data, expressed as trinucleotide parameters (Nm*10-8]
18. Sequence dependent bending propensity of DNA as revealed by DNAse I: Parameters for trinucleotides I.Brukner, R.Sanchez, D.Suck and S. Pongor EMBO J. 14, 1812-1818. (1995) Bendability of DNA determined from DNAse I digestion experiments expressed as trinucleotide parameters [arbitrary scale].
19. Validity of the nearest-neighbor approximation in the evaluation of the electrophoretic manifestation of DNA curvature. P.De Santis, A.Palleschi, M.Savino, A.Scipioni. Biochemistry, V.29, 9269--9273, 1990 Roll angle of DNA determined from conformational energy calculations expressed as dinucleotide parameters [degrees].
20. Validity of the nearest-neighbor approximation in the evaluation of the electrophoretic manifestation of DNA curvature. P.De Santis, A.Palleschi, M.Savino, A.Scipioni. Biochemistry, V.29, 9269--9273, 1990 Tilt of DNA determined from conformational energy calculations expressed as dinucleotide parameters [degrees].
21. Validity of the nearest-neighbor approximation in the evaluation of the electrophoretic manifestation of DNA curvature. P.De Santis, A.Palleschi, M.Savino, A.Scipioni. Biochemistry, V.29, 9269--9273, 1990 Twist of DNA determined from conformational energy calculations expressed as dinucleotide parameters [degrees].
22. Energy of electron interaction
23. B-DNA twisting correlates with base-pair morphology. A.Gorin, V.Zhurkin, W.Olson. J.Mol.Biol., V.247, 34-48, 1995 Roll angle of DNA determined from chemical constitution of base pairs expressed as dinucleotide parameters [degrees].
24. B-DNA twisting correlates with base-pair morphology. A.Gorin, V.Zhurkin, W.Olson. J.Mol.Biol., V.247, 34-48, 1995 Tilt of DNA determined from chemical constitution of base pairs expressed as dinucleotide parameters [degrees].
25. B-DNA twisting correlates with base-pair morphology. A.Gorin, V.Zhurkin, W.Olson. J.Mol.Biol., V.247, 34-48, 1995 Twist of DNA determined from chemical constitution of base pairs expressed as dinucleotide parameters [degrees].
26. Theoretical prediction of base sequence effects in DNA: experimental reactivity of Z-DNA and B-Z transition enthalpies. B.Hartmann, B.Malfoy and R.Lavery. J. Mol. Biol. 207, 433-444 (1989) Transition free energy determined by thermodynamic approach based on a two state statistical model expressed as dinucleotide parameters [kcal/mol]
27. Helix-Coil transition (Breslauer)
28. Decimal code controlling the B to A transition of DNA V.I.Ivanov, D.Yu.Krilov, A.K.Shchyolkina, B.K.Chernov and L.E.Minchenkova J. Biomolecular Structure and Dynamics, 12, a102 (1995) B to A transition free energy (delta G) obtained in water/ trifluoroethanol solution with spectroscopy, expressed as dinucleotde parameters [kcal/mol].
29. B->Z transition (Lisser)
30. DNA rigidity (Young's modulus) values based on a sequence dependent anisotropic bending model of DNA and calculated nucleosome positioning data, expressed as trinucleotide parameters (Nm*10-8]
31. Sequence periodicities in chicken nucleosome core DNA. S.Satchwell, H.Drew, A.Travers. J.Mol.Biol., V.191, 659-675, 1986 Bendability of DNA determined from nucleosome positioning data and Fourier analysis expressed as trinucleotide roll angles [degrees] using an arbitrary scaling to 0 to 10 degrees range.
32. Energy of polar interaction
33. Improved nearest-neighbor parameters for predicting DNAduplex stability. J.SantaLucia, H. Allawi, P.A.Seneviratne. Biochemistry, V.35, 3555-3562, 1996 Free energy change (delta G) of DNA melting determined from UV absorbance and temperature profiles of DNA expressed as dinucleotide parameters [kcal/mol].
34. Improved nearest-neighbor parameters for predicting DNA duplex stability. J.SantaLucia, H. Allawi, P.A.Seneviratne. Biochemistry, V.35, 3555-3562, 1996 Enthalpy change (delta H) of DNA determined from UV absorbance and temperature profiles of DNA expressed as dinucleotide parameters [kcal/mol].
35. Improved nearest-neighbor parameters for predicting DNA duplex stability. J.SantaLucia, H. Allawi, P.A.Seneviratne. Biochemistry, V.35, 3555-3562, 1996 Entropy change (delta S) of DNA melting determined from UV absorbance and temperature profiles of DNA expressed as dinucleotide parameters [eu].
36. Sequence dependence of DNA conformational flexibility. A.Sarai, J.Mazur, R.Nussinov, R.Jernigan. Biochemistry, V.28, 7842-7848, 1989 Flexibility of DNA obtained from conformational energy calculations, expressed as dinucleotide twist, roll and tilt angles [degrees].
37. Stabilities of nearest neighbour doublets in double helical DNA determined by fitting calculated melting profiles to observed profiles O. Gotoh and Y. Takashira Biopolymers 20, 1033-1042 DNA double helix stability determined from melting profiles expressed as dinucleotide parameters [degree C]
38. An optimized potential function for the calculation of nucleic acid interaction energies. I. Base stacking. R.L. Ornstein, R.Rein, D.L. Breen and R.D. MacElroy Biopolymers 17, 2341-2360 Base stacking energy obtained by quantum chemical calculations expressed as dinucleotide parameters [kcal/mol]
39. Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. N.Sugimoto, S. Nakano, M.Yoneyama, K.Honda. Nucl. Acids Res., V.24, 4501-4505, 1996 Free energy (change (delta G) of DNA determined from absorbance measurements in the UV region and melting curves of DNA expressed as dinucleotide parameters [kcal/mol].
40. Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. N.Sugimoto, S. Nakano, M.Yoneyama, K.Honda. Nucl. Acids Res., V.24, 4501-4505, 1996 Enthalpy change (delta H) of DNA determined from absorbance measurements in the UV region and melting curves of DNA expressed as dinucleotide parameters [kcal/mol].
41. Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. N.Sugimoto, S. Nakano, M.Yoneyama, K.Honda. Nucl. Acids Res., V.24, 4501-4505, 1996 Enthropy change (delta S) of DNA melting determined from absorbance measurements in the UV region and melting curves of DNA expressed as dinucleotide parameters [cal/mol/K].
42. Statistical analysis of DNA duplex structural features. N.Uljanov, T.James. Meth. in Enzymology, V.261, 90-115, 1995 Roll angle of DNA characterised by the internal geometry of the two consecutive base pairs determined from NMR data expressed as dinucleotide parameters [degrees].
43. Statistical analysis of DNA duplex structural features. N.Uljanov, T.James. Meth. in Enzymology, V.261, 90-115, 1995 Tilt of DNA characterised by the internal geometry of the two consecutive base pairs determined from NMR data expressed as dinucleotide parameters [degrees].
44. Statistical analysis of DNA duplex structural features. N.Uljanov, T.James. Meth. in Enzymology, V.261, 90-115, 1995 Twist of DNA characterised by the internal geometry of the two consecutive base pairs determined from NMR data expressed as dinucleotide parameters [degrees].
45. Geometry and energetics of DNA basepairs and triplets from first principles quantum molecular relaxations. J.Lewis, O.Sankey. Biophys.J., V.69, 1068-1076, 1995 Watson-Crick interaction energy, determined by quantum chemical calculations, expressed as dinucleotide parameters [kcal/mol].
Andrei Gabrielian, Kristian
Vlahovicek & Sándor Pongor