References and Footnotes
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- Major , F. , Turcotte , M. , Gautheret , D. , Lapalme , G. , Fillion , E. and Cedergren , R. 1991 . Science , 253 : 1255 – 1260 .
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- Hingerty , B. , Brown , R. S. and Jack , A. 1978 . J. Mol. Biol. , 124 : 523 – 534 .
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- Turner , D. H. , Sugimoto , N. and Freie , S. M. 1988 . Ann. Rev. Biophys. Chem. , 17 : 167 – 192 .
- All assigned free energies are for 37 deg C, where A·U (or U·A) pairs flanked by G·C, A·U and G·U pairs have values of −2.0, −1.0 and −0.5 kcal mol−1, respectively. The G·U (or U·G) pairs with an adjacent G·C pair or G·U pair have corresponding free energy values of −1.5 and −0.5 kcal mol−1. The G·C pairs flanked on the 3′ end of that G by G·C (or C·G) pairs or on the 5′ end of that G by a C·G pair have free energies of −3.0 and −2.0kcal mol−1, respectively
- Jaeger , J. A. , Turner , D. H. and Zuker , M. 1989 . Proc. Natl. Acad. Sci. USA , 86 : 7706 – 7710 .
- The base pair mid-point is taken at half the distance along the connection between the two lattice points that represent the pair of O3′-atoms. The minimum allowed distances between base pair mid-points here is 3.77 A and between base pair mid-points and lattice positions of an adjacent pair of nucleotides is 4.35 A The minimum allowed distance between the lattice positions of adjacent pairs that are on opposite strands is 10.65 A
- 1988 . Quanta including CHARMm from Polygen Corporation, Waltham, Mass
- Constraints, corresponding to the secondary structure pairings of the distorted structures shown in Figure 2B, 2E and 2F, were not successfully minimized. However, results are not conclusive, and more extensive manipulation and relaxation of the starting structure, followed by minimization, might have resulted in more stable structures
- The base pair mid-point is taken at half the distance along the connection between the two lattice points, that represent the 03′ atoms of that nucleotide pair. The minimum allowed distance between base pair midpoints is 3.77 and between base pair mid-points and the lattice positions of the other pair is 6.15 A The minimum distance between lattice positions that are on opposite strands is 10.65 A In addition, 4.35 A is the minimum distance between the tertiary base pair mid-points and stem base pair mid-points as well as among tertiary pairs not formed from neighbor or next nearest neighbor bases
- For more than two virtual bonds, the minimum distance for odd and even numbers of virtual bonds are 8.70 and 6.15 A respectively. For one virtual bond the minimum distance is 15.68 A and for two the minimum distance is 16.84 A. Here the limiting distances are actually taken as these minimum distances plus one lattice unit of 6.15 A
- Marky , N. L. and Olson , W. K. 1987 . Biopolymers , 26 : 415 – 438 .
- Guenther , R. H. , Hardin , C. C. , Sierzputowska-Gracz , H. , Dao , V. and Agris , P. F. 1992 . Biochemistry , 31 : 1104 – 11011 .
- Ke , S.-H. and Wartell , R. M. 1993 . Nucleic Acids Res. , 21 : 5137 – 5143 .