Allawi, H. T., & SantaLucia, J. Jr. (1997). Thermodynamics and NMR of internal G.T mismatches in DNA. Biochemistry, 36(34), 10581-10594.
Allawi, H. T., & SantaLucia, J. Jr. (1998). NMR solution structure of a DNA dodecamer containing single G.T mismatches. Nucleic Acids Res, 26(21), 4925-4934.
Allawi, H. T., & SantaLucia, J. Jr. (1998). Nearest-neighbor thermodynamics of internal A.C mismatches in DNA: sequence dependence and pH effects. Biochemistry, 37(26), 9435-9444.
Allawi, H. T., & SantaLucia, J. Jr. (1998). Thermodynamics of internal C.T mismatches in DNA. Nucleic Acids Res, 26(11), 2694-2701.
Allawi, H. T., & SantaLucia, J. Jr. (1998). Nearest neighbor thermodynamic parameters for internal G.A mismatches in DNA. Biochemistry, 37(8), 2170-2179.
Peyret, N., Seneviratne, P. A., Allawi, H. T., & SantaLucia, J. Jr. (1999). Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches. Biochemistry, 38, 3468-3477.
Plum, G. E., Grollman, A. P., Johnson, F., & Breslauer, K. J. (1995). Influence of the oxidatively damaged adduct 8-oxodeoxyguanosine on the conformation, energetics, and thermodynamic stability of a DNA duplex. Biochemistry, 34(49), 16148-16160.
Bolewska, K., Zielenkiewicz, A., & Wierzchowski, K. L. (1984). Deoxydodecanucleotide heteroduplex d(TTTTATAATAAA). d(TTTATTATAAAA) containing the promoter Pribnow sequence TATAAT. I. Double-helix stability by UV spectrophotometry and calorimetry. Nucleic Acids Res, 12(7), 3245-3256.
Breslauer, K. J., Frank, R., Blocker, H., & Marky, L. A. (1986). Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci USA, 83(11), 3746-3750.
Leonard, G. A., Thomson, J., Watson, W. P., & Brown, T. (1990). High-resolution structure of a mutagenic lesion in DNA. Proc Natl Acad Sci USA, 87(24), 9573-9576.
Tibanyenda, N., De Bruin, S. H., Haasnoot, C. A. G., Marel Van Der, G. A., Van Boom, J. H., & Hilbers, C. W. (1984). The effect of single base-pair mismatches on the duplex stability of d(T-A-T-T-A-A-T-A-T-C-A-A-G-T-T-G) . d(C-A-A-C-T-T-GA-T-A-T-T-A-A-T-A). Eur J Biochem, 139, 19-27.
Plum, G. E., Grollman, A. P., Johnson, F., & Breslauer, K. J. (1992). Influence of an exocyclic guanine adduct on the thermal stability, conformation, and melting thermodynamics of a DNA duplex. Biochemistry, 31(48), 12096-12102.
Arnold, F. H., Wolk, S., Cruz, P., & Tinoco, I. Jr. (1987). Structure, dynamics, and thermodynamics of mismatched DNA oligonucleotide duplexes d(CCCAGGG)2 and d(CCCTGGG)2. Biochemistry, 26(13), 4068-4075.
Ratmeyer, L., Vinayak, R., Zhong, Y. Y., Zon, G., & Wilson, W. D. (1994). Sequence specific thermodynamic and structural properties for DNA.RNA duplexes. Biochemistry, 33(17), 5298-5304.
Williams, A. P., Longfellow, C. E., Freier, S. M., Kierzek, R., & Turner, D. H. (1989). Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC. Biochemistry, 28(10), 4283-4291.
Sugimoto, N., Honda, K., & Sasaki, M. (1994). Application of the thermodynamic parameters of DNA stability prediction to double-helix formation of deoxyribooligonucleotides. Nucleosides & Nucleotides, 13, 1311-1317.
Wu, P., Nakano, S., & Sugimoto, N. (2002). Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation. Eur J Biochem, 269(12), 2821-2830.
Hall, K. B., & McLaughlin, L. W. (1991). Thermodynamic and structural properties of pentamer DNA.DNA, RNA.RNA, and DNA.RNA duplexes of identical sequence. Biochemistry, 30(44), 10606-10613.
Sugimoto, N., Nakano, S., Yoneyama, M., & Honda, K. (1996). Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res, 24(22), 4501-4505.
Bommarito, S., Peyret, N., & SantaLucia, J. Jr. (2000). Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res, 28(9), 1929-1934.
Senior, M., Jones, R. A., & Breslauer, K. J. (1988). Influence of dangling thymidine residues on the stability and structure of two DNA duplexes. Biochemistry, 27(10), 3879-3885.
Aboul-ela, F., Koh, D., Tinoco, I. Jr., & Martin, F. H. (1985). Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A, C, G,T). Nucleic Acids Res, 13(13), 4811-4824.
Riccelli, P. V., Hilario, J., Gallo, F. J., Young, A. P., & Benight, A. S. (1996). DNA and RNA oligomer sequences from the 3’ noncoding region of the chicken glutamine synthetase gene from intramolecular hairpins. Biochemistry, 35(48), 15364-15372.
Rentzeperis, D., Alessi, K., & Marky, L. A. (1993). Thermodynamics of DNA hairpins:contribution of loop size to hairpin stability and ethidium binding. Nucleic Acids Res, 21(11), 2683-2689.
Vallone, P. M., Paner, T. M., Hilario, J., Lane, M. J., Faldasz, B. D., & Benight, A. S. (1999). Melting studies of short DNA hairpins: influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability. Biopolymers, 50(4), 425-442.
Hilbers, C. W., Haasnoot, C. A., de Bruin, S. H., Joordens, J. J., Marel van der, G. A., & van Boom, J. H. (1985). Hairpin formation in synthetic oligonucleotides. Biochimie, 67(7-8), 685-695.
Antao, V. P., & Tinoco, I. Jr. (1992). Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. Nucleic Acids Res, 20, 819-824.
Antao, V. P., Lai, S. Y., & Tinoco, I. Jr. (1991). A thermodynamic study of unusually stable RNA and DNA hairpins. Nucleic Acids Res, 19, 5901-5905.
Moody, E. M., & Bevilacqua, P. C. (2003). Thermodynamic coupling of the loop and stem in unusually stable DNA hairpins closed by CG base pairs. J Am Chem Soc, 125(8), 2032-2033.
Nakano, M., Moody, E. M., Liang, J., & Bevilacqua, P. C. (2002). Selection for thermodynamically stable DNA tetraloops using temperature gradient gel electrophoresis reveals four motifs: d(cGNNAg), d(cGNABg), d(cCNNGg), and d(gCNNGc). Biochemistry, 41(48), 14281-14292.
LeBlanc, D. A., & Morden, K. M. (1991). Thermodynamic characterization of deoxyribooligonucleotide duplexes containing bulges. Biochemistry, 30(16), 4042-4047.
Morden, K. M., Chu, Y. G., Martin, F. H., & Tinoco, I. Jr. (1983). Unpaired cytosine in the deoxynucleotide duplex dCA3CA3G.dCT6G is outside of the helix. Biochemistry, 22, 5557-5563.
Li, Y., Zon, G., & Wilson, W. D. (1991). Thermodynamics of DNA duplexes with adjacent G.A mismatches. Biochemistry, 30(30), 7566-7572.
Li, Y., & Agrawal, S. (1995). Oligonucleotides containing G.A pairs: effect of flanking sequences on structure and stability. Biochemistry, 34(31), 10056-10062.
Kadrmas, J. L., Ravin, A. J., & Leontis, N. B. (1995). Relative stabilities of DNA three-way, four-way and five-way junctions (multi-helix junction loops): unpaired nucleotides can be stabilizing or destabilizing. Nucleic Acids Res, 23, 2212-2222.
Leontis, N. B., Kwok, W., & Newman, J. S. (1991). Stability and structure of three-way DNA junctions containing unpaired nucleotides. Nucleic Acids Res, 19, 759-766.
Ladbury, J. E., Sturtevant, J. M., & Leontis, N. B. (1994). The thermodynamics of formation of a three-strand, DNA three-way junction complex. Biochemistry, 33(22), 6828-6833.