Contributions of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp, XCCGGp, XGGCCYp, and XCCGGYp helixes.

The role of stacking in terminal base-pair formation was studied by comparison of the stability increments for dangling ends to those for fully formed base pairs. Thermodynamic parameters were measured spectrophotometrically for helix formation of the hexanucleotides AGGCCUp, UGGCCAp, CGGCCGp, GCCGGCp, and UCCGGAp and for the corresponding pentanucleotides containing a 5'-dangling end on the GGCCp or CCGGp core helix. In 1 M NaCl at 1 X 10(-4) M strands, a 5'-dangling nucleotide in this series increases the duplex melting temperature (Tm) only 0-4 degrees C, about the same as adding a 5'-phosphate. In contrast, a 3'-dangling nucleotide increases the Tm at 1 X 10(-4) M strands 7-23 degrees C, depending on the sequence [Freier, S. M., Burger, B. J., Alkema, D., Neilson, T., & Turner, D. H. (1983) Biochemistry 22, 6198-6206]. These results are consistent with stacking patterns observed in A-form RNA. The stability increments from terminal A.U, C.G, or U.A base pairs on GGCC or a terminal U.A pair on CCGG are nearly equal to the sums of the stability increments from the corresponding dangling ends. This suggests stacking plays a large role in nucleic acid stability. The stability increment from the terminal base pairs in GCCGGCp, however, is about 5 times the sum of the corresponding dangling ends, suggesting hydrogen bonding can also make important contributions.

[1]  D. Turner,et al.  Solvent effects on the stability of A7U7p. , 1985, Biochemistry.

[2]  G. A. van der Marel,et al.  Proton NMR study and conformational analysis of d(CGT), d(TCG) and d(CGTCG) in aqueous solution. The effect of a dangling thymidine and of a thymidine mismatch on DNA mini-duplexes. , 1984, Nucleic acids research.

[3]  T. Neilson,et al.  Relative stability of guanosine-cytidine diribonucleotide cores: a 1H NMR assessment. , 1984, Biochemistry.

[4]  D. Turner,et al.  Thermodynamic studies of RNA stability. , 1984, Journal of biomolecular structure & dynamics.

[5]  Douglas H. Turner,et al.  Effects of 3' dangling end stacking on the stability of GGCC and CCGG double helixes , 1983 .

[6]  Richard E. Dickerson,et al.  The DNA Helix and How it is Read , 1983 .

[7]  D. Turner,et al.  Solvent effects on the dynamics of (dG‐dC)3 , 1983, Biopolymers.

[8]  D. Turner,et al.  Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. , 1983, Biochemistry.

[9]  T. Neilson,et al.  Effects of flanking G . C base pairs on internal Watson-Crick, G . U, and nonbonded base pairs within a short ribonucleic acid duplex. , 1982, Biochemistry.

[10]  T. Neilson,et al.  TRIPLET GPCPA FORMS A STABLE RNA DUPLEX , 1981 .

[11]  D. Turner,et al.  Solvent effects on the kinetics and thermodynamics of stacking in poly(cytidylic acid). , 1981, Biochemistry.

[12]  D. Turner,et al.  Laser temperature-jump study of stacking in adenylic acid polymers. , 1979, Biochemistry.

[13]  P. Privalov,et al.  Thermodynamics of base interaction in (A)n and (A.U)n. , 1978, Journal of molecular biology.

[14]  T. Neilson,et al.  Stabilizing effect of dangling bases on a short RNA double helix as determined by proton nuclear magnetic resonance spectroscopy , 1978 .

[15]  O. Uhlenbeck,et al.  Enzymatic oligoribonucleotide synthesis with T4 RNA ligase. , 1978, Biochemistry.

[16]  O. Uhlenbeck,et al.  Polynucleotide kinase from a T4 mutant which lacks the 3' phosphatase activity. , 1978, Nucleic acids research.

[17]  M Levitt,et al.  How many base-pairs per turn does DNA have in solution and in chromatin? Some theoretical calculations. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[18]  E. Freire,et al.  Calorimetric determination of the heat capacity changes associated with the conformational transitions of polyriboadenylic acid and polyribouridylic acid , 1977, Biopolymers.

[19]  O. Uhlenbeck,et al.  3'-Phosphatase activity in T4 polynucleotide kinase. , 1977, Biochemistry.

[20]  T. Neilson,et al.  Oligoribonucleotide synthesis. X. An improved synthesis of the anticodon loop region of methionine transfer ribonucleic acid from E. coli , 1976 .

[21]  T. Neilson,et al.  Oligoribonucleotide synthesis. IX. Synthesis of sequences corresponding to the dihydrouridine loop neck region common in several transfer RNA molecules , 1976 .

[22]  I. Tinoco,et al.  Stability of ribonucleic acid double-stranded helices. , 1974, Journal of molecular biology.

[23]  J. Sturtevant,et al.  Heats of thermally induced helix–coil transitions of DNA in aqueous solution , 1973, Biopolymers.

[24]  P. Doty,et al.  Self-complementary oligoribonucleotides: adenylic acid-uridylic acid block copolymers. , 1971, Journal of molecular biology.

[25]  T. Ackermann,et al.  Experimental thermodynamics of the helix–random coil transition. III. Determination of the transition enthalpies of the helical complexes poly(I + C) and poly I in solution , 1970, Biopolymers.

[26]  E. Neumann,et al.  Thermodynamic investigation of the helix-coil transitions of a polyribonucleotide system , 1969 .

[27]  J. Sturtevant,et al.  Heats of the helix–coil transitions of the poly A–poly U complexes , 1968, Biopolymers.

[28]  P. Ross,et al.  Heat of the reaction forming the three‐stranded poly (A + 2U) complex , 1965, Biopolymers.

[29]  J. Sturtevant,et al.  The Heat of the Reaction between Polyriboadenylic Acid and Polyribouridylic Acid , 1963 .

[30]  H. C. Longuet-Higgins,et al.  Calculation of the rate of uncoiling of the DNA molecule , 1960 .

[31]  V. Cofman.  Biophysical chemistry. Part II , 1929 .

[32]  S. Shaner,et al.  Double helical DNA: conformations, physical properties, and interactions with ligands. , 1981, Annual review of biochemistry.

[33]  D M Crothers,et al.  Transient electric dichroism of rod-like DNA molecules. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[34]  O. C. Uhlenbeck,et al.  Equimolar addition of oligoribonucleotides with T4 RNA ligase , 1977, Nucleic Acids Res..

[35]  M. Sundaralingam,et al.  Structure and conformation of nucleic acids and protein-nucleic acid interactions , 1975 .

[36]  S. Izawa,et al.  [3] Hydrogen ion buffers , 1972 .