Polyadenylate polyuridylate helices with non-Watson-Crick hydrogen bonding

Ishikawa, Fumiyoshi; Frazier, Joe; Howard, Frank B.; Miles, H. Todd

doi:10.1016/0022-2836(72)90554-2

Cited by 31 publications

(18 citation statements)

References 17 publications

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“…Spectroscopic (884)(885)(886) as well as X-ray fiber diffraction methods (887) have been employed to derive the physical and structural characteristics of duplexes containing 2-substituted poly(A). These duplexes are thermodynamically less stable than their poly(A) analogs.…”

Section: A Double Helix With Parallel Chains and Hoogsteen Base-pairsmentioning

confidence: 99%

Principles of Nucleic Acid Structure

Saenger

1984

Springer Advanced Texts in Chemistry

5,967

312

6,279

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Section: A Double Helix With Parallel Chains and Hoogsteen Base-pairsmentioning

confidence: 99%

Principles of Nucleic Acid Structure

Saenger

1984

Springer Advanced Texts in Chemistry

5,967

312

6,279

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“…Models of the various hairpins optimized with force field calculations are described. mental evidence and model calculations support the existence of parallel stranded double helices stabilized by (i) hemiprotonation of C, as in the CpA-proflavin complex (4), and d(C-T)3 (5); (ii) protonation of poly(A) (6); and (iii) introduction of bulky substituents (x = dimethylamino, methyl, methylthio) in poly(x2A) poly(U) (7). Triple helices have also been proposed in which two of the strands are demonstrated or presumed to be associated in a parallel orientation stabilized by Hoogsteen base-pairing.…”

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confidence: 88%

Parallel Stranded DNA

Sande

Ramsing

Germann

et al. 1988

Science

231

150

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A series of four hairpin deoxyoligonucleotides was synthesized with a four-nucleotide central loop (either C or G) flanked by the complementary sequences d(T)10 and d(A)10. Two of the molecules contain either a 3'-p-3' or 5'-p-5' linkage in the loop, so that the strands in the stem have the same, that is, parallel (ps) polarity. The pair of reference oligonucleotides have normal phosphodiester linkages throughout and antiparallel (aps) stem regions. All the molecules adopt a duplex helical structure in that (i) the electrophoretic mobilities in polyacrylamide gels of the ps and aps oligomers are similar. (ii) The ps hairpins are substrates for T4 polynucleotide kinase, T4 DNA ligase, and Escherichia coli exonuclease III. (iii) Salt-dependent thermal transitions are observed for all hairpins, but the ps molecules denature 10 degrees C lower than the corresponding aps oligomers. (iv) The ultraviolet absorption and circular dichroism spectra are indicative of a base-paired duplex in the stems of the ps hairpins but differ systematically from those of the aps counterparts. (v) The bis-benzimidazole drug Hoechst-33258, which binds in the minor groove of B-DNA, exhibits very little fluorescence in the presence of the ps hairpins but a normal, enhanced emission with the aps oligonucleotides. In contrast, the intercalator ethidium bromide forms a strongly fluorescent complex with all hairpins, the intensity of which is even higher for the ps species. (vi) The pattern of chemical methylation is the same for both the ps and aps hairpins. The combined results are consistent with the prediction from force field analysis of a parallel stranded right-handed helical form of d(A)n.d(T)n with a secondary structure involving reverse Watson-Crick base pairs and a stability not significantly different from that of the B-DNA double helix. Models of the various hairpins optimized with force field calculations are described.

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“…In all the crystals of double-helical nucleic acid fragments studied so far, including the crystals of self-complementary dinucleoside phosphates (32,33) three-stranded complexes as well as in the complexes of poly-U with poly-2-methyladenylic acid (25) or poly-2-dimethylamino-adenylic acid (36), i.e. in the cases when the Watson-Crick pair has already been formed or cannot be formed owing to steric constraints.…”

Section: Calculation Proceduresmentioning

confidence: 99%

Simulation of Interactions between Nucleic Acid Bases by Refined Atom-Atom Potential Functions

Poltev

Shulyupina

1986

Journal of Biomolecular Structure and Dynamics

117

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Energy of interaction between nitrogen bases of nucleic acid has been calculated as a function of parameters determining the mutual position of two bases. Refined atom-atom potential functions are suggested. These functions contain terms proportional to the first (electrostatics), sixth (or tenth for the atoms forming a hydrogen bond) and twelfth (repulsion of all atoms) powers of interatomic distance. Calculations have shown that there are two groups of minima of the base interaction energy. The minima of the first group correspond to coplanar arrangement of the base pairs and hydrogen bond formation. The minima of the second group correspond to the position of bases one above the other in almost parallel planes. There are 28 energy minima corresponding to the formation of coplanar pairs with two (three for the G:C pair) almost linear N-H . . . O and (or) N-H . . . N hydrogen bonds. The position of nitrogen bases paired by two such H-bonds in any crystal of nucleic acid component in polynucleotide complexes and in tRNA is close to the position in one of these minima. Besides, for each pair there are energy minima corresponding to the formation of a single N-H . . . O or N-H . . . N and one C-H . . . O or C-H . . . N hydrogen bond. The form of potential surface in the vicinity of minima has been characterized. The results of calculations agree with the experimental data and with more rigorous calculations based on quantum-mechanical approach.

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Polyadenylate polyuridylate helices with non-Watson-Crick hydrogen bonding

Cited by 31 publications

References 17 publications

Principles of Nucleic Acid Structure

Principles of Nucleic Acid Structure

Parallel Stranded DNA

Simulation of Interactions between Nucleic Acid Bases by Refined Atom-Atom Potential Functions

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