Molecular structure of poly-2-thiouridylic acid, a double helix with non-equivalent polynucleotide chains

Μazumdar, S. Κ.; Saenger, Wolfram; Scheit, K. H.

doi:10.1016/0022-2836(74)90361-1

Cited by 59 publications

(25 citation statements)

References 33 publications

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“…4a) between the S atom at the C(2) position and the N(3) atom ofthe adjacent base in the poly(ms2A) chain. A similar sulfur-nitrogen interaction has been found in the poly(2-thiouridylic acid) duplex (23) and has been shown to have a stabilizing effect on the structure.…”

Section: Methodsmentioning

confidence: 63%

Molecular structure of a double helix that has non-Watson—Crick type base pairing formed by 2-substituted poly(A) and poly(U)

Hakoshima

Fukui

Ikehara

et al. 1981

Proc. Natl. Acad. Sci. U.S.A.

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ABSTRACr X-ray fiber diffraction studies of duplexes formed by 2-substituted poly(A) and poly(U) provide evidence for the existence of a double helical structure of poly(A)-poly(U) held together by Hoogsteen-type base pairing with parallel chain polarity. A variety of observations on duplex structures of polynucleotides have been interpreted by the single base-pairing scheme proposed by Watson and Crick (1) in 1953, and many biological phenomena are analyzed in the context of the molecular structure of the double helix. The precise manner by which guanine pairs with cytosine has been established by numerous experiments, but it is not always clear exactly how adenine pairs with uracil or thymine. Actually, base-pairing schemes other than the Watson-Crick type ( Fig. 1 b- Recently, it has been argued from spectroscopic experiments that a poly(A)-poly(U) duplex having non-Watson-Crick base pairs could be formed by introducing a substituent [e.g., methyl (5), methylthio (6), ethylthio (6), or dimethylamino (7)] group into the C(2) position ( Fig. 1) of the poly(A) to control the geometry ofthe base pairing by sterically blocking one side ofthe adenine ring [i.e., the N(1) side, which is used in the Watson-Crick and the reverse Watson-Crick pairings ( Fig. 1 a and b)]. UV absorption, circular dichroism, and infrared absorption spectra of the duplexes of these chemically modified poly(A)-poly(U)s have been examined, but little is known about the actual base-pairing fashions and the secondary structures.Here, we report x-ray fiber diffraction studies on the sodium salts ofthe double helices formed by poly(2-methylthioadenylic acid) [poly(ms2A)] and poly(U) [poly(ms2A).poly(U)] and poly(2-methyladenylic acid) [poly(m2A)] and poly(U) [poly(m2A)-poly(U)].We have obtained the similar diffraction patterns shown in Fig. 2 Upper and Lower for the two duplexes and have developed molecular models corresponding closely to the observed diffraction. It is shown that, in these duplexes, the two sugar-phosphate backbones are running in the same direction and held together by Hoogsteen-type hydrogen bonds between the 2-substituted adenine and the uracil bases (Fig. lc). in a manner similar to that of the double-helical portion having non-Watson-Crick base pairing of the triple-stranded helix, poly(U)poly(A)-poly(U) (9). MATERIALS AND METHODSThe synthesis and physicochemical properties ofpoly(m2A) and poly(ms2A) have been described (5,6). Fibers were drawn from a sticky pellet made by dissolving 0. 1 mg of the polymer in 20 Al of0.01 M NaCl and allowing the solution to dry in a closed dish containing saturated KNO3 (96% relative humidity) for several hours at 4°C. All diffiaction diagrams were obtained with nickel-filtered CuKa radiation using a-flat-film microcamera in which the temperature was kept at 0-2°C by a cooling apparatus and the relative humidity was controlled at -88% by helium gas constantly flushed through saturated KCl. The specimento-film distances were 30 mm and were calibrated by reference to the spacings of NaCl. ...

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Section: Methodsmentioning

confidence: 63%

Molecular structure of a double helix that has non-Watson—Crick type base pairing formed by 2-substituted poly(A) and poly(U)

Hakoshima

Fukui

Ikehara

et al. 1981

Proc. Natl. Acad. Sci. U.S.A.

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“…In contrast to poly(U), the X-ray diffraction pattern of poly(s2U) is of good quality and, in its characteristic features, similar to that of A-DNA (461). This points to an antiparallel double helix with 11 base-pairs per pitch of 28.8 A, base-pairs tilted in a negative sense with respect to the helix axis, and C3,-endo sugar puckering typical of A family structures (Figure 13-11).…”

Section: The Antiparallel A-rna-type Double Helices Of Poly(u) Poiymentioning

confidence: 95%

Principles of Nucleic Acid Structure

Saenger

1984

Springer Advanced Texts in Chemistry

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“…as messenger are readily detected in conditions such as high Mg2+ concentration (36) or in the presence of antibiotic (37 (40). Formation of a s2UxG wobble pair forces the S atom away from its favorable interactions with the pyrimidine N(1) on the middle anticodon base.…”

Section: (33) (We Have No Example Of a Vog Interaction)mentioning

confidence: 99%

On the physical basis for ambiguity in genetic coding interactions.

Grosjean¹,

Henau²,

Crothers³

1978

Proc. Natl. Acad. Sci. U.S.A.

264

126

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We report the relative stabilities, in the form of complex lifetimes, of complexes between two tRNAs complementary, or nearly so, in their anticodons. The results show striking parallels with the genetic coding rules, including the wobble interaction and the role of modified nucleotides sAU and V (a 5-oxyacetic acid derivative of U). One important difference between the genetic code and the pairing rules in the tRNAtRNA interaction is the stability in the latter of the short wobble pairs, which the wobble hypothesis excludes. We stress the potential of U for translational errors, and suggest a simple stereochemical basis for ribosome-mediated discrimination against short wobble pairs. Surprisingly, the stability of anticodon-anticodon complexes does not vary systematically with GC composition, unlike all other known double helices. How (10)(11)(12)(13)(14). Therefore, we selected this model system for more intensive study of base pairing rules; the observed strong parallels with the genetic coding rules justify our choice a posteriori."Recognition" between two tRNA anticodon loops can be expressed quantitatively by the association equilibrium constant, or by the kinetic constants for the association-dissociation reaction. Because the association rate constants are found to vary only moderately (by about a factor of five; unpublished results), the association equilibrium constant is approximately inversely proportional to the dissociation rate constant. Hence, we have selected a single parameter, the lifetime of the anticodonanticodon complex, determined by the temperature-jump technique, as a measure of the strength of association and therefore of the extent of recognition.In general we find that a "correct" base triplet interaction (as determined by the genetic coding rules) has a long lifetime. However, the lifetime of correct complexes frequently is not more than two orders of magnitude longer than the lifetime of some of the incorrect complexes that have mismatching bases. Therefore, to avoid errors, the ribosome must amplify the small difference in lifetime to produce a greater distinction between correct and incorrect pairings in protein synthesis. Specific mechanisms for such an amplification have been discussed under the heading of kinetic proofreading (15)(16)(17). MATERIALS AND METHODSThe procedures used in this work were described in a preceding paper (14). The concentration of each tRNA was 1.3-1.8 ,uM, based on amino acid acceptance activity. Temperature jumps of up to 100 were used, and relaxations were monitored at 266 nm. Control experiments on single samples of tRNA (not mixed with their complement) showed no slow relaxation signals between 00 and 150, except as reported explicitly below.The lifetimes (T*) of anticodon-anticodon complexes at 90 were determined from the relaxation time r, using the equation

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Molecular structure of poly-2-thiouridylic acid, a double helix with non-equivalent polynucleotide chains

Cited by 59 publications

References 33 publications

Molecular structure of a double helix that has non-Watson—Crick type base pairing formed by 2-substituted poly(A) and poly(U)

Molecular structure of a double helix that has non-Watson—Crick type base pairing formed by 2-substituted poly(A) and poly(U)

Principles of Nucleic Acid Structure

On the physical basis for ambiguity in genetic coding interactions.

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