Codon—Anticodon interaction studied with trinucleoside diphosphates containing 2-thiouridine, 4-thiouridine, 2,4-dithiouridine, or 2-thiocytidine

Vormbrock, Ria; Morawietz, R.; Gassen, Hans Günter

doi:10.1016/0005-2787(74)90280-9

Cited by 32 publications

(16 citation statements)

References 32 publications

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“…Replacement of the s2U+-A pair in tRNAPhe.tRNAGIu (Table 2A) by s2U+xG in tRNALeu-tRNAGlu (Table 2D) reduces the complex lifetime from 1640 to 6 msec. This is a much greater destabilization than provided by UoG wobble pairs, a result consistent with the weak codon response of s2U+ for G (29,30) or of s2U for G (31). Those authors did not present data on the codon response of s2U+ for U or C, but we note that s2U+xU and s2U+xC wobble pairs are considerably more stable than s2U+xG in the tRNA-tRNA interaction.…”

Section: Methodsmentioning

confidence: 47%

On the physical basis for ambiguity in genetic coding interactions.

Grosjean¹,

Henau²,

Crothers³

1978

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

265

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 Because the association rate constants are found to vary only moderately (by about a factor of five; unpublished results), the association equilibrium constant is approximately inversely proportional to the dissociation rate constant.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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Section: Methodsmentioning

confidence: 47%

On the physical basis for ambiguity in genetic coding interactions.

Grosjean¹,

Henau²,

Crothers³

1978

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

265

126

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“…In contrast to the thionated DNA derivatives, thionated RNA derivatives are among the most highly conserved and ubiquitous nucleobases in bacterial tRNAs (11). Since their discovery in the mid-1900s, thiopyrimidine derivatives have been employed in structural-biology studies (207)(208)(209)(210) and investigated for their potential pharmacological properties (5,(211)(212)(213)(214). 4-Thiouracil is widely used in photocrosslinking investigations to uncover in vivo RNA structures and important RNA-protein interactions (15,19,43,201,202,204,215).…”

Section: Thiobases As Phototherapeutic and Photocrosslinking Agentsmentioning

confidence: 99%

Photochemical and Photodynamical Properties of Sulfur‐Substituted Nucleic Acid Bases,

Ashwood

Pollum

Crespo‐Hernández

2018

Photochem & Photobiology

115

132

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Sulfur-substituted nucleobases (a.k.a., thiobases) are among the world's leading prescriptions for chemotherapy and immunosuppression. Long-term treatment with azathioprine, 6-mercaptopurine and 6-thioguanine has been correlated with the photoinduced formation of carcinomas. Establishing an in-depth understanding of the photochemical properties of these prodrugs may provide a route to overcoming these carcinogenic side effects, or, alternatively, a basis for developing effective compounds for targeted phototherapy. In this review, a broad examination is undertaken, surveying the basic photochemical properties and excited-state dynamics of sulfur-substituted analogs of the canonical DNA and RNA nucleobases. A molecular-level understanding of how sulfur substitution so remarkably perturbs the photochemical properties of the nucleobases is presented by combining experimental results with quantum-chemical calculations. Structure-property relationships demonstrate the impact of site-specific sulfur substitution on the photochemical properties, particularly on the population of the reactive triplet state. The value of fundamental photochemical investigations for driving the development of ultraviolet-A chemotherapeutics is showcased. The most promising photodynamic agents identified thus far have been investigated in various carcinoma cell lines and shown to decrease cell proliferation upon exposure to ultraviolet-A radiation. Overarching principles have been elucidated for the impact that sulfur substitution of the carbonyl oxygen has on the photochemical properties of the nucleobases.

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“…2; SS32) was assessed by the T m of the hybrid in three different solutions (Table 3). Relative to the hybrid with the unmodified RNA (T m = 54 C in 20% formamide), the introduction of nA + sU increased the stability of the probe-RNA hybrid by raising the T m to 84 C. This was expected because nA-T/U and sU-A base pairs are known to stabilize the A-form duplex (Vormbrock et al 1974;Howard and Miles 1984;Kumar and Davis 1997;Testa et al 1999). Hybrids in which the RNA was substituted with nA + sU, together with hX or cG, had T m s of 67 C and 80 C, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…Here, while the unmodified RNA was permissive for U-G formation, promoting 81% hybridization (panel 1), substitution of the RNA with sU prevented this mismatch, promoting only 9%-12% hybridization (panels 3-5). This is due to the fact that the sU-G pairing is less stable than U-G (Vormbrock et al 1974;Testa et al 1999). Thus, the presence of sU in the RNA increased the ability of the LNA probe to discriminate against the U-G mismatch.…”

Section: Resultsmentioning

confidence: 99%

Unrestricted accessibility of short oligonucleotides to RNA

Gamper¹

2005

RNA

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The propensity of RNA to fold into higher-order structures poses a major barrier to the use of short probes (<15 nucleotides) by preventing their accessibility. Introduction of the pseudo-complementary bases 2-aminoadenine (nA) and 2-thiouracil (sU) and the destabilizing base 7-deazaguanine (cG) into RNA provides a partial solution to this problem. While complementary in hydrogen bonding groups, nA and sU cannot form a stable base pair due to steric hindrance, and are thus pseudo-complementary. Each, however, recognizes the regular T/U and A complements, allowing pairing with oligonucleotides. Short pseudocomplementary RNAs can be prepared by in vitro transcription. Relative to standard transcripts, the modified transcripts possess reduced secondary structure and increased accessibility to short (8-mer) probes in the locked nucleic acid (LNA) configuration. They also hybridize to complementary probes with increased specificity and thermostability. Practical application of this strategy to oligonucleotide-based hybridization assays will require engineering of RNA polymerase for more efficient utilization of pseudo-complementary nucleoside triphosphates.

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Codon—Anticodon interaction studied with trinucleoside diphosphates containing 2-thiouridine, 4-thiouridine, 2,4-dithiouridine, or 2-thiocytidine

Cited by 32 publications

References 32 publications

On the physical basis for ambiguity in genetic coding interactions.

On the physical basis for ambiguity in genetic coding interactions.

Photochemical and Photodynamical Properties of Sulfur‐Substituted Nucleic Acid Bases,

Unrestricted accessibility of short oligonucleotides to RNA

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