Classification of the possible pairs between the first anticodon and the third codon positions based on a simple model assuming two geometries with which the pairing effectively potentiates the decoding complex

Takai, Kazuyuki

doi:10.1016/j.jtbi.2006.04.009

Cited by 9 publications

(14 citation statements)

References 98 publications

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“…Proposed topology of the base pairs according to the classical mode of Watson–Crick, a wobble mode (a pyrimidine unit directed toward the major groove) and WB* (a pyrimidine unit directed toward the minor groove), according to Takai (86). The U/S2U-A, U/S2U-G and X2U-G base pairs are positioned within the RNA helix (R = H or (c)mnm and X = S − , geS or H).…”

Section: Discussionmentioning

confidence: 99%

2-Thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in RNA and DNA duplexes

Sochacka

Szczepanowski

Cypryk

et al. 2015

Nucleic Acids Research

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2-Thiouracil-containing nucleosides are essential modified units of natural and synthetic nucleic acids. In particular, the 5-substituted-2-thiouridines (S2Us) present in tRNA play an important role in tuning the translation process through codon–anticodon interactions. The enhanced thermodynamic stability of S2U-containing RNA duplexes and the preferred S2U-A versus S2U-G base pairing are appreciated characteristics of S2U-modified molecular probes. Recently, we have demonstrated that 2-thiouridine (alone or within an RNA chain) is predominantly transformed under oxidative stress conditions to 4-pyrimidinone riboside (H2U) and not to uridine. Due to the important biological functions and various biotechnological applications for sulfur-containing nucleic acids, we compared the thermodynamic stabilities of duplexes containing desulfured products with those of 2-thiouracil-modified RNA and DNA duplexes. Differential scanning calorimetry experiments and theoretical calculations demonstrate that upon 2-thiouracil desulfuration to 4-pyrimidinone, the preferred base pairing of S2U with adenosine is lost, with preferred base pairing with guanosine observed instead. Therefore, biological processes and in vitro assays in which oxidative desulfuration of 2-thiouracil-containing components occurs may be altered. Moreover, we propose that the H2U-G base pair is a suitable model for investigation of the preferred recognition of 3′-G-ending versus A-ending codons by tRNA wobble nucleosides, which may adopt a 4-pyrimidinone-type structural motif.

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Section: Discussionmentioning

confidence: 99%

2-Thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in RNA and DNA duplexes

Sochacka

Szczepanowski

Cypryk

et al. 2015

Nucleic Acids Research

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“…Also, the R⅐R and Y⅐Y mismatches had reversed acceptability compared with the translational rules derived by Lim and Curran (46). The T box system also exhibits a preference for G⅐U over U⅐G, which is the opposite of what is found in translation (47)(48)(49). However, as in translation (50,51), mismatches at position 2 were the most deleterious.…”

Section: Discussionmentioning

confidence: 83%

Codon-Anticodon Recognition in the Bacillus subtilis glyQS T Box Riboswitch

Caserta¹,

Liu

Grundy

et al. 2015

Journal of Biological Chemistry

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Background:The T box riboswitch utilizes the cognate tRNA as its regulatory ligand. Results: Tolerance for mismatches at positions 1 and 3 differs from what is observed during translation. Conclusion: Regulation by the T box riboswitch utilizes codon-anticodon recognition rules that differ from those used in the ribosome. Significance: Understanding different mechanisms for RNA-RNA recognition provides insight into the constraints exerted by regulatory and translational machineries.

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“…Recognition of both pyrimidine-ending codons by one tRNA molecule is the wobbling behavior of G in the first position of the anticodon as proposed by Crick [1]. Modification of U (in the first position of the anticodon) to thio-U restricts the wobbling behavior of the tRNA molecule to recognition of both purine-ending codons [22], [23]. A second pattern of subdivision is presented by a box toward the bottom lefthand side of Table 1.…”

Section: Tablementioning

confidence: 94%

“…In eight boxes of Table 1 [25]. Takai [22] provides more information on these tRNAs which recognize all four members of a box: ". .…”

Section: Tablementioning

confidence: 99%

“…In summary, the wobbling behavior of tRNA molecules with unmodified anticodons allows subdivision of boxes with only sense codons in three ways: no subdivision, division in a pyrimidine-ending pair and a purine-ending pair, and division in a set of three codons in the top of a box, and a single codon at the bottom. Although extensive modifications of anticodons in contemporary organisms can lead to much more complex patterns of wobbling behavior [34], [35], [22], [24], for the purpose of enlarging Space 0, we do not take these aspects of the wobble phenomenon in account. These modifications are produced by proteins, and therefore were probably not present during the development of the coding system.…”

Section: Tablementioning

confidence: 99%

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Some Mathematical Refinements Concerning Error Minimization in the Genetic Code

Buhrman

Gulik

Kelk

et al. 2011

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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The genetic code is known to have a high level of error robustness and has been shown to be very error robust compared to randomly selected codes, but to be significantly less error robust than a certain code found by a heuristic algorithm. We formulate this optimization problem as a Quadratic Assignment Problem and use this to formally verify that the code found by the heuristic algorithm is the global optimum. We also argue that it is strongly misleading to compare the genetic code only with codes sampled from the fixed block model, because the real code space is orders of magnitude larger. We thus enlarge the space from which random codes can be sampled from approximately 2.433 × 10(18) codes to approximately 5.908 × 10(45) codes. We do this by leaving the fixed block model, and using the wobble rules to formulate the characteristics acceptable for a genetic code. By relaxing more constraints, three larger spaces are also constructed. Using a modified error function, the genetic code is found to be more error robust compared to a background of randomly generated codes with increasing space size. We point out that these results do not necessarily imply that the code was optimized during evolution for error minimization, but that other mechanisms could be the reason for this error robustness.

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Classification of the possible pairs between the first anticodon and the third codon positions based on a simple model assuming two geometries with which the pairing effectively potentiates the decoding complex

Cited by 9 publications

References 98 publications

2-Thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in RNA and DNA duplexes

2-Thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in RNA and DNA duplexes

Codon-Anticodon Recognition in the Bacillus subtilis glyQS T Box Riboswitch

Some Mathematical Refinements Concerning Error Minimization in the Genetic Code

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