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a tentative insight into the natural world; a concept that is not yet verified but that if true would explain certain facts or phenomena; "a scientific hypothesis that survives experimental testing becomes a scientific theory"; "he proposed a fresh theory (同)possibility, theory
a proposal intended to explain certain facts or observations
move unsteadily; "His knees wobbled"; "The old cart wobbled down the street" (同)coggle
an unsteady rocking motion
(of sound) fluctuating unsteadily; "a low-pitched wobbling sound"

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仮説,仮定,前提
よろよろする,ぐらぐらする,動揺する / 〈声などが〉震える / 〈意見・気持ちなどが〉ぐらつく / …‘を'よろよろ(ぐらぐら)させる / よろめき,ぐらつき,動揺

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出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2013/11/06 15:58:17」(JST)

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Wobble base pairs for inosine and guanine

In molecular biology, a wobble base pair is a non-Watson-Crick base pairing between two nucleotides in RNA molecules. The four main wobble base pairs are guanine-uracil (G-U), hypoxanthine-uracil (I-U), hypoxanthine-adenine (I-A), and hypoxanthine-cytosine (I-C). Because hypoxanthine is the nucleobase of inosine, "I" is used for the former in order to maintain consistency of nucleic acid nomenclature, which otherwise follows the names of the nucleobases (e.g., "G" for both guanine and guanosine).^[1] The thermodynamic stability of a wobble base pair is comparable to that of a Watson-Crick base pair. Wobble base pairs are fundamental in RNA secondary structure and are critical for the proper translation of the genetic code.

tRNA wobble[edit]

In the genetic code, there are = 64 possible codons (tri-nucleotide sequences). For translation, each of these codons requires a tRNA molecule with a complementary anticodon. If each tRNA molecule paired with its complementary mRNA codon using canonical Watson-Crick base pairing, then 64 types (species) of tRNA molecule would be required. In the standard genetic code, three of these 64 codons are stop codons, which terminate translation by binding to release factors rather than tRNA molecules, so canonical pairing would require 61 species of tRNA. Since most organisms have fewer than 45 species of tRNA,^[2] some tRNA species must pair with more than one codon. In 1966, Francis Crick proposed the Wobble hypothesis to account for this. He postulated that the 5' base on the anticodon, which binds to the 3' base on the mRNA, was not as spatially confined as the other two bases, and could, thus, have non-standard base pairing.^[3] Movement ("wobble") of the base in the 5' anticodon position is necessary for this capability.^[4]

As an example, yeast tRNA^Phe has the anticodon 5'-GmAA-3' and can recognize the codons 5'-UUC-3' and 5'-UUU-3'. It is, therefore, possible for non-Watson–Crick base pairing to occur at the third codon position, i.e., the 3' nucleotide of the mRNA codon and the 5' nucleotide of the tRNA anticodon.^[5]

tRNA Base pairing schemes[edit]

The original wobble pairing rules, as proposed by Crick. Watson-Crick base pairs are shown in bold, wobble base pairs in italic:

tRNA 5' anticodon base	mRNA 3' codon base
A	U
C	G
G	C or U
U	A or G
I	A or C or U

Revised pairing rules^[6]

tRNA 5' anticodon base	mRNA 3' codon base
G	U,C
C	G
k²C	A
A	U,C,(A),G
unmodified U	U,(C),A,G
xm⁵s²U,xm⁵Um,Um,xm⁵U	A,(G)
xo⁵U	U,A,G
I	A,C,U

References[edit]

^ Kuchin, Sergei (May 2011). "Covering All the Bases in Genetics: Simple Shorthands and Diagrams for Teaching Base Pairing to Biology Undergraduates". Journal of Microbiology & Biology Education (American Society for Microbiology) 12 (1). doi:10.1128/jmbe.v12i1.267. Retrieved October 16, 2013. "The correct name of the base in inosine (which is a nucleoside) is hypoxanthine, however, for consistency with the nucleic acid nomenclature, the shorthand [I] is more appropriate..."
^ http://gtrnadb.ucsc.edu/
^ Crick F (1966). "Codon–anticodon pairing: the wobble hypothesis". J Mol Biol 19 (2): 548–55. doi:10.1016/S0022-2836(66)80022-0. PMID 5969078.
^ Mathews, Christopher; Van Holde, K.E.; Appling, Dean; Anthony-Cahill, Spencer (2013). Biochemistry (4th ed.). Toronto, Canada: Pearson Education. p. 1181. ISBN 978-0-13-800464-4.
^ Varani G, McClain W (2000). "The G × U wobble base pair. A fundamental building-block of RNA structure crucial to RNA function in diverse biological systems". EMBO Rep 1 (1): 18–23. doi:10.1093/embo-reports/kvd001. PMC 1083677. PMID 11256617.
^ Murphy FV 4th, Ramakrishnan V (Dec 2004). "Structure of a purine-purine wobble base pair in the decoding center of the ribosome". Nat Struct Mol Biol 11 (12): 1251–1252. doi:10.1038/nsmb866. PMID 15558050.

External links[edit]

tRNA, the Adaptor Hypothesis and the Wobble Hypothesis
Wobble base-pairing between codons and anticodons

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English Journal

G/U and certain wobble position mismatches as possible main causes of amino acid misincorporations.

Zhang Z1, Shah B, Bondarenko PV.Author information 1Process and Product Development, Amgen Inc. , Thousand Oaks, California 91320, United States.AbstractA mass spectrometry-based method was developed to measure amino acid substitutions directly in proteins down to a level of 0.001%. When applied to recombinant proteins expressed in Escherichia coli, monoclonal antibodies expressed in mammalian cells, and human serum albumin purified from three human subjects, the method revealed a large number of amino acid misincorporations at levels of 0.001-0.1%. The detected misincorporations were not random but involved a single-base difference between the codons of the corresponding amino acids. The most frequent base differences included a change from G to A, corresponding to a G(mRNA)/U(tRNA) base pair mismatch during translation. We concluded that under balanced nutrients, G(mRNA)/U(tRNA) mismatches at any of the three codon positions and certain additional wobble position mismatches (C/U and/or U/U) are the main causes of amino acid misincorporations. The hypothesis was tested experimentally by monitoring the levels of misincorporation at several amino acid sites encoded by different codons, when a protein with the same amino acid sequence was expressed in E. coli using 13 different DNA sequences. The observed levels of misincorporation were different for different codons and agreed with the predicted levels. Other less frequent misincorporations may occur due to G(DNA)/U(mRNA) mismatch during transcription, mRNA editing, U(mRNA)/G(tRNA) mismatch during translation, and tRNA mischarging.
Biochemistry.Biochemistry.2013 Nov 12;52(45):8165-76. doi: 10.1021/bi401002c. Epub 2013 Oct 31.
A mass spectrometry-based method was developed to measure amino acid substitutions directly in proteins down to a level of 0.001%. When applied to recombinant proteins expressed in Escherichia coli, monoclonal antibodies expressed in mammalian cells, and human serum albumin purified from three human
PMID 24128183

Life without tRNAArg-adenosine deaminase TadA: evolutionary consequences of decoding the four CGN codons as arginine in Mycoplasmas and other Mollicutes.

Yokobori S1, Kitamura A, Grosjean H, Bessho Y.Author information 1Laboratory of Extremophiles, Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan. yokobori@ls.toyaku.ac.jpAbstractIn most bacteria, two tRNAs decode the four arginine CGN codons. One tRNA harboring a wobble inosine (tRNA(Arg)ICG) reads the CGU, CGC and CGA codons, whereas a second tRNA harboring a wobble cytidine (tRNA(Arg)CCG) reads the remaining CGG codon. The reduced genomes of Mycoplasmas and other Mollicutes lack the gene encoding tRNA(Arg)CCG. This raises the question of how these organisms decode CGG codons. Examination of 36 Mollicute genomes for genes encoding tRNA(Arg) and the TadA enzyme, responsible for wobble inosine formation, suggested an evolutionary scenario where tadA gene mutations first occurred. This allowed the temporary accumulation of non-deaminated tRNA(Arg)ACG, capable of reading all CGN codons. This hypothesis was verified in Mycoplasma capricolum, which contains a small fraction of tRNA(Arg)ACG with a non-deaminated wobble adenosine. Subsets of Mollicutes continued to evolve by losing both the mutated tRNA(Arg)CCG and tadA, and then acquired a new tRNA(Arg)UCG. This permitted further tRNA(Arg)ACG mutations with tRNA(Arg)GCG or its disappearance, leaving a single tRNA(Arg)UCG to decode the four CGN codons. The key point of our model is that the A-to-I deamination activity had to be controlled before the loss of the tadA gene, allowing the stepwise evolution of Mollicutes toward an alternative decoding strategy.
Nucleic acids research.Nucleic Acids Res.2013 Jul;41(13):6531-43. doi: 10.1093/nar/gkt356. Epub 2013 May 8.
In most bacteria, two tRNAs decode the four arginine CGN codons. One tRNA harboring a wobble inosine (tRNA(Arg)ICG) reads the CGU, CGC and CGA codons, whereas a second tRNA harboring a wobble cytidine (tRNA(Arg)CCG) reads the remaining CGG codon. The reduced genomes of Mycoplasmas and other Mollicut
PMID 23658230

Design and implementation of a control system reflecting the level of analgesia during general anesthesia.

Janda M1, Schubert A, Bajorat J, Hofmockel R, Nöldge-Schomburg GF, Lampe BP, Simanski O.Author information 1Department of Anesthesiology and Intensive Care Medicine, University of Rostock, Rostock, Germany.AbstractINTRODUCTION: Measuring and ensuring an adequate level of analgesia in patients are of increasing interest in the area of automated drug delivery during general anesthesia. Therefore, the aim of this investigation was to develop a control system that may reflect the intraoperative analgesia value. Our hypothesis was that a feedback controller could be applied in clinical practice safely and at an adequate quality of analgesia. The purpose of this study was to evaluate the practical feasibility of such a system in a clinical setting.
Biomedizinische Technik. Biomedical engineering.Biomed Tech (Berl).2013 Feb;58(1):1-11. doi: 10.1515/bmt-2012-0090.
INTRODUCTION: Measuring and ensuring an adequate level of analgesia in patients are of increasing interest in the area of automated drug delivery during general anesthesia. Therefore, the aim of this investigation was to develop a control system that may reflect the intraoperative analgesia value. O
PMID 23314499

Japanese Journal

Molecular mechanism of stop codon recognition by eRF1 : a wobble hypothesis for peptide anticodons

MURAMATSU T.
FEBS Lett. 488, 105-109, 2001
NAID 80012150792

チャンドラ-極運動の周波数変動仮説の検定とそのQに関する研究〔英文〕

大久保修平
東京大学地震研究所彙報 57(1), p1-47, 1982-00-00
… The Chandler wobble is one of the elastic-gravitational normal modes of the Earth. … The eigenperiod is about 435 sidereal days, larger than the other modes by a factor 104, which gives the Chandler wobble an exotic status in the group of normal modes. …
NAID 120000871635