Studies on oligonucleotides: Thermodynamic and optical properties of the oligoinosinate polycytidylate complexes

Tazawa, Ichiro; Tazawa, Setsuko; Ts’o, Paul O. P.

doi:10.1016/s0022-2836(72)80010-x

Cited by 33 publications

(13 citation statements)

References 46 publications

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“…Using the data of Tazawa et al (25) for model compounds, we calculate that replacing a G-C pair by I-C should reduce the stability by a factor of 90, compared to the average observed reduction by a factor of 20 for tRNA-tRNA complexes. Evidently the unknown factors that increase the stability of A-U pairs in RNA loop-loop interactions operate less effectively on I-C pairs, and even less so on C-C pairs.…”

Section: Methodsmentioning

confidence: 98%

“…One factor that may help produce standardization of the lifetimes of triplet pairings is the presence of modified purines moval of the Y base from yeast tRNAPhe reduces the lifetime of the tRNAPhe tRNAGIu complex by a factor of seven (Table 2A3) There is other evidence that I-C pairs are less stable than G-C (8,25). Using the data of Tazawa et al (25) for model compounds, we calculate that replacing a G-C pair by I-C should reduce the stability by a factor of 90, compared to the average observed reduction by a factor of 20 for tRNA-tRNA complexes.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

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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Section: Methodsmentioning

confidence: 98%

Section: Methodsmentioning

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

View full text Add to dashboard Cite

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“…On the other hand, the ethidium residue stabilized the complexes more efficiently when directed to a longer unpaired region (seven unpaired nucleotide residues) of a complementary oligonucleotide target than to a shorter one (two unpaired residues; compare complexes (VII) and (VIII) or (IX) and (X); R = Etd-1; Table 1). It is known that the interaction of short oligonucleotides with the complementary sequence of a polynucleotide may be significantly stabilized by the presence of another oligonucleotide bound to the adjacent sequence (Gupta et a[., 1968;Tasawa et al, 1972;Springgate and Poland, 1973). This stabilization originates from the co-operative end-to-end interaction.…”

Section: Melting Experimentsmentioning

confidence: 99%

“…This is approximately equal to the energy of interaction of one or two base pairs. The effect of cooperative binding of short oligonucleotides to singlestranded polynucleotides is well known (Gupta et af., 1968;Tasawa et al, 1972) and as 'effector approach' was successfully used to increase the efficiency of sequence-specific modification of single-stranded nucleic acids (Kutyavin e f al., 1988). From the data presented in this paper one can conclude that the presence of ethidium residue attached to an oligonucleotide results in significantly higher co-operativity when compared to oligonucleotides without attached ethidium dye (0.1 kcal/mol at 37 "C; -2.1 kcal/mol at 25 "C).…”

Section: Melting Experimentsmentioning

confidence: 99%

Ethidium and azidoethidium oligonucleotide derivatives: Synthesis, complementary complex formation and sequence‐specific photomodification of the single‐stranded and double‐stranded target oligo‐ and polynucleotides

Kropachev

et al. 1994

J of Molecular Recognition

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Oligodeoxyribonucleotide derivatives containing ethidium or azidoethidium residues attached to 3' and/or 5' end were prepared. These derivatives formed tight specific complexes with complementary oligodeoxyribonucleotides where each attached ethidium residue led to an increase of complex Tm by 20-30 degrees C. Tandem complexes of two oligodeoxyribonucleotides containing ethidium residues with an oligodeoxyribonucleotide having two adjacent complementary sequences for these oligonucleotides were investigated. Photoinduced reactions of a number of ethidium and azidoethidium oligodeoxyribonucleotide derivatives with target complementary single-stranded and double-stranded oligo- and polydeoxyribonucleotides were investigated. The irradiation led to direct photocleavage of the target oligo- or polynucleotide, to formation of hidden (piperidine cleavable) modifications of the target and to formation of covalent adducts between ethidium oligodeoxyribonucleotide derivative and the target. In a number of experiments, azidoethidium dyes were demonstrated to be considerably stronger photosensitizers than ethidium ones. Depending on the nature of the target (single- or double-stranded DNA) and on the irradiation conditions, the total damages to the target oligo- or polydeoxyribonucleotides ranged from 10-70% (for ethidium dyes) to 30-80% (for azidoethidium dyes).

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“…The data we use originally comes from the work of Tazawa, Tazawa, and Ts'o. 13 A statistical mechanical model based on this data was given by Springgate and Poland,14 and it is parameters from this study that we will use here.…”

Section: Binding Of I M To Poly-cmentioning

confidence: 99%

Ligand binding distributions in nucleic acids

Poland

2001

Biopolymers

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Studies on oligonucleotides: Thermodynamic and optical properties of the oligoinosinate polycytidylate complexes

Cited by 33 publications

References 46 publications

On the physical basis for ambiguity in genetic coding interactions.

On the physical basis for ambiguity in genetic coding interactions.

Ethidium and azidoethidium oligonucleotide derivatives: Synthesis, complementary complex formation and sequence‐specific photomodification of the single‐stranded and double‐stranded target oligo‐ and polynucleotides

Ligand binding distributions in nucleic acids

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