Nearest-Neighbor Effects in the Structure and Function of Nucleic Acids

Bubienko, Edward; Cruz, Phillip; Thomason, J.F.; Borer, Philip N.

doi:10.1016/s0079-6603(08)60683-2

Cited by 26 publications

(9 citation statements)

References 153 publications

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“…Another model that includes interactions beyond nearest neighbors is the R-Y model (Cruz et al, 1982;Bubienko et al, 1983). This model attributes special stability to sequences with patterns of continuous stacking.…”

Section: Discussionmentioning

confidence: 99%

Polymer-supported RNA synthesis and its application to test the nearest-neighbor model for duplex stability

Kierzek¹,

Caruthers²,

Longfellow³

et al. 1986

Biochemistry

148

100

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A solid-phase method using a phosphoramidite approach is described for synthesis of oligoribonucleotides. The method was used to synthesize pairs of oligomers with identical nearest neighbors but different sequences. Comparison of thermodynamic parameters for these pairs provides a test of the nearest-neighbor hypothesis for prediction of helix stability. In general, pairs of sequences with identical nearest neighbors have enthalpy and entropy changes for helix formation that differ by 8% on average, delta Go37 that differ by 6% on average, and melting temperatures within 0-5 degrees C of each other. These limits are typical of the accuracy that should be expected from nearest-neighbor predictions of RNA helix stability. UCAUGA and UGAUCA have the same nearest neighbors but melting temperatures that differ by 7 degrees C. This suggests some sequences will not be approximated well by the nearest-neighbor model.

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Section: Discussionmentioning

confidence: 99%

Polymer-supported RNA synthesis and its application to test the nearest-neighbor model for duplex stability

Kierzek¹,

Caruthers²,

Longfellow³

et al. 1986

Biochemistry

148

100

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“…Application of the RY Model. Two recent publications propose a model to account for the sequence dependence of duplex stability in terms of both intrastrand and interstrand overlap between adjacent base pairs (Cruz et al, 1982;Bubienko et al, 1983). Instead of the regular 30°w inding angle between base pairs in the A' helix, the authors postulate that the winding angle varies according to the sequence and, using NMR data, have determined the best fit of the winding angle to the data.…”

Section: Discussionmentioning

confidence: 99%

Relative stability of guanosine-cytidine diribonucleotide cores: a proton NMR assessment

Sinclair¹,

Alkema²,

Ra³

et al. 1984

Biochemistry

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Proton NMR was used to study the secondary structure and melting behavior of six self-complementary oligoribonucleotide tetramers, each containing two guanosine and two cytidine residues (GGCC, CCGG, GCCG, CGGC, GCGC, and CGCG). GGCC and CCGG formed perfect duplexes containing four G.C base pairs with Tms of 54 and 47.8 degrees C, respectively; GCCG and CGGC formed staggered duplexes with two G.C base pairs and four 3' double-dangling bases, with Tms of 35.5 and 29.2 degrees C, respectively; GCGC formed a perfect duplex with a Tm of 49.9 degrees C, while CGCG formed a staggered duplex with a Tm of 36.9 degrees C. From these results, an order of stability of the cores containing two G.C base pairs was proposed: GC:GC is more stable than GG:CC which is more stable than CG:CG. The RY model for secondary structure stability prediction was applied to the above tetramers with reasonable success. Suggestions for refinements are discussed.

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“…Our results are more consistent with the second notion. Were the rest of the anticodon arm to modify the anticodon configuration to that which is optimal for binding to a particular codon, this modification should be propagated through the secondary structure, via stereochemical and stacking interactions between nearest neighbor base-pairs (Bubienko et al, 1983). Effects of a substitution under this otherwise plausible model would be expected to decline with distance from the anticodon.…”

Section: Each Extended Anticodon Alteration Improves Efficiencymentioning

confidence: 99%

Systematic alterations in the anticodon arm make tRNA(Glu)-Suoc a more efficient suppressor.

Raftery¹,

Yarus²

1987

The EMBO Journal

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Using site-specific mutagenesis, we constructed five more efficient variants of tRNAGlu_Suo, an extremely inefficient ochre suppressor. Each variant has an extended anticodon, or region of the anticodon arm, which is more similar to that found in normal tRNAs which translate codons Uxx. Suppressor efficiency invariably increases with similarity of the extended anticodon to that of a normal Uxx-translating tRNA. Altered nucleotides in both helix and loop strongly affect effi'ciency, with no position dependence and no significant interaction between substitutions. The variant with all substitutions is 230-fold more efficient (in one context) than the parental tRNAGIu_Su"". Two other unexpected variants seem to be 'context mutants', having altered response to message context. Key words: anticodon/extended/RNA/suppressor/tRNA Introduction Termination suppressor tRNAs in Escherichia coli facilitate in vivo study of tRNA function. Our laboratory has focused in particular on the influence of the anticodon arm on the ribosomal function of the tRNA. The results may have implications not only for the influence of tRNA structure on the specificity of codon -anticodon pairing but also for other specific RNA -RNA interactions such as the control of colEl plasmid replication or, perhaps, the splicing of eukaryotic transcripts.

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Nearest-Neighbor Effects in the Structure and Function of Nucleic Acids

Cited by 26 publications

References 153 publications

Polymer-supported RNA synthesis and its application to test the nearest-neighbor model for duplex stability

Polymer-supported RNA synthesis and its application to test the nearest-neighbor model for duplex stability

Relative stability of guanosine-cytidine diribonucleotide cores: a proton NMR assessment

Systematic alterations in the anticodon arm make tRNA(Glu)-Suoc a more efficient suppressor.

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