A model for base overlap in RNA

Cruz, Phillip; Bubienko, Edward; Borer, Philip N.

doi:10.1038/298198a0

Cited by 17 publications

(8 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Most non-exchangeable base protons in oligonucleotide duplexes exhibit 6 vs. T profiles with positive slopes, similar to those displayed by GC8 and GC5 in Fig. 3 (24,28,29). Such profiles Nucleic Acids Research are consistent with a decrease in ring current and steric shielding upon melting the double helix (23, 30).…”

Section: Discussionmentioning

confidence: 54%

Hydrogen-bonding effects and 13 of the DNA double helix

Borer¹,

LaPlante²,

Zanatta³

et al. 1988

Nucl Acids Res

Self Cite

View full text Add to dashboard Cite

13C-nmr chemical shifts of the nucleotides in DNA are sensitive to hydrogen bonding, especially for three of the carbons immediately bonded to exocyclic oxygen or nitrogen atoms acting as H-bond acceptors or donors. GuoC2, GuoC6 and ThdC4 are strongly deshielded (about 1 ppm) upon Watson-Crick pairing in oligodeoxynucleotide duplexes, regardless of the base sequence. Deshielding at these sites may be useful to distinguish bases involved in Watson-Crick pairs from unpaired bases.

show abstract

Section: Discussionmentioning

confidence: 54%

Hydrogen-bonding effects and 13 of the DNA double helix

Borer¹,

LaPlante²,

Zanatta³

et al. 1988

Nucl Acids Res

Self Cite

View full text Add to dashboard Cite

show abstract

“…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

View full text Add to dashboard Cite

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.

show abstract

“…The great sensitivity of the predictions to the values assigned to G.U's can be rationalized as follows. A fully c-).l;plementary segment of nucleic acid is presurmiably quite flexible, and cap a ble of adoptiinb, several dcifferent conformations (29,30). Thus, long ran,e interactions will intervene in shaping the structure, and it is not possible to pinpoint an unique energy value to describe a particular stacking interaction.…”

Section: Discussionmentioning

confidence: 99%

An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules

1984

View full text Add to dashboard Cite

A new set of energy values to predict the secondary structures in RNA molecules has been derived through a multiple-step refinement procedure. It achieves more than 80% success in predicting the cloverleaf pattern in tRNA (200 sequences tested) and more than 60% success in predicting the consensus folding of 5S RNA (100 sequences). Improvements in our initial program for predicting secondary structures, based on the principle of the "incompatibility islets" made possible the work on 5S RNA. The program was speeded up by introducing a dynamic grouping of the islets into three disjoint blocks. The novel features in the energy model include i) an evaluation of the contribution of odd pairs according to their position within a segment ii) a penalty for internal loops related to their dissymmetry iii) a bonus for bulge loops when the two terminal paired bases at the junction point are both pyrimidines.

show abstract

A model for base overlap in RNA

Cited by 17 publications

References 27 publications

Hydrogen-bonding effects and 13 of the DNA double helix

Hydrogen-bonding effects and 13 of the DNA double helix

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

An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules

Contact Info

Product

Resources

About