Triple helix formation by oligopurine-oligopyrimidine DNA fragments

Manzini, Giorgio; Xodo, Luigi E.; Gasparotto, Daniela; Quadrifoglio, Franco; Marel, Gijs A. van der; Boom, Jacques H. van

doi:10.1016/s0022-2836(05)80267-0

Cited by 168 publications

(99 citation statements)

References 35 publications

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“…4B), with the exception of affinity cleavage data, even though the ionic conditions are not uniform. In many thermal melting and calorimetric experiments, we are able to predict the melting temperature (21,23,(26)(27)(28) within 6°C, only slightly worse than the members of our data set (Fig. 4B). Once again, the model shows no apparent bias in GC content or pH.…”

Section: Methodscontrasting

confidence: 65%

Prediction of the stability of DNA triplexes.

Roberts

Crothers²

1996

Proc. Natl. Acad. Sci. U.S.A.

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We present rules that allow one to predict the stability of DNA pyrimidine-purine-pyrimidine (Y-R-Y) triple helices on the basis of the sequence. The rules were derived from van Prediction of macromolecular physical properties using only the sequence is one of the primary goals of biophysical chemistry. The utility of such models is in the ability to predict the stability of RNA or DNA helices based on the sequence alone (1, 2), the flexibility of the DNA duplex (3), local helical geometry (4,5), and the propensity of a particular sequence to undergo a structural transition between different helical forms (6). A predictive model for triple-helix stability could have broad application as well. Triple-helix formation can be used to recognize DNA duplexes highly specifically (for reviews, see refs. 7-10) and has potential for antisense and therapeutic applications. In this paper, we present a model for predicting DNA triplex stability using only the sequence.In developing a predictive model, two features are important: (i) the appropriateness of the parameters used to construct the model and (ii) the distribution of the sequences used as the basis set in its parameterization. For the prediction of the enthalpy of triplex formation (AH°), a nearest neighbor model was used, whereas a combination model (one containing a mixture of mono-and dinucleotide parameters) was found to be best for prediction of the free energy of the triplex (AG° [Na+] cacodylate/cacodylic acid, 1 mM EDTA (experiments at pH 6.25-7.0). The Na+ concentration was held constant at 100 mM because it is known to affect the triplex tm (10, 12) Melting experiments were performed by heating from low temperature to high temperature at -0.5°C per min and data were taken every 0.5°C. tm values were reproducible +0.5°C.Determination of Triplex Stability. The stability of the 23 intermolecular triplexes was determined by van't Hoff analysis of absorbance melting curves over a pH range from 4.75 to 7.0. Between pH 4.75 and 5.5, curves were analyzed as described (11,13). Briefly, the melting data were treated with a statistical mechanical approach where the equilibrium is broken up into discrete states (11,14)

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Section: Methodscontrasting

confidence: 65%

Prediction of the stability of DNA triplexes.

Roberts

Crothers²

1996

Proc. Natl. Acad. Sci. U.S.A.

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“…The fact that the spectrum of 20GT: 30RY is different from the sum of individual 30RY and 20GT spectra suggests that there is an interaction between the two components of the mixture, thus forming a triplehelical complex. Interestingly, an intense and negative ellipticity at 212 nm is induced upon triplex formation, as previously observed for other triplex structures [5,6,24]. Another outstanding feature present in the 20GT: 30RY spectrum is the presence of a negative ellipticity at 277 nm, which according to a study on poly(dG).poly(dC) has been attributed to the formation of triplex helices containing G. GC triads [20,21,32,33].…”

Section: Polyacrylamide Gel Electrophoresis and Ha Chromatographysupporting

confidence: 65%

“…Such DNA structures have been studied with different methods including eletrophoresis [2~], UV-spectroscopy [5][6][7][8][9][10][11][12][13] and NMR [14,15].…”

Section: Introductionmentioning

confidence: 99%

Characterization of the DNA triplex formed by d(TGGGTGGGTGGTTGGGTGGG) and a critical R · Y sequence located in the promoter of the murine Ki‐ras proto‐oncogene

Xodo

1995

FEBS Letters

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“…Synthesis of 3'-phosphate and 5'-phosphate precursors. The target polypyrimidine sequence was selected from a triplex studied by Xodo et al [13,14]. The same sequence has been 4 used to characterize the binding properties of both parallel [15] and antiparallel hairpins [16] (Scheme 2).…”

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confidence: 99%