Thermodynamics of DNA Triplex Formation in Oligomers with and without Cytosine Bases: Influence of Buffer Species, pH, and Sequence

Wilson, W. David; Hopkins, Harry P.; Mizan, Shaikh; Hamilton, David; Zon, Gerald

doi:10.1021/ja00087a060

Cited by 43 publications

(36 citation statements)

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“…Also included in the table are the parameters exhibited by the interaction between dT 18 and 20 -2(TAT)FE. As previously reported (22,29,30), triplex formation reveals negative ⌬S and ⌬H values, indicating that the process is characterized by an unfavorable entropy change and is, as such, driven by a large negative enthalpy change. Conspicuous differences are, however, observed in the magnitude of the thermodynamic parameters exhibited by the various processes.…”

Section: Thermodynamic Effects Of Flanking Sequences On the Formationsupporting

confidence: 82%

Contextual Equilibrium Effects in DNA Molecules

Goobes

Minsky

2001

Journal of Biological Chemistry

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The thermodynamic parameters of DNA triplex formation between oligonucleotides and double-stranded DNA segments containing adenine runs (A-tracts) were investigated to explore equilibrium structural effects exerted by flanking segments upon the A-tracts. Results obtained from isothermal titration calorimetry, temperature-dependent circular dichroism (CD), and UV melting experiments indicate that A-tracts, considered as a uniquely robust and inflexible DNA motif, can be structurally perturbed by neighboring sequences in a way that significantly affects the propensity of this motif to interact with triplex-forming oligonucleotides. These contextual equilibrium effects, which depend upon the composition and location of the flanking sequences, are likely to apply not only to the interaction of A-tracts with single-stranded DNA molecules but also to interactions with drugs and proteins. As such, the current results refine the guidelines for the design of triplexforming oligonucleotides used for antigene strategies. More generally, they substantiate the notion that significant data might be encoded by structural DNA parameters.The demonstrated in vivo existence of non-B-DNA morphologies and the potential involvement of such altered structures in the regulation and fine-tuning of cellular processes (1, 2) elicited intensive studies on the factors that affect and modulate DNA conformational transitions. It is well established that the physical chemistry of these transitions is determined by an intricate array of environmental conditions and intrinsic factors, including the ionic strength, relative humidity, pH, and torsional strain. The actual structure exhibited by a given DNA segment is, however, generally considered to be dictated by the particular composition and sequential order of the base pairs within this segment. Indeed, left-handed DNA conformations, cruciforms, intramolecular triplexes, as well as bent or macroscopically curved motifs are detected predominantly in nonrandom DNA sequences such as alternating purine-pyrimidine segments, direct or inverted repeats, and purine-rich tracts (2). Several studies have indicated, however, that the kinetics of a conformational change, as well as the features of the resulting DNA structure, may be influenced or even dominated by sequences that are removed from those directly participating in the transition.The first evidence that structural information can be transmitted along the DNA molecule was provided by the observation that the melting of a DNA segment can be strongly affected by the base composition of a contiguous region (3). The kinetics of cruciform extrusion (4), as well as of the formation of intramolecular triple-stranded DNA motifs (5), were found to be dominated by sequences flanking the region that undergoes the transition. The effects were shown to operate over relatively long distances and to be independent of polarity. Right-to-lefthanded transitions of alternating d(G-C) n and d(A-T) n segments were also found to be significantly modulated by regions...

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Section: Thermodynamic Effects Of Flanking Sequences On the Formationsupporting

confidence: 82%

Contextual Equilibrium Effects in DNA Molecules

Goobes

Minsky

2001

Journal of Biological Chemistry

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“…-2 to -7 kcal/(mol of base). 25 The ∆H i (ionization) of the buffer and the pH used in the experiments influence the observed triplex thermodynamic parameters. Unlike the results with the mixed sequences, the T m values and calorimetric ∆H for triplex formation from the A‚T duplex are independent of pH and buffer species.…”

Section: Discussionmentioning

confidence: 99%

Association of Short-Strand DNA Oligomers with Guanidinium-Linked Nucleosides. A Kinetic and Thermodynamic Study

et al. 1996

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Complementary short-strand DNA homooligomers and guanidinium-linked homonucleosides associate and form triplexes in solution. The melting temperatures, T m , the association and dissociation kinetic and thermodynamic parameters, and activation energies were determined by UV thermal analysis for the triplexes of short strand DNA homooligomers {d(pA) 5 -d(pA) 12-18 } and poly(dA) with the guanidinium-linked nucleoside d(Tg) 4 -T-azido {DNG 5 }. The melting and cooling curves exhibit hysteresis behavior in the temperature range of 5-95°C at 0.2 deg/min thermal rate. From these curves the rate constants and the energies of activation for association (k on , E on ) and dissociation (k off , E off ) processes were obtained. The T m decreases with the ionic strength and increases slightly with increase in concentration of the monomers. A greater increase in the T m results from an increase in the length of the DNA strand d(pA) x . In the case of d(pA) 5 and d(pA) 6 , triplexes are formed, with T m ) 34 and 39°C, respectively, only above 0.063 mM/(adenine base) concentration when ionic strength is 0.08. The rate constants k on and k off at a reference temperature (288 K) are dependent on the DNA strand length and also decrease and increase respectively with the ionic strength. The energies of activation for the association and dissociation processes are in the range of -10 to -50 and 17 to 44 kcal/mol, respectively. The equilibrium for the formation of the triplexes {(d(Tg) 4 -T-azido) 2 ‚d(pA) x , x ) 5-10)} is favored by several orders of magnitude when compared to the triplexes of DNA. The standard molar enthalpies for triplex formation have larger negative values at low ionic strength than at high ionic strength indicating that at lower µ values the formation of triplexes of d(Tg) 4 -T-azido with d(pA) x is more favored. The values of ∆H°(288) calculated from the activation parameters are between -30 and -60 kcal/ (mol base) and the values of ∆G°(288) are between -8 and -13 kcal/(mol base) for short-strand DNA. There is a linear relationship in the enthalpy-entropy compensation for the triplex-melting thermodynamics.

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“…The primary difference between many of these triplex models resides in the molecularity of the complex, which in turn influ ences the nature of the duplex and triplex ends. For example, the litera ture contains reports of three-stranded complexes with contiguous dupie x extensions (21,41,110,145,(149)(150)(151)(152) and with so-called blunt ends (52, 60, 104,136,175,184). Other triplex constructs include Wat son-Crick hairpins paired with oligopyrimidine strands (82,133,134,181), an all-pyrimidine hairpin paired with an oligopurine (180), circular oligonucleotides paired with linear oligonucleotides (64), and single stranded intramolecular triplexes (9, 42, 74-77, 109, 119-122, 125-127, 153, 169, 170).…”

Section: Model Oligonucleotide Triple-helix Constructsmentioning

confidence: 99%

“…Despite these prob lems, inspection of the enthalpy data reveals some patterns that may prove to be general. To be specific, calorimetric studies of oligo(pyri midine) DNA third-strand hybridization with mixing calorimetry (175) and DSC (52, 109, 110, 170) , at or near neutral pH, yield enthalpy values of 2.0-4.2 kcallmol of Hoogsteen-forming nucleotide. Comparisons of these model-independent calorimetric enthalpies with the corresponding model-dependent van't Hoff values under identical conditions re veal that t:J.. HvH is systematically larger than t:J.…”

Section: Temperature Sensitivity Of Triple-helix Stabilitymentioning

confidence: 99%

Nucleic Acid Hybridization: Triplex Stability and Energetics

Plum¹,

Pilch²,

Singleton³

et al. 1995

Annu. Rev. Biophys. Biomol. Struct.

143

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In this chapter, we review the current state of the thermodynamic database for triple helical oligonucleotide hybridization reactions and present a critical assessment of the methods used to obtain the relevant data. The thermodynamic stability of triple-helix oligonucleotide constructs is discussed in terms of its dependence on temperature, chain length, pH, salt, base sequence, base and backbone modifications, and ligand binding. In particular, we examine the coupling of hybridization equilibria to proton, cation, and drug-binding equilibria. Throughout the chapter, we emphasize that a detailed understanding of the endogenous and exogenous variables that control triplex stability is required for the rational design of oligonucleotides for specific therapeutic, diagnostic, and/or biotechnological applications, as well as for elucidating the potential cellular roles of these higher-order nucleic acid complexes.

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Thermodynamics of DNA Triplex Formation in Oligomers with and without Cytosine Bases: Influence of Buffer Species, pH, and Sequence

Cited by 43 publications

References 1 publication

Contextual Equilibrium Effects in DNA Molecules

Contextual Equilibrium Effects in DNA Molecules

Association of Short-Strand DNA Oligomers with Guanidinium-Linked Nucleosides. A Kinetic and Thermodynamic Study

Nucleic Acid Hybridization: Triplex Stability and Energetics

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