Predicting sequence‐dependent melting stability of short duplex DNA oligomers

Owczarzy, Richard; Vallone, Peter M.; Gallo, Frank J.; Paner, Teodoro M.; Lane, Michael J.; Benight, Albert S.

doi:10.1002/(sici)1097-0282(1997)44:3<217::aid-bip3>3.3.co;2-k

Cited by 71 publications

(144 citation statements)

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“…24 The duplex thermal stability is also predicted to increase logarithmically with increasing oligo concentration. 8,9 Three states of aggregation were reported for the LUVs (no aggregation, stable aggregates, and continual growth to flocculation) and it is reasonable to assume that these are the analogous states to those we observe for the GUVs, even though different regions of phase space are explored. All LUV experiments were conducted at [Na + ] ) 125 mM, and the DNA coverage from 2.5 to 39 DNA per vesicle corresponds to surface concentrations in the range from 2.5 × 10 -5 to 4.0 × 10 -4 DNA per lipid.…”

Section: Resultsmentioning

confidence: 99%

“…DNA binding stability is also affected by other controllable parameters, such as the ionic strength of the solution and the concentration of DNA. 8,9 The prospect exists for having numerous different singlestranded DNA (ssDNA) sequences expressed by different colloid populations to program the assembly of superstructures with high degrees of complexity. 10 A DNA-mediated approach would be an effective solution to the controllable association of different populations of lipid vesicles.…”

Section: Introductionmentioning

confidence: 99%

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Specific Binding of Different Vesicle Populations by the Hybridization of Membrane-Anchored DNA

2007

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We demonstrate a method of heterogeneous vesicle binding using membrane-anchored, single-stranded DNA that can be used over several orders of magnitude in vesicle size, as demonstrated for large 100 nm vesicles and giant vesicles several microns in diameter. The aggregation behavior is studied for a range of DNA surface concentrations and solution ionic strengths. Three analogous states of aggregation are observed on both vesicle size scales. We explain the existence of these three regimes by a combination of DNA binding favorability, vesicle collision kinetics, and lateral diffusion of the DNA within the fluid membrane. The reversibility of the DNA hybridization allows dissociation of the structures formed and can be achieved either thermally or by a reduction in the ionic strength of the external aqueous environment. Difficulty is found in fully unbinding giant vesicles by thermal dehybridization, possibly frustrated by the attractive van der Waals minimum in the intermembrane potential when brought into close contact by DNA binding. This obstacle can be overcome by the isothermal reduction of the ionic strength of the solution: this reduces the Debye screening length, coupling the effects of DNA dehybridization and intermembrane repulsion due to the increased electrostatic repulsion between the highly charged DNA backbones.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Specific Binding of Different Vesicle Populations by the Hybridization of Membrane-Anchored DNA

2007

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“…Traditional thermodynamic models for sequence-dependent DNA melting [79][80][81] were modified to take into account inter-membrane interactions by applying a Bell-type model [82] to account for the tilting of the free energy landscape by an applied force [77]: …”

Section: B Influence Of Membrane Interactions Upon Dna Thermodynamicmentioning

confidence: 99%

Application of nucleic acid–lipid conjugates for the programmable organisation of liposomal modules

Beales

Vanderlick

2014

Advances in Colloid and Interface Science

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“…These deficiencies are of particular concern because ⌬C P , ⌬V, and ⌬K s provide unique insights into the role of solvent in duplex stabilization (12)(13)(14)(15) and because quantitative knowledge of ⌬C P is required to compare thermodynamic properties of nucleic acids at a common reference temperature (16)(17)(18). This latter capacity is of specific practical value because thermodynamic databases reported at a given temperature often are used to predict hybridization properties at a different temperature as part of various diagnostic and therapeutic protocols (19). Without a significant body of directly measured heat capacity values, this parameter generally has been assumed to be zero for the melting of duplex structures to their component single strands (1)(2)(3).…”

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confidence: 99%

A more unified picture for the thermodynamics of nucleic acid duplex melting: A characterization by calorimetric and volumetric techniques

Chalikian

Völker

Plum

et al. 1999

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

234

219

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We use a combination of calorimetric and volumetric techniques to detect and to characterize the thermodynamic changes that accompany helix-to-coil transitions for five polymeric nucleic acid duplexes. Our calorimetric measurements reveal that melting of the duplexes is accompanied by positive changes in heat capacity (⌬C P ) of similar magnitude, with an average ⌬C P value of 64.6 ؎ 21.4 cal deg ؊1 mol ؊1 . When this heat capacity value is used to compare significantly different transition enthalpies (⌬H o ) at a common reference temperature, T ref , we find ⌬H T ref for duplex melting to be far less dependent on duplex type, base composition, or base sequence than previously believed on the basis of the conventional assumption of a near-zero value for ⌬C P . Similarly, our densimetric and acoustic measurements reveal that, at a given temperature, all the ATand AU-containing duplexes studied here melt with nearly the same volume and compressibility changes. In the aggregate, our results, in conjunction with literature data, suggest a more unified picture for the thermodynamics of nucleic acid duplex melting. Specifically, when compared at a common temperature, the apparent large differences present in the literature for the transition enthalpies of different duplexes become much more compressed, and the melting of all-AT-and all-AU-containing duplexes exhibits similar volume and compressibility changes despite differences in sequence and conformation. Thus, insofar as thermodynamic properties are concerned, when comparing duplexes, the temperature under consideration is as important as, if not more important than, the duplex type, the base composition, or the base sequence. This general behavior has significant implications for our basic understanding of the forces that stabilize nucleic acid duplexes. This behavior also is of practical significance in connection with the use of thermodynamic databases for designing probes and for assessing the affinity and specificity associated with hybridization-based protocols used in a wide range of sequencing, diagnostic, and therapeutic applications.Thermodynamic studies of nucleic acids have produced data of both fundamental and practical importance. On the fundamental side, such studies have provided insight into the nature and strength of the forces that stabilize nucleic acids in the myriad of structural states they can assume (1-7). On the practical side, such studies have produced databases that are used to predict the stability and selectivity of hybridization events required in a broad range of nucleic acid-based diagnostic and therapeutic protocols (3, 8-11, 19, 42-44).Three aspects of the current nucleic acid thermodynamic library that are conspicuously deficient are values for the heat capacity change(s), ⌬C P , the volume changes, ⌬V, and the compressibility changes, ⌬K s , which accompany nucleic acid conformational transitions. These deficiencies are of particular concern because ⌬C P , ⌬V, and ⌬K s provide unique insights into the role of solvent i...

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Predicting sequence‐dependent melting stability of short duplex DNA oligomers

Cited by 71 publications

References 0 publications

Specific Binding of Different Vesicle Populations by the Hybridization of Membrane-Anchored DNA

Specific Binding of Different Vesicle Populations by the Hybridization of Membrane-Anchored DNA

Application of nucleic acid–lipid conjugates for the programmable organisation of liposomal modules

A more unified picture for the thermodynamics of nucleic acid duplex melting: A characterization by calorimetric and volumetric techniques

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