Extracting Thermodynamic Data From Equilibrium Melting Curves for Oligonucleotide Order-Disorder Transitions

Kj, Breslauer

doi:10.1007/978-1-59259-513-6_14

Cited by 94 publications

(86 citation statements)

References 45 publications

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“…The optical and calorimetric melting profiles were analyzed as previously described 36,37 to extract melting temperatures, T,,, and T,,, (from uv and DSC) as well as direct, model-independent transition enthalpies, AH,,, (from DSC), and model-dependent, van't Hoff enthalpies, AHvH (from uv and DSC). We also have combined the calorimetrically determined AH value with the optically derived concentration dependence of T,,, data to evaluate the effective molecularity of the duplex melting process, as well as to evaluate the free energy change, AG, associated with duplex disruption.…”

Section: Duplex Meltingmentioning

confidence: 99%

The impact of a bistrand abasic lesion on DNA duplex properties

et al. 1996

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Section: Duplex Meltingmentioning

confidence: 99%

The impact of a bistrand abasic lesion on DNA duplex properties

et al. 1996

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“…The effects of these mutations on the stability of the TAR RNA-aptamer complex were analyzed by thermal denaturation monitored by UV-absorption spectroscopy (26,27). The binding kinetics were determined by using surface plasmon resonance (SPR).…”

mentioning

confidence: 99%

Is a Closing “GA Pair” a Rule for Stable Loop-Loop RNA Complexes?

Ducongé

Primo

Toulmé

2000

Journal of Biological Chemistry

118

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Intermolecular interactions between structured RNA play key roles in the regulation of gene expression. In Escherichia coli, the replication of the ColE1 plasmid is regulated by the interaction of two RNA transcripts, RNA I and RNA II, which fold as hairpins (1, 2). The interaction starts with base pairing between the complementary loops of these RNAs and leads to the formation of a double-stranded RNA along the entire length of RNA I, thus disrupting the RNA II hybridization with the template DNA required for replication (3,4). Even if the stability of these so-called "kissing" complexes is primarily based on loop complementarity (2), factors such as the orientation of the loops (5), the loop closing base pair, and the sequence of each stem next to the loop (6), are crucial for stability. For instance, the loop inversion 5Ј to 3Ј induces a 350-fold increased stability of the RNA I-RNA II complex.In HIV-1, 1 the dimerization of the genomic RNA involves the formation of a loop-loop complex between two structured regions (7). The dimerization initiation site of HIV-1 RNA folds as a hairpin, which is closed by a noncanonical AA pair. The 9-nt-long loop contains a 6-nt self-complementary sequence flanked by two 5Ј and one 3Ј purines, which, together with loop complementarity, are crucial for the dimerization process (8). Non-Watson-Crick interactions in RNA molecules have been also reported in the viral RNA element bound by the Rev protein of HIV-1 (9), in GRNA tetraloops (10, 11), tRNAs (12-14), and tandem mismatches within duplexes (15-17). All these results indicate that interactions other than canonical base pairs contribute to the structural diversity displayed by RNAs, which, as a matter of fact, is crucial for activity. The contribution of such noncanonical interactions can actually be conveniently explored by in vitro selection, since neither the structure of the target nor the interactions between the target and the interacting aptamer need to be known (18,19). This strategy was successfully used in our laboratory to identify DNA aptamers against DNA (20 -22) and RNA hairpin structures (23).Recently, RNA aptamers specific for the trans-activationresponsive (TAR) RNA (24) were selected by in vitro selection (25). The TAR RNA element is a 59-nt-long imperfect stem loop structure located at the 5Ј end of the retroviral RNA. A 3-nt bulge in the upper part of the hairpin constitutes part of the binding site of the viral protein Tat, which recruits cyclin T 1 . Together with additional TAR-bound cellular proteins, this complex prevents abortion of the transcription of the retroviral genome. Therefore, TAR plays a key role in the life cycle of HIV-1 and constitutes a valid target for the development of ligands, which could inhibit its interaction with viral and cellular proteins, thus ultimately preventing the development of the virus. The isolated high affinity anti-TAR aptamers were shown to fold as imperfect hairpins and form kissing complexes with the targeted RNA at physiological magnesium concentration. The ...

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“…6 The transitions are accompanied by large energy change ( 8-10 kcal/mol for the sequences being discussed) and a clear melting point, characteristic of single-stranded self-transition for hairpin formation, as opposed to loose interstrand aggregation or self-helix formation which exhibit small energy variation and broad melting. 26 Overall it is observed that of the two families, the (GACX) motif can direct the formation of structures stabilized under acidic conditions provided that the CG base stack is absent from the repeat motif. These structures have the potential to differ from classical W-C DNA duplexes, due to the abundance of non-canonical pairings between the protonated bases.…”

Section: Structural Properties Of Dna Oligomers 163mentioning

confidence: 96%

“…24 The Marquardt nonlinear least squares method, implemented within the program was used to fit the absorbance versus temperature curves. The melting temperature, T m , was also calculated using a two-state analysis method for non self-complementary associations, 25,26 (See Supporting Information).…”

Section: Determination Of Thermodynamic Parameters Using Meltwin 35mentioning

confidence: 99%

Structural properties of DNA oligomers containing (GACX)_n and (GAXC)_n tandem repeats

2011

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The antisense DNA sequence of mature mouse micro RNA, miR341, includes three repeats of the tetranucleotide (GACC). The -GAC- repeat is known to form a parallel duplex, in acidic environments. The thermal melting profile of miR341 DNA, at pH 4, 5, and 6 indicates the formation of a very stable structure, which loses its stability when pH is increased. Thus, the addition of a cytosine at the 3' end of the (GAC) motif preserves the molecule's potential to fold into an unusual structure at low pH. The effect of modifying the nucleotide composition of the GACC sequence on the secondary structures formed by oligomers containing seven tandem repeats of the altered motifs was examined here. UV melting profiles were determined, as a function of pH, for 28-mers of the two series (GAXC)(7) and (GACX)(7) (X= A/C/T/G)(.) The sequence (GACC)(7) was found to be extremely sensitive to pH variations, with a stable structure formed at pH 5 (T(m) ≥ 60°C). NMR spectroscopy established that the low pH structure is not B-DNA. (GACA)(7) and (GACT)(7) also formed stable structures at low pH but the addition of guanine at the 3'end, as seen in the (GACG) series resulted in the loss of this property. Introducing a break in the 5'-GAC-3' motif, explored in the (GAXC) series, also inhibits formation of stable structures under acidic conditions.

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Extracting Thermodynamic Data From Equilibrium Melting Curves for Oligonucleotide Order-Disorder Transitions

Cited by 94 publications

References 45 publications

The impact of a bistrand abasic lesion on DNA duplex properties

The impact of a bistrand abasic lesion on DNA duplex properties

Is a Closing “GA Pair” a Rule for Stable Loop-Loop RNA Complexes?

Structural properties of DNA oligomers containing (GACX)_n and (GAXC)_n tandem repeats

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Extracting Thermodynamic Data From Equilibrium Melting Curves for Oligonucleotide Order-Disorder Transitions

Cited by 94 publications

References 45 publications

The impact of a bistrand abasic lesion on DNA duplex properties

The impact of a bistrand abasic lesion on DNA duplex properties

Is a Closing “GA Pair” a Rule for Stable Loop-Loop RNA Complexes?

Structural properties of DNA oligomers containing (GACX)n and (GAXC)n tandem repeats

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Product

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Structural properties of DNA oligomers containing (GACX)_n and (GAXC)_n tandem repeats