Sequence Dependent Rigidity of Single Stranded DNA

Goddard, Noël L.; Bonnet, Grégoire; Krichevsky, Oleg; Libchaber, Albert

doi:10.1103/physrevlett.85.2400

Cited by 281 publications

(428 citation statements)

References 15 publications

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“…To isolate the thermodynamic contribution of order in the triplet repeat loop regions of these hairpins, we have compared these hairpins to the similarly constructed hairpin, X[TTT] 6 X. Implicit in the choice of X[TTT] 6 X as a thermodynamic reference is the assumption that the all-T loop resembles, more than any other base combination, an unstructured loop (47,(49)(50)(51)(52)(53)(54). In support of this assumption, we note that the measured enthalpy for X[TTT] 6 X is in good agreement with the enthalpy predicted by nearest-neighbor data (55,56) for the hairpin stem.…”

Section: Resultsmentioning

confidence: 99%

Conformational energetics of stable and metastable states formed by DNA triplet repeat oligonucleotides: Implications for triplet expansion diseases

Völker

Makube

Plum

et al. 2002

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

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We have embedded the hexameric triplet repeats (CAG)6 and (CTG) 6 between two (GC)3 domains to produce two 30-mer hairpins with the sequences d[(GC) 3(CAG)6(GC)3] and d[(GC)3(CTG)6(GC)3]. This construct reduces the conformational space available to these repetitive DNA sequences. We find that the (CAG) 6 and (CTG)6 repeats form stable, ordered, single-stranded structures. These structures are stabilized at 62°C by an average enthalpy per base of 1.38 kcal⅐mol ؊1 for the CAG triplet and 2.87 kcal⅐mol ؊1 for the CTG triplet, while being entropically destabilized by 3.50 cal⅐K ؊1 ⅐mol ؊1 for the CAG triplet and 7.6 cal⅐K ؊1 ⅐mol ؊1 for the CTG triplet. Remarkably, these values correspond, respectively, to 1͞3 (for CAG) and 2͞3 (for CTG) of the enthalpy and entropy per base values associated with Watson-Crick base pairs. We show that the presence of the loop structure kinetically inhibits duplex formation from the two complementary 30-mer hairpins, even though the duplex is the thermodynamically more stable state. Duplex formation, however, does occur at elevated temperatures. We propose that this thermally induced formation of a more stable duplex results from thermal disruption of the single-stranded order, thereby allowing the complementary domains to associate (perhaps via "kissing hairpins"). Our melting profiles show that, once duplex formation has occurred, the hairpin intermediate state cannot be reformed, consistent with our interpretation of kinetically trapped hairpin structures. The duplex formed by the two complementary oligonucleotides does not have any unusual optical or thermodynamic properties. By contrast, the very stable structures formed by the individual single-stranded triplet repeat sequences are thermally and thermodynamically unusual. We discuss this stable, triplet repeat, single-stranded structure and its interconversion with duplex in terms of triplet expansion diseases.

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Section: Resultsmentioning

confidence: 99%

Conformational energetics of stable and metastable states formed by DNA triplet repeat oligonucleotides: Implications for triplet expansion diseases

Völker

Makube

Plum

et al. 2002

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

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“…Such increase in entropy of ssDNA has been observed earlier upon binding to protein 46,47 . Also the entropic and enthalpic rigidity of the polyA and polyT sequence is well known from various single molecule fluorescence studies 48 .…”

Section: Sequence Dependence Of Complexationmentioning

confidence: 99%

Structure and Dynamics of DNA−Dendrimer Complexation: Role of Counterions, Water, and Base Pair Sequence

2006

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“…This can be understood from the persistence length being highly sensitive to other factors such as base sequence 45 and the experimental set-up used to measure the persistence length, for example fluorescence spectroscopy 39 , laser tweezers 40 , hairpin loops 41 and gel electrophoresis 42 . Fig.…”

Section: A Persistence Length Of Ssdna and Dsdnamentioning

confidence: 99%

A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality

Morriss-Andrews

Rottler

Plotkin

2010

The Journal of Chemical Physics

118

165

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We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with minimal phenomenology. Persistence length, degree of stacking, and twist are studied by molecular dynamics simulation as functions of temperature, salt concentration, sequence, interaction potential strength, and local position along the chain, for both single-and double-stranded DNA where appropriate. The model of DNA shows several phase transitions and crossover regimes in addition to dehybridization, including unstacking, untwisting, and collapse which affect mechanical properties such as rigidity and persistence length. The model also exhibits chirality with a stable right-handed and metastable left-handed helix.

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Sequence Dependent Rigidity of Single Stranded DNA

Cited by 281 publications

References 15 publications

Conformational energetics of stable and metastable states formed by DNA triplet repeat oligonucleotides: Implications for triplet expansion diseases

Conformational energetics of stable and metastable states formed by DNA triplet repeat oligonucleotides: Implications for triplet expansion diseases

Structure and Dynamics of DNA−Dendrimer Complexation: Role of Counterions, Water, and Base Pair Sequence

A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality

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