Persistence Length of Single-Stranded DNA

Tinland, B.; Pluen, Alain; Sturm, Jürgen; Weill, G.

doi:10.1021/ma970381+

Cited by 505 publications

(526 citation statements)

References 15 publications

(20 reference statements)

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“…4. The values for (dT) 30 , (dT) 40 , and (dT) 50 match each other and are larger than previous results between 0.75 and 4 nm (28,29,(31)(32)(33) (variations primarily due to differences in buffers and sequence). In theoretical models, l P is divided into intrinsic l P 0 and electrostatic l P el components, l P ϭ l P 0 ϩ l P el .…”

Section: And 4; See Sample Preparation and Characterization Insupporting

confidence: 74%

Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins

Laurence

Kong²,

Jäger³

et al. 2005

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

220

227

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We study protein and nucleic acid structure and dynamics using single-molecule FRET and alternating-laser excitation. Freely diffusing molecules are sorted into subpopulations based on singlemolecule signals detected within 100 s to 1 ms. Distance distributions caused by fluctuations faster than 100 s are studied within these subpopulations by using time-correlated singlephoton counting. Measured distance distributions for dsDNA can be accounted for by considering fluorophore linkers and fluorophore rotational diffusion, except that we find smaller fluctuations for internally labeled dsDNA than DNA with one of the fluorophores positioned at a terminal site. We find that the electrostatic portion of the persistence length of short single-stranded poly(dT) varies approximately as the ionic strength (I) to the ؊1͞2 power (I ؊1/2 ), and that the average contribution to the contour length per base is 0.40 -0.45 nm. We study unfolded chymotrypsin inhibitor 2 (CI2) and unfolded acyl-CoA binding protein (ACBP) even under conditions where folded and unfolded subpopulations coexist (contributions from folded proteins are excluded by using alternating-laser excitation). At lower denaturant concentrations, unfolded CI2 and ACBP are more compact and display larger fluctuations than at higher denaturant concentrations where only unfolded proteins are present. The experimentally measured fluctuations are larger than the fluctuations predicted from a Gaussian chain model or a wormlike chain model. We propose that the larger fluctuations may indicate transient residual structure in the unfolded state.conformational dynamics ͉ protein folding ͉ single-molecule fluorescence spectroscopy ͉ nucleic acid structure ͉ fluorescence resonance energy transfer I n contrast to neutral homopolymers (1), biopolymers such as proteins and nucleic acids have long-range Coulomb interactions (2) and specific, intrachain interactions that strongly affect their structure and dynamics. Protein folding is the most spectacular manifestation of these interactions (3). Understanding biopolymer energy landscapes requires measurements of fluctuating distance distributions occurring over short distances (0.1-100 nm) and many time scales (picoseconds to minutes) (4). The structure and dynamics of charged polymer chains (polyelectrolytes), including dsDNA and ssDNA, are strongly affected by long-range, electrostatic repulsion (2). Because simulations and theory have focused on dilute, single-chain properties, a regime difficult to access by conventional methods, experimental validation of many predictions has been lacking (5). In protein folding studies, folded, unfolded, and partially folded species may be simultaneously present and rapidly interconverting, obscuring the properties of individual species. An experimental method that unravels distance distributions and fast conformational fluctuations is therefore much-needed.Previous protein folding studies with single-molecule FRET (6-8) measured distance distributions with time resolutions of Ϸ100 s. Using ...

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Section: And 4; See Sample Preparation and Characterization Insupporting

confidence: 74%

Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins

Laurence

Kong²,

Jäger³

et al. 2005

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

220

227

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“…From the energy landscape and extension histograms, we obtained predictions for ⌬x, ⌬G, the barrier heights at F 0 and F 1/2 , and the barrier location along the reaction coordinate. For all hairpins, model predictions were averaged over the same range of WLC parameters consistent with previous measurements: ssDNA persistence length of 1.0-1.5 nm (33,(41)(42)(43)(44) and contour length per nucleotide of 0.58-0.67 nm (45).…”

Section: Resultsmentioning

confidence: 99%

Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins

Woodside

Behnke-Parks²,

Larizadeh³

et al. 2006

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

426

545

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Nucleic acid hairpins provide a powerful model system for probing the formation of secondary structure. We report a systematic study of the kinetics and thermodynamics of the folding transition for individual DNA hairpins of varying stem length, loop length, and stem GC content. Folding was induced mechanically in a highresolution optical trap using a unique force clamp arrangement with fast response times. We measured 20 different hairpin sequences with quasi-random stem sequences that were 6 -30 bp long, polythymidine loops that were 3-30 nt long, and stem GC content that ranged from 0% to 100%. For all hairpins studied, folding and unfolding were characterized by a single transition. From the force dependence of these rates, we determined the position and height of the energy barrier, finding that the transition state for duplex formation involves the formation of 1-2 bp next to the loop. By measuring unfolding energies spanning one order of magnitude, transition rates covering six orders of magnitude, and hairpin opening distances with subnanometer precision, our results define the essential features of the energy landscape for folding. We find quantitative agreement over the entire range of measurements with a hybrid landscape model that combines thermodynamic nearest-neighbor free energies and nanomechanical DNA stretching energies.DNA hairpin ͉ energy landscape ͉ force clamp ͉ optical tweezers ͉ single molecule H airpins formed from self-complementary sequences supply a model system for studying folding and duplex formation, the most fundamental processes for generating structure in nucleic acids. Using hairpins, repeated measurements can be made on the same molecule, facilitating single-molecule studies. Furthermore, by simply altering the nucleotide sequence, physical properties such as folding energies, kinetic rates, and distances to transition states all can be changed systematically. Hairpins also play essential roles in vivo. DNA hairpins bind proteins to regulate transcription (1), and hairpin intermediates are involved in both replication and recombination (2, 3). RNA hairpins form tertiary contacts (4), bind to proteins (2), regulate transcription (5), and mediate RNA interference (6). Understanding the factors that influence hairpin folding should therefore not only elucidate principles of structure formation in nucleic acids but may also shed light on the biological roles played by these structures.Extensive calorimetric and melting studies have been carried out to generate predictive rules for the thermodynamic stability of arbitrary nucleic acid duplexes (7). The kinetic properties of duplex formation, however, remain less well understood, particularly those related to the nature of the transition state. Temperature-jump studies of annealing in short duplexes have been interpreted in terms of the nucleation of a transition state consisting of Ϸ1-3 bp, followed by zippering of the remaining stem (8). This interpretation, however, rests on the assumption that the enthalpy of activation arises ...

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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

117

162

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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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Persistence Length of Single-Stranded DNA

Cited by 505 publications

References 15 publications

Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins

Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins

Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins

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

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