Structural Features of the DNA Hairpin d(ATCCTA-GTTA-TAGGAT): Formation of a G-A Base Pair in the Loop

Dongen, M.J.P. van; Mooren, M.M.W.; Willems, Edwin; Marel, Gijs A. van der; Boom, Jacques H. van; Wijmenga, Sybren S.; Hilbers, Cornelis W.

doi:10.1093/nar/25.8.1537

Cited by 51 publications

(53 citation statements)

References 37 publications

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“…A repulsive Morse potential (39) was added to model fluctuation-driven compression of the stem helix (i.e., negative extension), and the energy associated with stretching the fully unfolded state was included, using a WLC approximation. We then subtracted the mechanical work performed by the trap on the hairpin during unfolding, calculating the extension of the partially unzipped hairpin from previous FEC measurements of ssDNA (33) but taking into account the finite width of the stem helix as measured from NMR structures (40). Finally, we incorporated the effect of thermal fluctuations in the extension of the partially unzipped hairpin by smoothing the energy landscape by an amount proportional to the ssDNA stiffness, estimated by a WLC approximation.…”

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.

444

556

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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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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.

444

556

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“…1a). The native structure of this hairpin was obtained from NMR measurements (protein data bank entry 1AC7), [35,36] except for a point mutation in which the adenine at position 10 was replaced with a cytosine. The hairpin was chosen to enable comparison of the KIS model predictions with MD simulations (see below) starting from this NMR structure.…”

Section: Application Of the Modelmentioning

confidence: 99%

Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes

Lin

Meinhold

Shorokhov

et al. 2008

Phys. Chem. Chem. Phys.

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SummaryA 2D free energy landscape model is presented to describe the (un)folding transition of DNA/RNA hairpins, together with molecular dynamics simulations and experimental findings. The dependence of the (un)folding transition on the stem sequence and the loop length is shown in the enthalpic and entropic contributions to the free energy. Intermediate structures are well defined by the two coordinates of the landscape during (un)zipping. Both the free energy landscape model and the extensive molecular dynamics simulations totaling over 10 μs predict the existence of temperaturedependent kinetic intermediate states during hairpin (un)zipping and provide the theoretical description of recent ultrafast temperature-jump studies which indicate that hairpin (un)zipping is, in general, not a two-state process. The model allows for lucid prediction of the collapsed state(s) in simple 2D space and we term it the kinetic intermediate structure (KIS) model.

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“…1,2 Recently, an increasing number of studies were reported on DNA hairpins comprising a two-residue loop (or minihairpin) [3][4][5][6][7][8][9][10][11] or even a one-residue loop. [12][13][14][15] In fact, it seems that DNA preferably adopts small hairpin loops whenever possible.…”

Section: Introductionmentioning

confidence: 99%

“…In addition, a reduction of the space required to fit in the closing base pair is another way to remove steric strain in the loop. This is the reason why noncanonical base pairs like a G-A, 11 a wobble T-T, 9,16,17 a Hoogsteen T-A, 18 and a G(syn)-C ϩ10 closing base pair can effectively stabilize tight hairpin loops with the aid of their unusual base pairing schemes consisting of a reduced intrastrand C1Ј-C1Ј distance compared to that in canonical Watson-Crick base pairs. In our terminology a minihairpin is defined as a two-residue loop, in which the bases closing the loop lie in an approximately planar geometry and are connected by at least one hydrogen bond.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Structural similarities and differences between H1- and H2-family DNA minihairpin loops: NMR studies of octameric minihairpins

et al. 1998

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TheDNA sequences 5′‐d(CGC‐AC‐GCG)‐3′ (HPAC), 5′‐d(CGC‐AA‐GCG)‐3′ (HPAA), 5′‐d(CGC‐TC‐GCG)‐3′ (HPTC), and 5′‐d(CGC‐CT‐GCG)‐3′ (HPCT), were studied by means of nmr spectroscopy. At low DNA concentration and no added salt all four molecules adopt a minihairpin structure, containing three Watson–Crick base pairs and a two‐residue loop. The structure of the HPAC hairpin is based on quantitative distance restraints, derived by a full relaxation matrix approach (iterative relaxation matrix approach), together with torsion angles obtained from coupling constant analysis. The loop folding is of the H1‐family type, characterized by continuous 3′‐5′ stacking of the loop bases on the duplex stem. The structure of the HPAA hairpin is similar to that of HPAC, but is more flexible and has a lower thermodynamic stability (Tm 326 K vs 320 K). According to “weakly” distance‐constrained simulations in water on the HPAC minihairpin, the typical H1‐family loop folding remains intact during the simulation. However, residue‐based R factors of simulated nuclear Overhauser effect spectroscopy spectra, free molecular dynamics simulations in vacuo, and unusual chemical shift profiles indicate partial destacking of the loop bases at temperatures below the overall melting midpoint. The dynamic nature of the loop bases gives insight into the geometrical tolerances of stacking between bases in H1‐family minihairpin loops. The HPTC and HPCT minihairpins, both containing a pyrimidine base at the first position in the loop, adopt a H2‐family type folding, in which the first loop base is loosely bound in the minor groove and the second loop base is stacked upon the helix stem. The thermal stability for these two hairpins corresponds to 327–329 K, but depends on local base sequence. Preference for the type of folding depends on a single substitution from a pyrimidine (H2 family) to a purine (H1 family) at the first position of the miniloop and is explained by differences in base stacking energies, steric size, and the number of possible candidates for hydrogen bonds in the minor groove. In view of newly collected data, previous models of the H1‐family and H2‐family hairpins had to be revised and are now compatible with the reported HPTC and HPAC structures. The structural difference between the refined structure of HPAC and HPTC show that a conversion between H1‐family and H2‐family hairpins is geometrically possible by a simple pivot point rotation of 270° along two torsion angles, thereby swiveling the first loop base from a stacked position in a H1‐family folding toward a position in the minor groove in a H2‐family folding. The second loop residue subsequently shifts to the position of the first base in a concerted fashion. © 1998 John Wiley & Sons, Inc. Biopoly 46: 375–393, 1998

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Structural Features of the DNA Hairpin d(ATCCTA-GTTA-TAGGAT): Formation of a G-A Base Pair in the Loop

Cited by 51 publications

References 37 publications

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

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

Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes

Structural similarities and differences between H1- and H2-family DNA minihairpin loops: NMR studies of octameric minihairpins

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