Minihairpin Loops in DNA: Experimental and Theoretical Studies

Altona, C.; Beuzekom, Aart A. van; Orbons, Leonard P. M.; Pieters, Jane M. L.

doi:10.1007/978-94-009-3117-6_8

Cited by 4 publications

(2 citation statements)

References 45 publications

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“…This peculiar loop structure is characterized by atypical NOEs between the loop residues and the 3' side of the stem on the one hand and by relatively large downfield shifts of H6 (4) (6 = 4.847 ppm) and Hl'(4) (6 = 3.363 ppm) signals and by large upfield shifts of the sugar-proton resonances of residue dA5 on the other hand (Pieters et al, unpublished results). Recently, we reported the structural details of the hairpin form of the mismatched DNA octamer d(mSCGm5CGTGmS-CG) [28,[36][37][38] in solution. Again, this hairpin has three regular base pairs making up the stem, leaving the two central residues to form the loop.…”

Section: Tlzr Hairpin Formmentioning

confidence: 99%

Conformational consequences of the incorporation of arabinofuranosylcytidine in DNA

Pieters

Vroom

Marel

et al. 1989

European Journal of Biochemistry

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The self-complementary octamers d(CGCTAGCG) and d(CGaCTAGCG) (aC, arabinofuranosylcytidine) were studied by means of NMR spectroscopy. It is shown that d(CGaCTAGCG), under suitable conditions of oligonucleotide concentration, ionic strength and temperature, exclusively adopts a hairpin structure. However, under the same experimental conditions (5 mM DNA, no added salt, 295 K) d(CCCTAGCG) mainly adopts a B-DNA-type duplex. At lower temperatures (G290 K) the hairpin form of d(CGaCTACCG) occurs in slow exchange with an intact B-DNA-type duplex. When the DNA concentration of d(CGCTAGCG) is dramatically reduced (GO.5 mM) the hairpin form becomes highly favoured at the expense of the dimer. Moreover, protonchemical-shift considerations indicate that the structural features of the hairpin structure of d(CGCTAGCG) mimic, in part, those of the modified octamer d(CGaCTAGCG), i.e. a loop comprising only the two central residues with the thymine located into the minor groove (Pieters, J. M. L., de Vroom, E., van Recently, we carried out an NMR and model-building study on the modified octamer d(CGaCTAGCG) at low DNA concentration, ionic strength and temperature (Pieters et al., unpublished results). Under these experimental conditions the DNA compound exclusively prefers to adopt a monomeric hairpin structure. It was demonstrated that this hairpin structure consists of a double-helical stem formed by two WatsonCrick-type dC . dG base pairs and one aC . dG base pair, which closes the loop formed by the two remaining residues (Fig. 2). The vertical base stacking is not propagated into the loop region; instead, the thymine swings into the minor groove.In order to obtain detailed information regarding the effect of incorporation of aC into the DNA strand upon the Correspondence to C .

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Section: Tlzr Hairpin Formmentioning

confidence: 99%

Conformational consequences of the incorporation of arabinofuranosylcytidine in DNA

Pieters

Vroom

Marel

et al. 1989

European Journal of Biochemistry

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“…(Many molecular biologists use "hairpin" to refer to a stem with a loop of size 0 or 1 at the end, i.e., a stem with virtually no loop. These structures are not allowed within our model, and it is not certain that such structures occur in vivo [Altona et al, 1988]. )…”

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confidence: 99%

Artificial intelligence and molecular biology

1994

Choice Reviews Online

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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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Minihairpin Loops in DNA: Experimental and Theoretical Studies

Cited by 4 publications

References 45 publications

Conformational consequences of the incorporation of arabinofuranosylcytidine in DNA

Conformational consequences of the incorporation of arabinofuranosylcytidine in DNA

Artificial intelligence and molecular biology

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

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