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Blommers, Marcel J. J.; Haasnoot, C. A. G.; Walters, J. A. L. I.; Marel, G.A. van der; Boom, Jacques H. van; Hilbers, C. W.

doi:10.1021/bi00422a011

Cited by 37 publications

(36 citation statements)

References 12 publications

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“…a 180" turn) in the direction of the phosphate backbone. This has been observed for the first time in the crystal structures of the riboniicleotides UpA [29] and A' pApA [30] and in the crystal structure [31] and NMR structure [32] of the cyclic deoxyribonucleotide d(pApA). In all of these examples, the remaining part of the backbone in the dinucleotide unit exhibits an A-type backbone conformation.…”

mentioning

confidence: 86%

“…In the latter case, the sugar(s) may switch of a S-type conformation, while retaining 4 3 ' ) and ((5') in the gauche' domain and preserving the 180" turn in the backbone. This requires adjustment of the other torsion angles otherwise severe steric hindrance of the H3' atoms of the adjacent sugars will occur [33]. In d(ATCCTATTRTATAGGAT) the sugar moieties of the L3 and L4 residues are S puckered (Tables 2 and 6) NMR spectra were recorded at the Dutch National Hf-NMR Facility (Nijmegen, The Netherlands) supported by the Stichting Scheikundig Onderzoek Nederland (SON).…”

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confidence: 99%

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The three‐dimensional structure of a DNA hairpin in solution

Blommers¹,

Ven²,

Marel

et al. 1991

European Journal of Biochemistry

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The hairpin formed by d(ATCCTATTTATAGGAT) was studied by means of two-dimensional NMR spectroscopy and conformational analysis. Almost all 'H resonances of the stem region could be assigned, while the 'H and 31P spectra of the loop region were interpreted completely; this includes the stereospecific assignment of the H5' and H5" resonances. The derivation of the detailed loop structure was carried out in a stepwise fashion including some improved and new methods for structure determination from NMR data. In the first step, the mononucleotide structures were examined. The conformational space available to the mononucleotide was scanned systematically by varying the glycosidic torsion angle and pseudorotational parameters. Each generated conformer was tested against the experimental J coupling constants and NOE parameters. In the following stage, the structures of dinucleotides and longer fragments were derived. Inter-residue distances between protons were calculated by means of a procedure in which the simulated NOEs, obtained via a relaxation-matrix approach, were fitted to the experimental NOEs without the introduction of a molecular model. In addition, the backbone torsion angles fl, y and c were deduced from homocoupling and heterocoupling constants. These data served as constraints in the next step, in which the loop sequence was subjected to a multi-conformer generation procedure. The resulting structures were tested against the mentioned constraints and disregarded if these constraints were violated. This yielded a family of structures for the loop region, confined to a relatively narrow conformational space. A representative conformation was subsequently docked on a B-type stem which fulfilled the structural constraints (derived from the NMR experiments for the stem region) to yield the hairpin structure. Results obtained from subsequent restrained-molecular-mechanics as well as free-molecular-mechanics calculations are in accordance with those obtained by means of the analysis described above.The structure of the hairpin loop is a compactly folded conformation and the first base of the central TTTA region forms a Hoogsteen T-A pair with the fourth base. This Hoogsteen base pair is stacked upon the sixth base pair of the B-type double-helical stem. The second base of the loop is folded into the minor groove, whereas the third base of the loop is partly stacked on the first and fourth bases. The phosphate backbone exhibits a sharp turn between the third and fourth nucleotides of the loop. The peculiar structure of this hairpin loop is discussed in relation to loop folding in DNA and RNA hairpins and in relation to a general model for loop folding.Loop structures in RNA and DNA hairpins have been the subject of numerous studies. We have been interested in these structures because they may serve as models for the folding which occurs in RNA and DNA molecules in the cell, and also because they may provide insight into the mechanism underlying the folding. Our initial studies were concerned with the hairpin fo...

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mentioning

confidence: 86%

mentioning

confidence: 99%

The three‐dimensional structure of a DNA hairpin in solution

Blommers¹,

Ven²,

Marel

et al. 1991

European Journal of Biochemistry

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“…The individual s, C, a, 1, and y values for the 9C-p-1OA backbone conformation in the loop are -170°, 1240, 720, -1080, and -1790, respectively. From crystallographic (25)(26)(27) and NMR (19,(28)(29)(30) studies of various sized loops, it would appear that the last (3') loop phosphodiester that links it to the 5'-end of the stem is generally close to the C(g+) a(g+-t) P3(t-g-) conformation.…”

Section: Structural Featuresmentioning

confidence: 99%

A single G-to-C change causes human centromere TGGAA repeats to fold back into hairpins.

Zhu

Chou

Reid

1996

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

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Recently, we established that satellite III (TGGAA). tandem repeats, which occur at the centromeres of human chromosomes, pair with themselves to form an unusual "self-complementary" antiparallel duplex containing (GGA)2 motifs in which two unpaired guanines from opposite strands intercalate between sheared GoA base pairs. In separate studies, we have also established that the GCA triplet does not form bimolecular (GCA)2 motifs but instead promotes the formation of hairpins containing a GCA-turn motif in which the loop contains a single cytidine closed by a sheared GoA pair. Since TGCAA is the most frequent variant of TGGAA found in satellite III repeats, we reasoned that the potential of this variant to form GCA-turn miniloop fold-back structures might be an important factor in modulating the local structure in natural (TGGAA The classical satellite III of human DNA, which has been located in the centromere region of chromosomes (1), is composed of (TGGAA)n repeats with the consensus sequence 5'-CAACCCGAM(TGGAA), (2). From the cooperative UVmelting transition Grady et al. (1) found that, in the absence of the complementary TTCCA strand, (TGGAA)6 alone can somehow pair with itself to form a stable duplex with a Tm of 65°C. We recently solved the solution structure of the antiparallel "self-complementary" (TGGAATGGAA)2 duplex containing a tandem TGGAA repeat; this structure contains two (GGA)2 motifs in which the central guanines from opposite strands are unpaired and intercalatively stacked on each other between flanking GoA pairs (3, 4). The flanking G°A pairs are in the sheared, or side-by-side, configuration (5-7) and the guanines of the (GGA)2 motif form a four-guanine interstrand stack. Although the (TGGAA)n repeat is highly conserved in satellite III, perfect repeats rarely continue for more than 12-15 repeats (60-75 bp) with several variants that differ from the consensus pentamer by only a single base. The most frequent among these variants is TGCAA-i.e., the central GGA triplet [which forms the self-paired (GGA)2 motifl is changed to GCA. Interestingly, we recently found that the triplet GCA is a very strong hairpin promoter (8, 9). Among the four GNA triplets in a d(NAATGNAATG) sequence context, GGA predominantly forms bimolecular duplexes containing a (GGA)2 motif, as described previously (3, 4), while GCA forms a unimolecular hairpin (8, 9) and GAA and GTA form a mixture of mostly hairpin in equilibrium with a minor (GNA)2 duplex form (9). If (TGGAA), repeats self-pair to form antiparallel (GGA)2 motifs in vivo, we reasoned that occasional TGCAA pentamers interspersed among (TG-GAA), repeats might promote folding back of the chain on itself by forming GCA-turn loops, and thus modulate centromere folding. In the present paper, we have used NMR, distance geometry, restrained molecular dynamics, and backcalculation refinement to study the solution structure of the DNA heptadecamer (G)TGGAATGCAATGGAA(C), which contains three centromeric pentamer repeats, the middle one of which is changed from TG...

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“…12 [246]. From an almost complete assignment of the 2D spectrum of the hexadecanucleotide in combination with a J coupling analysis, it could be derived that all of the sugars except the terminal ones are predominantly in an S-type conformation, indicating that the stem region adopts a B-type structures.…”

Section: N a Hairpinsmentioning

confidence: 98%

“…Three-dimensional model of the hairpinjormed by the sequence f( ATCCTATTTTTAGGAT). This model was derived from analysis if J coupling constants and NOE data, and was refined by means of nolecular mechanics calculations [246] Jase of the loop. The sharp turn in the loop is accommodated by the unusual value of the torsion angle, y, of the fourth nucleotide which adopts a trans conformation in contrast to the usual gauche' conformation in normal B-type helices.…”

Section: N a Hairpinsmentioning

confidence: 99%