Parallel and Antiparallel A*A-T Intramolecular Triple Helices

Dagneaux, C; Gousset, Hervé; Shchyolkina, Anna K.; Ouali, Mohammed Assam; Letellier, R.; Liquier, J.; Florentiev, V. L.; Taillandier, E.

doi:10.1093/nar/24.22.4506

Cited by 28 publications

(19 citation statements)

References 45 publications

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“…1(a, b) the melting profiles and their first derivatives are presented. In agreement with Dagneaux et al (1996), who studied similar paperclips, and, assuming their interpretation is correct, we assign the transition of paperclip (I) at 58.3°C to duplex melting (A T) and the small transition at 28.4°C to the melting of an antiparallel triplex T A Â A (the known purine motif). This interpretation is supported by the melting behaviour of paperclip (II) with the mismatch (TG) in the third strand region, since only the low temperature transition is shifted to lower temperatures (22.4°C) and is broadened.…”

Section: Paperclips Containing Two Adenine and One Thymine Strandssupporting

confidence: 87%

“…In our investigations of similar systems [d(T 12 C 4 A 12 C 4 A 12 ) and d(A 12 C 4 T 12 C 4 A 12 )], we also found two T m values in the antiparallel system [ Fig. 1(a, b)] comparable to the corresponding values of Dagneaux et al (1996). In the parallel system, however, we found only a single melting transition with a T m value (60°C) higher than the duplex to coil T m (58°C) of the antiparallel system.…”

Section: Pyrimidine Motifsupporting

confidence: 75%

“…Studies on paperclips with the purine strands composed of alternating AG bases have shown that the parallel triplex is significantly less stable than the antiparallel one (Shchyolkina et al, 1995). Dagneaux et al (1996) carried out melting experiments on the paperclip triplexes d(A 10 )-L-d(A 10 )-L-d(T 10 ) and d(A 10 )-L-d(T 10 )-L-d(A 10 ) at 0.1 M Mn 2 [L = -pO(CH 2-CH 2 O) 3 p-, a triethylene glycol linker]. They found too that the T m values for the parallel triplex are lower than those for the antiparallel triplex.…”

Section: Pyrimidine Motifmentioning

confidence: 99%

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Evidence for a DNA triplex in a recombination‐like motif: I. Recognition of Watson–Crick base pairs by natural bases in a high‐stability triplex

Walter

Schütz

Simon

et al. 2001

J of Molecular Recognition

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Data are presented on a triplex type with two parallel homologous strands for which triplex formation is almost as strong as duplex formation at least for some sequences and even at pH 7 and 0.2 M NaCl. The evidence mainly rests upon comparing thermodynamic properties of similar systems. A paperclip oligonucleotide d(A12C4T12C4A12) with two linkers C4 obviously can form a triplex with parallel back-folded adenine strand regions, because the single melting transition of this complex splits in two transitions by introducing mismatches only in the third strand region. Respectively, a hairpin duplex d(A12C4T12) and a single strand d(A12) form a triplex as a 1:1 complex in which the second adenine strand is parallel oriented to the homologous one in the Watson-Crick paired duplex. In this system the melting temperature T(m) of the triplex is practically the same as that of the duplex d(A12)-d(T12), at least within a complex concentration range of 0.2-4.0 microM. The melting behaviour of complexes between triplex stabilizing ligand BePI and the system hairpin duplex plus single strand supports the triplex model. Non-denaturing gel electrophoresis suggests the existence of a triplex for a system in which five of the twelve A-T*A base triads are substituted by C-G*C base triads. The recognition between any substituted Watson-Crick base pair (X-Y) in the hairpin duplex d(A4XA7C4T7YT4) and the correspondingly replaced base (Z) in the third strand d(A4ZA7) is mutually selective. All triplexes with matching base substitutions (Z = X) have nearly the same stability (T(m) values from 29 to 33.5 degrees C), whereas triplexes with non-matching substitutions (Z not equal X) show a clearly reduced stability (T(m) values from 15 to 22 degrees C) at 2microM equimolar oligonucleotide concentration. Most nucleic acid triple helices hitherto known are limited to homopurine-homopyrimidine sequences in the target duplex. A stable triplex formation is demonstrated for inhomogeneous sequences tolerating at least 50% pyrimidine content in the homologous strands. On the basis of the surprisingly similar thermodynamic parameters for duplex and triplex, and of the fact that this triplex type seems to be more stable than many other natural DNA triplexes known, and on the basis of semiempirical and molecule mechanical calculations, we postulate bridging interactions of the third strand with the two other strands in the triplex according to the recombination motif. This triplex, denoted by us 'recombination-like form', tolerates heterogeneous base sequences.

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Section: Paperclips Containing Two Adenine and One Thymine Strandssupporting

confidence: 87%

Section: Pyrimidine Motifsupporting

confidence: 75%

Section: Pyrimidine Motifmentioning

confidence: 99%

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Evidence for a DNA triplex in a recombination‐like motif: I. Recognition of Watson–Crick base pairs by natural bases in a high‐stability triplex

Walter

Schütz

Simon

et al. 2001

J of Molecular Recognition

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“…In the spectral range between 1750 and 1500 cm -1 , the adenine residues gave only one band at 1621 cm -1 ( Figure 3). This mode, assigned to ND 2 scissoring coupled to ring CdC and CdN stretching vibrations, has been used previously to follow the melting of DNA duplexes and triplexes (21,22). In addition to the C6dO6 stretching band, the guanine residues have a band at 1576 cm -1 assigned to Cd N (except C8dN7) and C-N bond stretching vibrations (23,24).…”

Section: Results and Discusionmentioning

confidence: 95%

FTIR and UV Spectroscopy of Parallel-Stranded DNAs with Mixed A•T/G•C Sequences and Their A•T/I•C Analogues

et al. 1998

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The infrared spectra of parallel-stranded (ps) hairpin duplexes with mixed A*T/G*C composition and either isolated or sequential G*C pairs were studied in comparison with antiparallel-stranded (aps) duplexes and a corresponding set of molecules with hypoxanthine as a G base analogue lacking the exocyclic amino group. The ps duplexes showed the characteristic bands for the C2=O2 and C4=O4 stretching vibrations of thymine residues in trans-Watson-Crick A*T pairing at 1683 and 1668 cm-1. The latter band was superimposed on the stretching vibration of the free C6=O6 group of guanine. Substitution of guanine by hypoxanthine inhibited the formation of ps hairpin duplexes whatever the sequence, demonstrating that in the H-bonding between G and C the 2-NH2 group is necessary for stabilizing all of the investigated ps duplexes. This result is in agreement with a model of trans-Watson-Crick G*C base pairs with two H-bonds [N2H2(G)-N3(C) and N1H(G)-O2(C)]. However, trans-Watson-Crick A*T and G*C base pairs with two H-bonds are not isomorphous, which may explain the decreased stability of the ps, but not the aps, duplexes upon increasing the number of A*T/G*C steps. Molecular modeling studies performed on two of the ps duplexes reveal the existence of propeller twist for avoiding a clash between the N2(G) and N4(C) amino groups, and favorable stacking of sequential G*C base pairs. The optimized hairpin ps duplexes invariably incorporated G*C base pairs with two H-bonds, regardless of the initial structures adopted for the force field calculations.

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“…To date, the evidence for the existence of such a ªparallelº triplex is brief, and comes mainly from foldback molecules [2], crystals [3], or homopolymeric sequences containing just one type of triplet [4,5]. In spite of the lack of exhaustive physical-chemical evidence, triplex affinity capture of poly(dG-dA), poly(dTdC)-containing tracts from human chromosome restriction digests is thought to rely on parallel triplex formation [6].…”

mentioning

confidence: 99%