Four-Stranded DNA Helices: Conformational Analysis of Regular Poly(dT) · Poly(dA) · Poly(dA) · Poly(dT) Helices with Various Types of Base Binding

Chernyi, A. A.; Lysov, Yu. P.; Il'ychova, I. A.; Zibrov, A. S.; Shchyolkina, Anna K.; Borisova, O. F.; Мамаева, О. К.; Florentiev, V. L.

doi:10.1080/07391102.1990.10507826

Cited by 9 publications

(11 citation statements)

References 9 publications

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“…This structure was described earlier for some free homo-and alternatingpolynucleotides (25)(26)(27)(28). In fact, the base pairs of different molecules in the type VII structures can form one or two weak hydrogen bonds with each other.…”

Section: Tetramer Complexesmentioning

confidence: 94%

Homology in Trivaline Complex Formation with dsDNA and ssRNA

Streltsov¹,

Semenov

Moroz

1993

Journal of Biomolecular Structure and Dynamics

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It has been shown by the equilibrium dialysis that at a polyU concentration above the "critical" one, the complete polymer saturation with trivaline reaches approximately 0.7 trivaline molecules per one phosphate group. i.e. at these conditions peptide dimer occupies on polyU a site of three bases (phosphates) in length. The trivaline complex with polyU at a concentration lower than the "critical" one does not reveal any noticeable fluorescence, but has rather significant positive linear dichroism at 265 and 330 nm. The trivaline-nucleic acids complex has a significant fluorescence at any dsDNA concentration while with polyU it is only so at a concentration above the "critical" one. Electron microscopy has shown that at a rather high concentration of dsDNA molecules in solution a "biduplex" structure undergoes an additional stage of compaction, during which the extended particles more than 30 nm in diameter are formed.

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Section: Tetramer Complexesmentioning

confidence: 94%

Homology in Trivaline Complex Formation with dsDNA and ssRNA

Streltsov¹,

Semenov

Moroz

1993

Journal of Biomolecular Structure and Dynamics

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“…Thus the hairpin dimers with G3 stems are different from the hairpin dimers with G4 stems, where all three types of dimer can be symmetric because of the even number of guanines in the stem (Mohanty and Bansal, 1994;Smith and Feigon, 1993). In the symmetric hairpin dimers with two loops on the same side the thymines and adenines can form a TATA tetrad (Chernyi et al, 1990), which is nearly isostructural to the G tetrad and can accommodate maximum number of hydrogen bonds between the adenines and thymines that form the tetrad. Such symmetric dimer structures with TATA tetrads can be obtained by dimerization of hairpins with the loop across the large groove (i.e., the groove in which donor atoms N2 and Ni of the guanine in the anti conformation are hydrogen bonded to acceptors N7 and 06 of the guanine in the syn conformation ( Fig.…”

Section: Model Buildingmentioning

confidence: 99%

“…The various types of TATA tetrad (Chernyi et al, 1990) that are expected from symmetry considerations are the following: Two Watson-Crick (Fig. 3 b) (or Hoogsteen (Fig.…”

Section: Model Buildingmentioning

confidence: 99%

Chain folding and A:T pairing in human telomeric DNA: a model-building and molecular dynamics study

Mohanty

Bansal

1995

Biophysical Journal

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The various types of chain folding and possible intraloop as well as interloop base pairing in human telomeric DNA containing d(TTAG3) repeats have been investigated by model-building, molecular mechanics, and molecular dynamics techniques. Model-building and molecular mechanics studies indicate that it is possible to build a variety of energetically favorable folded-back structures with the two TTA loops on same side and the 5' end thymines in the two loops forming TATA tetrads involving a number of different intraloop as well as interloop A:T pairing schemes. In these folded-back structures, although both intraloop and interloop Watson-Crick pairing is feasible, no structure is possible with interloop Hoogsteen pairing. MD studies of representative structures indicate that the guanine-tetraplex stem is very rigid and, while the loop regions are relatively much more flexible, most of the hydrogen bonds remain intact throughout the 350-ps in vacuo simulation. The various possible TTA loop structures, although they are energetically similar, have characteristic inter proton distances, which could give rise to unique cross-peaks in two-dimensional nuclear Overhauser effect spectroscopy (NOESY) experiments. These folded-back structures with A:T pairings in the loop region help in rationalizing the data from chemical probing and other biochemical studies on human telomeric DNA.

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“…5), the unusual cytosine motif in I-DNA, 6 or poly-dA and poly-dT. 7 In addition, multistranded species can be formed that are based on the Holliday junction; 8 these molecules contain a unique branch point flanked by three or more double helices, 9 but the strands are not coaxial in these molecules. Nevertheless, two Holliday junctions joined at two adjacent arms produce double crossover (DX) molecules.…”

Section: Introductionmentioning

confidence: 99%

Paranemic Crossover DNA: A Generalized Holliday Structure with Applications in Nanotechnology

et al. 2004

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Paranemic crossover (PX) DNA is a four-stranded coaxial DNA structure containing a central dyad axis that relates two flanking parallel double helices. The strands are held together exclusively by Watson-Crick base pairing. The key feature of the structure is that the two adjacent parallel DNA double helices form crossovers at every point possible. Hence, reciprocal crossover points flank the central dyad axis at every major or minor groove separation. This motif has been modeled and characterized in an oligonucleotide system; a minor groove separation of 5 nucleotide pairs and major groove separations of 6, 7, or 8 nucleotide pairs produce stable PX DNA molecules; a major groove separation of 9 nucleotide pairs is possible at low concentrations. Every strand undergoes a crossover every helical repeat (11, 12, 13 or 14 nucleotides), but the structural period of each strand corresponds to two helical repeats (22, 24, 26 or 28 nucleotides). Non-denaturing gel electrophoresis shows that the molecules are stable, forming well-behaved complexes. PX DNA can be produced from closed dumbbells, demonstrating that the molecule is paranemic. Ferguson analysis indicates that the molecules are similar in shape to DNA double crossover molecules. Circular dichroism spectra are consistent with B-form DNA. Thermal transition profiles suggest a premelting transition in each of the molecules. Hydroxyl radical autofootprinting analysis confirms that there is a crossover point at each of the positions expected in the secondary structure. These molecules are generalized Holliday junctions that have applications in nanotechnology.

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Four-Stranded DNA Helices: Conformational Analysis of Regular Poly(dT) · Poly(dA) · Poly(dA) · Poly(dT) Helices with Various Types of Base Binding

Cited by 9 publications

References 9 publications

Homology in Trivaline Complex Formation with dsDNA and ssRNA

Homology in Trivaline Complex Formation with dsDNA and ssRNA

Chain folding and A:T pairing in human telomeric DNA: a model-building and molecular dynamics study

Paranemic Crossover DNA: A Generalized Holliday Structure with Applications in Nanotechnology

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