Salt-induced conformational changes of poly(dA-dT)

Vorlı́čková, Michaela; Kypr, Jaroslav; Kleinwächter, V.; Paleček, Emil

doi:10.1093/nar/8.17.3965

Cited by 58 publications

(36 citation statements)

References 21 publications

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“…In addition, we compare in fig. I the CD spectra of poly(dG-dC).poly(dG-dC) and poly(dA-dT).poly(dA-dT) in 60% ethanol in the presence of Cs a These spectra correspond to a strongly altered CD with negative bands at 290 nm as already known for poly(dG-dC) poly(dG-dC) (7,9,16) and at 278 im for poly(dA-dT).poly(dA-dT) (18,19) in high salt media or in ethanolic solutions.…”

Section: Resultsmentioning

confidence: 57%

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Conformational transitions of poly(dA-dC).poly(dG-dT) induced by high salt or in ethanolic solution

Zimmer¹,

Tymen²,

Marck³

et al. 1982

Nucl Acids Res

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Poly(dA-dC)*poly(dG-dT) was studied by circular dichroism in the presence of high CsCl concentrations and in ethanolic solutions. This alternating purine-pyrimidine duplex may undergo two conformational transitions from a B-type to a novel stucture and subsequently into an A-form. Cs+ ions or increasing ethanol concentrations induced a change of the B-type CD spectrum and an inversion of the long wavelength CD band. Lowering the temperature below OCor addition of small amounts of Ca++ ions were particularly potent in producing a large negative CD band. A modified B-type structure or a conversion into a left-handed Z-form is considered for this conformational transition.The variability and dynamics of the DNA conformation is dependent on the nucleotide sequence (1-5). Discovery of left-handed Z-DNA in crystals of alternating d.(G-C)n sequences (1-3) has recently focused attention on sequence controlled conformational transitions of DNA between the right-handed B-and A-forms and Z-type or B-type left-handed structures (4-6). Poly(dG-dC)X poly(dG-dC) may assume a left-handed Z-helix in fibres (6,8) and in solution (9) under conditions of reduced water activity. Drastic CD changes of this alternating duplex had first indicated a left-right conversion in solution (9) at high salt concentrations. 31P-NMR studies (10) presented support that the high salt form of poly(dG-dC).poly(dG-dC) may be a Z-DNA. Formation of Z-DNA is strongly favoured by modification of deoxyguanosine residues (11-13) or deoxycytidine residues (14). Poly(dG-m5dC).poly(dG-m5dC) undergoes a B to Z transition close to physiological ionic strength conditions (14). X-ray fibre diffraction data (6,8) showed that other alternating purine-pyrimidine sequences, like poly(dA-dC)'poly(dG-dT) may adopt the left handed Z-helix. For poly(dA-dT)-poly(dA-dT) which is believed to exist mainly in the B-form (6), changes in its geometry have been suggested (15) and were observed in solution at high CsF concentrations (16).In the present paper, first results by circular dichroism (CD) on conformational transitions of poly(dA-dC).poly(dG-dT) induced by high salt or

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Section: Resultsmentioning

confidence: 57%

“…An alternative explanation could be a change of the geometry within the B-type family as regard to the sugar-phosphate conformation in alternating pvrine-pyrimidine nucleotides in the polymer. In this case poly(dA-dC)*poly(dG-dT) would behave similar to poly(dA-dT).poly(dA-dT) (18,19).…”

Section: Discussionmentioning

confidence: 97%

Conformational transitions of poly(dA-dC).poly(dG-dT) induced by high salt or in ethanolic solution

Zimmer¹,

Tymen²,

Marck³

et al. 1982

Nucl Acids Res

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“…This model was constructed for poly(dA-dT) on the basis of x-ray data for pdA-dT-dA-dT (9) and may be adopted by poly(dG-dG) as well. The "Z-DNA" conformation By contrast, the circular dichroism studies (11) and the 31P NMR studies in Fig. 4 demonstrate that poly(dA-dT) undergoes a noncooperative structural transition on addition of molar amounts of CsF.…”

Section: Resultsmentioning

confidence: 87%

“…Poly(dA-dT) conformation in CsF solution Vorlickova' and coworkers (11) recently reported on a noncooperative inversion of the long-wavelength circular dichroism spectrum of poly(dA-dT) at high concentrations of CsF solution that was not observed for the corresponding homopolymer duplex poly(dA)'poly(dT) under the same conditions. These workers proposed that poly(dA-dT) adopts a conformation with different geometries at the purine and pyrimidine residues in 6 M CsF solution (11).…”

Section: Resultsmentioning

confidence: 99%

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Right-handed alternating DNA conformation: poly(dA-dT) adopts the same dinucleotide repeat with cesium, tetraalkylammonium, and 3 alpha, 5 beta, 17 beta-dipyrrolidinium steroid dimethiodide cations in aqueous solution.

Patel¹,

Kozlowski²,

Suggs³

et al. 1981

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

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Right-handed alternating DNA conformation: Poly(dA-dT) adopts the same dinucleotide repeat with cesium, tetraalkylammonium, and 3a,5,3,17,8-dipyrrolidinium Communicated by Frank Bovey, March 11, 1981 ABSTRACT We demonstrate that poly(dA-dT) can adopt two conformations in solution, with the relative proportions dependent on the nature and concentration of the counter ion and cationic ligands. The synthetic DNA exhibits a dinucleotide repeat conformation on addition of CsF and Me4NCl at molar concentrations, with the NMR spectral changes reflecting a common conformational change at one glycosidic torsion angle and one phosphodiester linkage. We also observe the same dinucleotide repeat in the neighbor-exclusion 3a,17I3dipyrrolidin-1'-yl-5,3-A9"1-androstene dimethiodide (3a,5,,17frdipyrandenium) complex, with the steroid diammonium ligand binding in the groove of the stacked poly(dA-dT) duplex and the complex stabilized through the interaction of one of the charged ends with the backbone phosphate. We demonstrate further that 3a,5,8,17,-dipyrandenium bound to poly(dA-dT) at low binding ratios induces a switch to the dinucleotide repeat conformation at adjacent steroidfree duplex regions. This observation contrasts with a previous demonstration that the diastereoisomeric 3,B,5a,178-dipyrandium binds to poly(dA-dT) by partial insertion between unstacked tilted base pairs. The NMR parameters rule out a left-handed alternating DNA structure (Z DNA) for the observed poly(dA-dT) dinucleotide repeat conformation, but right-handed alternating DNA models are under consideration. The facile interconversion of poly(dA-dT) between two conformations, one of which exhibits a dinucleotide repeat and can be induced by ligand binding, may provide a mechanism for the recognition of specific nucleic acid sequences by DNA-binding proteins.

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Highly Stable Double‐Stranded DNA Containing Sequential Silver(I)‐Mediated 7‐Deazaadenine/Thymine Watson–Crick Base Pairs

et al. 2016

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The oligonucleotide d(TX)9 , which consists of an octadecamer sequence with alternating non-canonical 7-deazaadenine (X) and canonical thymine (T) as the nucleobases, was synthesized and shown to hybridize into double-stranded DNA through the formation of hydrogen-bonded Watson-Crick base pairs. dsDNA with metal-mediated base pairs was then obtained by selectively replacing W-C hydrogen bonds by coordination bonds to central silver(I) ions. The oligonucleotide I adopts a duplex structure in the absence of Ag(+) ions, and its stability is significantly enhanced in the presence of Ag(+) ions while its double-helix structure is retained. Temperature-dependent UV spectroscopy, circular dichroism spectroscopy, and ESI mass spectrometry were used to confirm the selective formation of the silver(I)-mediated base pairs. This strategy could become useful for preparing stable metallo-DNA-based nanostructures.

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Salt-induced conformational changes of poly(dA-dT)

Cited by 58 publications

References 21 publications

Conformational transitions of poly(dA-dC).poly(dG-dT) induced by high salt or in ethanolic solution

Conformational transitions of poly(dA-dC).poly(dG-dT) induced by high salt or in ethanolic solution

Right-handed alternating DNA conformation: poly(dA-dT) adopts the same dinucleotide repeat with cesium, tetraalkylammonium, and 3 alpha, 5 beta, 17 beta-dipyrrolidinium steroid dimethiodide cations in aqueous solution.

Highly Stable Double‐Stranded DNA Containing Sequential Silver(I)‐Mediated 7‐Deazaadenine/Thymine Watson–Crick Base Pairs

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