Salt-induced co-operative conformational change of a synthetic DNA: Equilibrium and kinetic studies with poly(dG-dC)

Pohl, Fritz M.; Jovin, Thomas M.

doi:10.1016/0022-2836(72)90457-3

Cited by 1,226 publications

(735 citation statements)

References 43 publications

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“…If in an aqueous solution of poly d(G-C) * poly d(G-C) the salt concentration is raised beyond 2.5 M NaCl or 0.7 M MgC12, or if mM amounts of Co(NH&+ or 60% alcohol are added, a direct B-Z transition is observed without indication of an A form [4,5]. The Z-DNA form is also found in fibers under high-salt conditions [2,3].…”

Section: Introduction Poly D(g-c) -Poly D(g-c) Adopts the Canonical Rmentioning

confidence: 99%

Raison d'être and structural model for the B‐Z transition of poly d(G‐C)^∗poly d(G‐C)

Heinemann

1989

FEBS Letters

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In DNA oligonucleotides crystallized in the A form, the nucleotides adopt standard conformation except for steps 5'‐CpG‐3' where reduced base‐pair twist and a sliding motion of the base pairs along their long axes causes pronounced interstrand guanine‐guanine overlap. As a consequence, torsion angles α,β and γ are consistently trans, trans, trans instead of the common ‐gauche, trans, + gauche. This conformation significantly increases the intraresidue distance between the guanine base and the 5'‐phosphate group. A molecular model of poly d(G‐C)·poly d(G‐C) built with these structural characteristics in the A form, which we call A2‐DNA, shows that rotation of the guanosine sugar into the syn orientation is easily achieved and pushes the base pair across the helix axis. If successive guanosines are changed this way, a smooth transformation occurs to the left‐handed Z‐DNA. We suggest that A‐ and A2‐DNA forms of poly d(G‐C)·poly d(G‐C) are metastable and that the actual transition is B ⇌ (A ⇌ A2) ⇌ Z‐DNA.

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Section: Introduction Poly D(g-c) -Poly D(g-c) Adopts the Canonical Rmentioning

confidence: 99%

Raison d'être and structural model for the B‐Z transition of poly d(G‐C)^∗poly d(G‐C)

Heinemann

1989

FEBS Letters

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“…Yeast tRNAPhe was purchased from Boehringer Mannheim Biochemicals and dissolved in 10 mM Tris buffer, pH 7.5. The Z conformation of DNA was promoted by the addition of [CO(NH3)6] 3+ to B-form poly(dG*dC)=poly(dG*dC) and characterized through the negative Cotton effect seen at 290 nm in the circular dichroic spectrum (Pohl & Jovin, 1972). Oligonucleotides used in the triple-helix experiments were synthesized using either a Pharmacia gene assembler or an Applied Biosystems DNA synthesizer Model 392 and were purifed using reversed phase HPLC.…”

mentioning

confidence: 99%

Characterization of dipyridophenazine complexes of ruthenium(II): The light switch effect as a function of nucleic acid sequence and conformation

Jenkins¹,

Friedman²,

Turro³

et al. 1992

Biochemistry

440

368

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Spectroscopic parameters for two novel ruthenium complexes on binding to nucleic acids of varying sequences and conformations have been determined. These complexes, R~( b p y )~d p p z~+ and Ru(phen)zdppz2+ (bpy = 2,2'-bipyridine; phen = 1,lO-phenanthroline; dppz = dipyrido[3,2:a-2',3':~]-phenazine) serve as "molecular light switches" for DNA, displaying no photoluminescence in aqueous solution but luminescing intensely in the presence of DNA. The luminescent enhancement observed upon binding is attributed to the sensitivity of the excited state to quenching by water; in DNA, the metal complex, upon intercalation into the helix, is protected from the aqueous solvent, thereby preserving the luminescence. Correlations between the extent of protection (depending upon the DNA conformation) and the luminescence parameters are observed. Indeed, the strongest luminescent enhancement is observed for intercalation into DNA conformations which afford the greatest amount of overlap with access from the major groove, such as in triple helices. Differences are observed in the luminescent parameters between the two complexes which also correlate with the level of water protection. In the presence of nucleic acids, both complexes exhibit biexponential decays in emission. Quenching studies are consistent with two intercalative binding modes for the dppz ligand from the major groove: one in which the metal-phenazine axis lies along the DNA dyad axis and another where the metal-phenazine axis lies almost perpendicular to the DNA dyad axis. Ru(bpy)zdppz2+ and Ru(phen)2dppzz+ are shown here to be unique reporters of nucleic acid structures and may become valuable in the design of new diagnostics for DNA.Considerable attention has been given to the design of small molecules that bind to DNA with site selectivity so as to develop novel therapeutics and chemical probes for nucleic acid sites and structures, as well as novel diagnostic agents targeted to double-helical DNA (Pyle & Dervan, 1986;Moser & Dervan, 1987;Hecht, 1986;Tullius, 1988). Our laboratory has focused in part on the development of transitionmetal complexes as probes of nucleic acid structure (Chow & Barton, 1992;Mei & Barton, 1986;Kirshenbaum et al., 1988;Barton, 1986). We have found that ruthenium complexes serve as very sensitive luminescent reporters of DNA in aqueous solution and may become particularly useful in developing new diagnostics.Ruthenium complexes are ideally suited for application as sensitive noncovalent probes for polymer structure. The complexes are water-soluble, coordinatively saturated, and inert to substitution. Polypyridyl complexes of ruthenium-(11) furthermore are intensely colored owing to a wellcharacterized, localized metal-to-ligand charge transfer (MLCT) transition (Juris et al., 1988). Importantly, this transition is perturbed on binding to DNA, providing a sensitive spectroscopic handle for interactions with nucleic acids (Pyle et al., 1989). Tris( 1 ,IO-phenanthroline)ruthenium(II), Ru-(phen)j2+, has been established, primar...

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“…It has been found that long stretches of alternating purine‐pyrimidine sequences have a tendency to form Z‐DNA 21. In our initial study, the commercially available polynucleotide poly(dG‐dC)‐poly(dG‐dC) (polyGC) was chosen as a model sequence.…”

Section: Resultsmentioning

confidence: 99%

The Cucurbit[7]Uril‐Based Supramolecular Chemistry for Reversible B/Z‐DNA Transition

Wang

et al. 2018

Advanced Science

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As a left‐handed helical structure, Z‐DNA is biologically active and it may be correlated with transcription and genome stability. Until recently, it remained a significant challenge to control the B/Z‐DNA transition under physiological conditions. The current study represents the first to reversibly control B/Z‐DNA transition using cucurbit[7]uril‐based supramolecular approach. It is demonstrated that cucurbit[7]uril can encapsulate the central butanediamine moiety [HN(CH2)4NH] and reverses Z‐DNA caused by spermine back to B‐DNA. The subsequent treatment with 1‐adamantanamine disassembles the cucurbit[7]uril/spermine complex and readily induces reconversion of B‐ into Z‐DNA. The DNA conformational change is unequivocally demonstrated using different independent methods. Direct evidence for supramolecular interactions involved in DNA conformational changes is further provided. These findings can therefore open a new route to control DNA helical structure in a reversible way.

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Salt-induced co-operative conformational change of a synthetic DNA: Equilibrium and kinetic studies with poly(dG-dC)

Cited by 1,226 publications

References 43 publications

Raison d'être and structural model for the B‐Z transition of poly d(G‐C)^∗poly d(G‐C)

Raison d'être and structural model for the B‐Z transition of poly d(G‐C)^∗poly d(G‐C)

Characterization of dipyridophenazine complexes of ruthenium(II): The light switch effect as a function of nucleic acid sequence and conformation

The Cucurbit[7]Uril‐Based Supramolecular Chemistry for Reversible B/Z‐DNA Transition

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Salt-induced co-operative conformational change of a synthetic DNA: Equilibrium and kinetic studies with poly(dG-dC)

Cited by 1,226 publications

References 43 publications

Raison d'être and structural model for the B‐Z transition of poly d(G‐C)∗poly d(G‐C)

Raison d'être and structural model for the B‐Z transition of poly d(G‐C)∗poly d(G‐C)

Characterization of dipyridophenazine complexes of ruthenium(II): The light switch effect as a function of nucleic acid sequence and conformation

The Cucurbit[7]Uril‐Based Supramolecular Chemistry for Reversible B/Z‐DNA Transition

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Raison d'être and structural model for the B‐Z transition of poly d(G‐C)^∗poly d(G‐C)

Raison d'être and structural model for the B‐Z transition of poly d(G‐C)^∗poly d(G‐C)