Structural specificity effects of trivalent polyamine analogues on the stabilization and conformational plasticity of triplex DNA

Thekkumkat Thomas, Gayathri D. Kulkarni, Norma J. Greenfield, Akira Shirahata, Thresia Thomas

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

Natural polyamines, i.e. putrescine, spermidine and spermine, are excellent promoters of triplex DNA. Using melting temperature (T(m)) measurements and CD spectroscopy, we found that structural alterations on spermidine backbone, including methylation, or acetylation at the N1-, N4- and/or N8-positions had a profound influence on the stability and conformation of poly(dA).2poly(dT) triplex. The conformation of the polynucleotide complex underwent sequential changes from B-DNA to triplex DNA as the concentration of spermidine increased from 0 to 50 μM in a buffer containing 10 mM sodium cacodylate and 1 mM EDTA (pH 7.2). At 60 μM spermidine, the CD spectrum of triplex DNA was comparable with that of Ψ-DNA, with a strong positive band centred around 260 nm. A negative band was also found at 295 nm. At higher concentrations of spermidine, however, the intensity of the positive band progressively decreased and the peak intensity was found at a 1:0.3 molar ratio of DNA phosphate:spermidine. Temperature-dependent CD analysis showed that the Ψ-DNA structure melted to single-stranded DNA at temperatures above the T(m) determined from the absorbance versus temperature profile. Comparable effects were exerted on the conformation of triplex DNA by Co(NH3)63+, an inorganic trivalent cation. Substitution of the N4-hydrogen of spermidine by a cyclohexyl ring or the fusion of the N4-nitrogen in a cyclic ring system, as in piperidine, enhanced the ability of spermidine analogues to stabilize triplex and Ψ-DNA forms over a wider concentration range compared with spermidine. These data demonstrate a differential effect of trivalent cations in stabilizing triplex DNA and provoking unusual conformations such as Ψ-DNA. Synthetic homologues of spermidine that stabilize triplex DNA over a wider range of concentrations than that stabilized by spermidine itself might have potential therapeutic applications in the development of an anti-gene strategy against several diseases, including cancer and AIDS.

Original languageEnglish (US)
Pages (from-to)591-599
Number of pages9
JournalBiochemical Journal
Volume319
Issue number2
DOIs
StatePublished - Oct 15 1996

Fingerprint

Spermidine
Polyamines
Plasticity
Stabilization
Conformations
Temperature
DNA
Cations
triplex DNA
Cacodylic Acid
B-Form DNA
Polynucleotides
Putrescine
Spermine
Acetylation
Single-Stranded DNA
Methylation
Edetic Acid
Freezing
Temperature measurement

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Biochemistry
  • Cell Biology

Cite this

Thomas, Thekkumkat ; Kulkarni, Gayathri D. ; Greenfield, Norma J. ; Shirahata, Akira ; Thomas, Thresia. / Structural specificity effects of trivalent polyamine analogues on the stabilization and conformational plasticity of triplex DNA. In: Biochemical Journal. 1996 ; Vol. 319, No. 2. pp. 591-599.
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abstract = "Natural polyamines, i.e. putrescine, spermidine and spermine, are excellent promoters of triplex DNA. Using melting temperature (T(m)) measurements and CD spectroscopy, we found that structural alterations on spermidine backbone, including methylation, or acetylation at the N1-, N4- and/or N8-positions had a profound influence on the stability and conformation of poly(dA).2poly(dT) triplex. The conformation of the polynucleotide complex underwent sequential changes from B-DNA to triplex DNA as the concentration of spermidine increased from 0 to 50 μM in a buffer containing 10 mM sodium cacodylate and 1 mM EDTA (pH 7.2). At 60 μM spermidine, the CD spectrum of triplex DNA was comparable with that of Ψ-DNA, with a strong positive band centred around 260 nm. A negative band was also found at 295 nm. At higher concentrations of spermidine, however, the intensity of the positive band progressively decreased and the peak intensity was found at a 1:0.3 molar ratio of DNA phosphate:spermidine. Temperature-dependent CD analysis showed that the Ψ-DNA structure melted to single-stranded DNA at temperatures above the T(m) determined from the absorbance versus temperature profile. Comparable effects were exerted on the conformation of triplex DNA by Co(NH3)63+, an inorganic trivalent cation. Substitution of the N4-hydrogen of spermidine by a cyclohexyl ring or the fusion of the N4-nitrogen in a cyclic ring system, as in piperidine, enhanced the ability of spermidine analogues to stabilize triplex and Ψ-DNA forms over a wider concentration range compared with spermidine. These data demonstrate a differential effect of trivalent cations in stabilizing triplex DNA and provoking unusual conformations such as Ψ-DNA. Synthetic homologues of spermidine that stabilize triplex DNA over a wider range of concentrations than that stabilized by spermidine itself might have potential therapeutic applications in the development of an anti-gene strategy against several diseases, including cancer and AIDS.",
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Structural specificity effects of trivalent polyamine analogues on the stabilization and conformational plasticity of triplex DNA. / Thomas, Thekkumkat; Kulkarni, Gayathri D.; Greenfield, Norma J.; Shirahata, Akira; Thomas, Thresia.

In: Biochemical Journal, Vol. 319, No. 2, 15.10.1996, p. 591-599.

Research output: Contribution to journalArticle

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AB - Natural polyamines, i.e. putrescine, spermidine and spermine, are excellent promoters of triplex DNA. Using melting temperature (T(m)) measurements and CD spectroscopy, we found that structural alterations on spermidine backbone, including methylation, or acetylation at the N1-, N4- and/or N8-positions had a profound influence on the stability and conformation of poly(dA).2poly(dT) triplex. The conformation of the polynucleotide complex underwent sequential changes from B-DNA to triplex DNA as the concentration of spermidine increased from 0 to 50 μM in a buffer containing 10 mM sodium cacodylate and 1 mM EDTA (pH 7.2). At 60 μM spermidine, the CD spectrum of triplex DNA was comparable with that of Ψ-DNA, with a strong positive band centred around 260 nm. A negative band was also found at 295 nm. At higher concentrations of spermidine, however, the intensity of the positive band progressively decreased and the peak intensity was found at a 1:0.3 molar ratio of DNA phosphate:spermidine. Temperature-dependent CD analysis showed that the Ψ-DNA structure melted to single-stranded DNA at temperatures above the T(m) determined from the absorbance versus temperature profile. Comparable effects were exerted on the conformation of triplex DNA by Co(NH3)63+, an inorganic trivalent cation. Substitution of the N4-hydrogen of spermidine by a cyclohexyl ring or the fusion of the N4-nitrogen in a cyclic ring system, as in piperidine, enhanced the ability of spermidine analogues to stabilize triplex and Ψ-DNA forms over a wider concentration range compared with spermidine. These data demonstrate a differential effect of trivalent cations in stabilizing triplex DNA and provoking unusual conformations such as Ψ-DNA. Synthetic homologues of spermidine that stabilize triplex DNA over a wider range of concentrations than that stabilized by spermidine itself might have potential therapeutic applications in the development of an anti-gene strategy against several diseases, including cancer and AIDS.

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