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Gene-therapy Inspired Polycation Coating for Protection of DNA Origami Nanostructures
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Ionic microenvironmental effects on triplex DNA stabilization: cationic counterion effects on

Amanda Beck1, Veena Vijayanathan, Thresia Thomas

  • 1Department of Medicine, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, 125 Paterson St, New Brunswick, NJ 08903, USA.

Biochimie
|March 5, 2013
PubMed
Summary
This summary is machine-generated.

Metal ions and ammonium salts stabilize triplex DNA structures, influencing their melting temperatures. Different cations show varying effectiveness in stabilizing both triplex and duplex DNA, with implications for gene silencing techniques.

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Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
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Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids

Published on: September 21, 2017

Area of Science:

  • Molecular Biology
  • Biophysics
  • Biochemistry

Background:

  • Nucleic acid structure and conformation are significantly influenced by factors like metal ions, polyamines, and the surrounding microenvironment.
  • Poly(purine) · poly(pyrimidine) sequences, such as poly(dA) · poly(dT), are known to form triplex DNA structures, a process facilitated by various ligands.
  • Understanding the stabilization mechanisms of DNA structures is crucial for applications in molecular biology and gene technology.

Purpose of the Study:

  • To investigate the effects of mono- and di-valent metal ions, as well as ammonium salts, on the stability of triplex and duplex DNA structures.
  • To quantify the impact of different cations on the melting temperatures (Tm) of poly(dA) · poly(dT) triplex and duplex forms.
  • To explore the potential of these findings for developing novel gene silencing strategies using triplex-forming oligonucleotides.

Main Methods:

  • Melting temperature (Tm) measurements were used to assess the stability of triplex and duplex DNA structures.
  • Absorbance versus temperature profiles were analyzed to determine Tm1 (triplex to duplex/single strand) and Tm2 (duplex to single strand) transitions.
  • Circular dichroism (CD) spectroscopy was employed to study conformational changes in triplex DNA.
  • Thermodynamic analysis, including calculation of Δn (number of ions released), was performed using 1/Tm1 versus ln[M(+,2+)] plots.

Main Results:

  • Monovalent cations (Li+, Na+, K+, Rb+, Cs+, NH4+) stabilized triplex DNA at concentrations ≥150 mM, with varying effects on Tm1.
  • Ammonium (NH4+) was highly effective in stabilizing triplex DNA, with efficacy decreasing upon substitution of hydrogen atoms.
  • Divalent cations (Mg2+, Ca2+, Sr2+, Ba2+) also stabilized triplex DNA in a concentration-dependent manner, with Mg2+ being the most effective.
  • All tested cations increased the melting temperature of duplex DNA.
  • Calculated Δn values indicated differential ion release upon melting of triplex and duplex DNA for mono- and di-valent cations.
  • CD studies revealed distinct conformational alterations in triplex DNA stabilized by different ions.

Conclusions:

  • Metal ions and ammonium salts significantly influence the stability of triplex and duplex DNA structures.
  • The effectiveness of cations in stabilizing triplex DNA varies, providing insights into ion-DNA interactions.
  • The observed stabilization effects and conformational changes suggest potential applications in the design of triplex-forming oligonucleotide-based gene silencing techniques.