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Related Concept Videos

Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
DNA Topoisomerases02:02

DNA Topoisomerases

Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
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Nucleic Acid Structure01:25

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
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Homologous Recombination02:31

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The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
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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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Potent triple helix stabilization by 5',3'-modified triplex-forming oligonucleotides.

Nouha Ben Gaied1, Zhengyun Zhao, Simon R Gerrard

  • 1School of Chemistry, University of Southampton, Highfield, SO17 1BJ, Southampton, UK.

Chembiochem : a European Journal of Chemical Biology
|June 26, 2009
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Summary

Anthraquinone and pyrene modifications enhance triplex-forming oligonucleotide (TFO) stability. These simple modifications significantly increase the melting temperature of parallel triple helices, with implications for biology and nanotechnology.

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Area of Science:

  • Biochemistry
  • Oligonucleotide Chemistry
  • Nanotechnology

Background:

  • Triple helices are DNA structures with potential applications in molecular biology and nanotechnology.
  • Enhancing the stability of these structures is crucial for their practical use.
  • Existing methods for stabilizing triple helices can be complex or require specialized base analogues.

Purpose of the Study:

  • To investigate the impact of anthraquinone and pyrene analogues on the stability of parallel triple helices.
  • To develop simple and efficient methods for modifying triplex-forming oligonucleotides (TFOs).
  • To assess the selectivity and thermal stability of modified TFOs.

Main Methods:

  • Chemical synthesis of TFOs modified with anthraquinone and pyrene analogues at termini.
  • Standard solid-phase oligonucleotide synthesis techniques.
  • Melting temperature (Tm) analysis to determine triplex stability and selectivity.

Main Results:

  • Anthraquinone and pyrene modifications significantly increased the stability of parallel triple helices.
  • Doubly modified TFOs showed the most potent stabilization, with melting temperature increases up to 30°C.
  • Modified TFOs maintained high selectivity for their target DNA duplexes.
  • Achieved stable triplexes with melting temperatures of 40°C at pH 7 without specialized base analogues.

Conclusions:

  • Anthraquinone and pyrene analogues are effective modifications for enhancing TFO stability.
  • These modifications are readily incorporated using standard oligonucleotide synthesis.
  • The developed TFOs offer improved stability and selectivity, broadening their potential applications in biology and nanotechnology.