Identification of ssDNA aptamers specific for anti-neuroexcitation peptide III and molecular modeling studies: insights into structural interactions

Arch Pharm Res. 2008 Sep;31(9):1120-8. doi: 10.1007/s12272-001-1278-2. Epub 2008 Sep 20.

Abstract

Twelve ssDNA aptamers specific for a novel recombinant anti-neuroexcitation peptide (ANEPIII) were identified using the SELEX method from a 79-nucleotide ssDNA pool to purify ANEPIII in a more efficient way. To further understand the binding modes between ssDNA and ANEPIII, fully flexible dinucleotides were docked onto the homology-modeled ANEPIII structure. AutoDocking identified favorable binding sites on ANEPIII for nucleotides, which was valuable for designing more potent ligands.

MeSH terms

  • Aptamers, Nucleotide / chemistry*
  • Aptamers, Nucleotide / pharmacology*
  • Cloning, Molecular
  • DNA, Single-Stranded / drug effects*
  • Electrophoretic Mobility Shift Assay
  • Enzyme-Linked Immunosorbent Assay
  • Models, Molecular
  • Nucleic Acid Conformation
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / pharmacology
  • Scorpion Venoms / chemistry*
  • Scorpion Venoms / pharmacology*
  • Serum Albumin, Bovine / chemistry

Substances

  • Aptamers, Nucleotide
  • DNA, Single-Stranded
  • Recombinant Proteins
  • Scorpion Venoms
  • anti-epilepsy peptide, Buthrus martensii
  • Serum Albumin, Bovine