Single-stranded DNA aptamers specific for antibiotics tetracyclines

Javed H. Niazi, Su Jin Lee, Man Bock Gu

Research output: Contribution to journalArticle

86 Citations (Scopus)

Abstract

Tetracyclines (TCs) are a group of antibiotics comprising of a common tetracycline (TET) nucleus with variable X1 and X2 positions on 5 and 6 carbon atoms, such as oxytetracycline (OTC) and doxycycline (DOX). In this study, the tetracycline group specific (TGS) ssDNA aptamers were identified by modified SELEX method by employing tosylactivated magnetic beads (TMB) coated with OTC, TET, and DOX, respectively, as targets and counter targets. Twenty TGS-aptamers were selected, of which seven aptamers, designated as T7, T15, T19, T20, T22, T23, and T24, showed high affinity to the basic TET backbone (Kd = 63-483 nM). The specificity of these TGS-aptamers to structural analogues followed the order in which the TCs was employed during SELEX process (OTC > TET > DOX) except aptamer T22, which was highly specific to TET than OTC or DOX. Aptamers that were specific to one target molecule but fail to bind the other structurally related TCs were eliminated during counter selection steps. Three aptamers, T7, T19, and T23 contained palindromic consensus sequence motif GGTGTGG. The remaining TGS-aptamers showed many consensus sequences that are truncated forms of this palindrome forming mirror image or inverted sequences. For example, GTGG or its inverted form, GGTG motif was found in all TGS-aptamers. A consensus sequence motif TGTGCT or its truncated terminal T-residue was found in most TGS-aptamers, which is predicted to be essential for high affinity and group specificity. These TGS-aptamers have potential applications such as target drug delivery, and detection of TCs in pharmaceutical preparations and contaminated food products.

Original languageEnglish
Pages (from-to)7245-7253
Number of pages9
JournalBioorganic and Medicinal Chemistry
Volume16
Issue number15
DOIs
Publication statusPublished - 2008 Aug 1

Fingerprint

Nucleotide Aptamers
Tetracyclines
Single-Stranded DNA
Tetracycline
Anti-Bacterial Agents
Oxytetracycline
Doxycycline
Consensus Sequence
Sequence Inversion
Drug delivery
Pharmaceutical Preparations

Keywords

  • Antibiotics
  • Aptamer
  • SELEX
  • ssDNA
  • Tetracyclines

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Organic Chemistry
  • Drug Discovery
  • Pharmaceutical Science

Cite this

Single-stranded DNA aptamers specific for antibiotics tetracyclines. / Niazi, Javed H.; Lee, Su Jin; Gu, Man Bock.

In: Bioorganic and Medicinal Chemistry, Vol. 16, No. 15, 01.08.2008, p. 7245-7253.

Research output: Contribution to journalArticle

Niazi, Javed H. ; Lee, Su Jin ; Gu, Man Bock. / Single-stranded DNA aptamers specific for antibiotics tetracyclines. In: Bioorganic and Medicinal Chemistry. 2008 ; Vol. 16, No. 15. pp. 7245-7253.
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