Design of Triplex Forming Oligonucleotide
Triplex forming oligonucleotide (TFO) is formed by the interaction of a chain containing polypurines in classic Watson-Crick double helix with a third strand through Hoogsteen and trans-Hoogsteen hydrogen bonds. The third chain is located in the large gully of the Watson-Crick double chain. Two forms of TFO are found, that is the pyrimidine · purine-pyrimidine type (Y·RY) and the purine · purine-pyrimidine type (R·RY). The structure of TFO is extremely valuable in the medical field. Homologous deoxynucleotides containing antigenic proteins are used to locate in double-stranded DNA, which is easy to form three-stranded DNA.
As a professional and technical service company for gene function research, Creative Biolabs provides TFO design and quality services to scientists and pharmaceutical companies in the field of life sciences worldwide.
Our TFO service:
Creative Biolabs provides TFO design and optimization services. The constructed TFOs can be used directly for further drug development research.
- Design and synthesize customized TFO. TFO interacts with the purine-rich region of the double-stranded target DNA, entangled in the deep groove of the DNA through hydrogen and anti-Hoogsteen hydrogen. Prevents target DNA from binding to nucleic acid polymerase, transcription factors, and other proteins, thereby inhibiting replication and target gene expression.
- Target DNA fragment labeling and purification. The sense sequence and antisense strand of the designed complementary oligonucleotides are synthesized and hybridized to double stranded target DNA. The hybridization is confirmed by polyacrylamide gel electrophoresis. Target DNA is labeled with 3' terminal filling method and then purified by chromatography. The concentration of the marker is measured and the specific radiation activity of target DNA is estimated.
- The specificity of TFO binding to target sequence is verified by tri-strand DNA formation and gel retention tests.
- The enzyme footprint test confirms that the typical base triplet binding in the synthetic TFO is strong. The A+G sequence of target DNA is measured by fast Maxam- Gilbort sequencing method.
- Define and optimize the conditions of TFO design: Creative Biolabs provides customers with a variety of personalized solutions to define and optimize the key conditions at TFO design.
- Located in the gene regulatory region (optional promoter).
- Target sequences of TFO which is similar to homopurine sequences.
- The effect of base pairing on the stability of base triplet. Creative Biolabs can help you avoid the formation of atypical triplet.
- Optimize TFO chain length. Because G in these three-chain oligonucleotides is easy to form its own related structure, such as G tetrmer and dimer, the effective concentration of TFO binding with target sequence is reduced. In a certain range, increasing the length of TFO chain is helpful to improve the affinity of TFO binding to target sequence. Creative Biolabs assists clients in selecting the right length of nucleotide chain to achieve optimal results.
- Antigene technique. Oligodexyribonucleotides (ODN) specifically with the double helix of DNA sequence to form three spiral structures. ODN regards the particular sequence of DNA double helix molecular as targets. Through combined with the target sequence to form three helical DNA, OND disturb or block the combination of RNA polymerase or transcription factors and DNA, and affect transcription start or extended, thereby inhibit gene transcription.
References
- Chandrasekaran AR, et al. Triplex-forming oligonucleotides: a third strand for DNA nanotechnology. Nucleic Acids Res. 2018, 46(3):1021-1037.
- Goñi JR, et al. Triplex-forming oligonucleotide target sequences in the human genome. Nucleic Acids Res. 2004, 32(1):354-360.
*For Research Use Only. Not for use in diagnostic procedures.