# TTSBBC: triplex target site biomarkers and barcodes in cancer

## TL;DR

This paper introduces TTSBBC, a new tool for analyzing and visualizing DNA sites where triplex-forming molecules can bind, helping researchers design better gene-targeting strategies in cancer.

## Contribution

The novel TTSBBC platform enables exploration and validation of triplex-forming DNA sequences for gene manipulation in cancer research.

## Key findings

- Triplex-forming oligonucleotides bind to specific DNA sites with poly-purine sequences.
- TTSBBC provides a web-based tool for analyzing and visualizing these target sites.
- The platform supports design and validation of TTSs for gene regulation and DNA manipulation.

## Abstract

The technology of triplex-forming oligonucleotides (TFOs) provides an approach to manipulate genes at the DNA level. TFOs bind to specific sites on genomic DNA, creating a unique intermolecular triple-helix DNA structure through Hoogsteen hydrogen bonding. This targeting by TFOs is site-specific and the locations TFOs bind are referred to as TFO target sites (TTS). Triplexes have been observed to selectively influence gene expression, homologous recombination, mutations, protein binding, and DNA damage. These sites typically feature a poly-purine sequence in duplex DNA, and the characteristics of these TTS sequences greatly influence the formation of the triplex. We introduce TTSBBC, a novel analysis and visualization platform designed to explore features of TTS sequences to enable users to design and validate TTSs. The web server can be freely accessed at https://kowalski-labapps.dellmed.utexas.edu/TTSBBC/.

Graphical Abstract