Team:OUC-R/Description

• PROJECT
  • Description
  • Design
  • Results
  • Contribution
  • Engineering
  • Implementation
  • Proof of Concept
  • Medal Equirement
• WET LAB
  • Experiments
  • Safety
  • Measurement
• MODEL
  • Overview
  • Sequence Design
  • ODE
  • Furthermore
  • Software
• PARTS
  • Overview
  • Improvement
• HUMAN PRACTICES
  • Human Practices
  • Education
  • Online Lectures
  • Comics
  • Scientific Videos
  • Communication
• COLLABORATIONS
  • Collaborations
  • OUC-China_Team
  • Tongji-Software Team
  • ICJFLS Team
  • ECUST_China Team
• TEAM
  • Members
  • Attributions

Project Principle

Basic knowledge about B-DNA and Z-DNA

Z-DNA is a secondary structure of left-handed helical DNA, named after its phosphoric acid skeleton in the "Z" shape. More and more data indicate that Z-DNA exists in organisms and plays important biological functions (such as regulating transcription and inducing chromosome recombination).However, its stability under physiological conditions is lower than that of conventional right-handed spiral B-DNA, and it is generally difficult to exist stably, which makes the relevant research progress slow. It is generally believed that only alternating purine/pyrimidine sequence (APP sequence) can form this special structure, and it requires high concentration of salt ions and other special conditions to induce it.Under physiological conditions, Z-DNA can only be obtained in the presence of artificially modified APP sequences or high-density negative superhelix.

Main theory of our project

Z-DNA is a secondary structure of left helical DNA, which is generally difficult to exist stably due to its lower stability than the common right helical B-DNA under physiological conditions. It is generally believed that only alternating purine-pyrimidine sequences (App sequences) can form this special structure, and special conditions such as high concentration of salt are required to induce it. In addition, other factors that can promote Z-DNA formation include polyvalent cations, chemical modification of bases, induction of chiral molecules such as metalloporphyrin complexes, and high-density negative superhelix introduced by DNA unchain during replication and transcription.

Recently, with the discovery of Z-DNA specific binding proteins and the development of biomolecular marker technology, many functions of Z-DNA have been gradually revealed, such as participating in gene regulation, inducing DNA damage, inducing cancer and a variety of genetic diseases.

In The past 20 years since the discovery of anti-Z-DNA antibodies, researchers have discovered a class of proteins containing The Zα domain, which can specifically bind Z-DNA and are collectively called Z-DNA binding proteins. Currently known Z-DNA binding proteins include vertebrate adenosine deaminase acting on RNA(ADAR1), mammalian Z-DNA binding protein 1(ZBP1/DLM-1), protein kinase containing Z-DNA binding domain (PKZ) and Vaccinia virus E3L protein. There are also ruthenium complex [Ru(dip)2dppz]2+, porphyrin zinc, nickel complex and so on. In addition, positively charged polyamines such as spermine, spermidine and putrescine can also stabilize Z -DNA structure.

Our project intends to use a DNA double-loop structure with hairpins, with a total of 86nt and a Linking number of 6.

Resulting from the binding between ZBP1, antibody or other inducers and the purine-pyrimidine sequence(APP sequence), APP sequences are forced to transform from right-handed helix into left-handed helix. That is, the LK value of APP sequence changes from +1 to -1, and to ensure the Linking number of the system being 6, the promoter sequence on the hairpin structure changes to right helix, which turns the LK value of the hairpin structure from 0 to +2, and the hammerhead Ribozyme gene can be expressed normally. With the formation of the transcription bubble, LK value of APP sequence will be changed back to +1. The tightness of the inducer binding will affect the way of transcription. If the inducer binding is loose, rolling loop transcription may occur. By detecting the presence and concentration of hammerhead Ribozyme, we can predict the concentration of large detection substance and its binding ability with APP sequence. At the same time, we can increase the concentration of magnesium ion in the reaction condition, so that the Z-DNA exists before the inducer is added, and then we can further study it. For comparison, we also replaced the APP sequence with a random sequence and conducted the same experiment. And we tested the formation of our structure at different temperatures to find its optimal conditions.

This structure can be used to construct a novel biosensor for the screening and enrichment of Z-DNA specific binding substances. At the same time, the conformational changes of B-DNA and Z-DNA can be used to treat diseases and provide new diagnostic and therapeutic ideas for Alzheimer's disease and breast cancer, or other diseases related to DNA conformational changes.