How is DNA Quantified?

DNA can be quantified through gel electrophoresis, a process that separates proteins in a sample by charge and molecular weight - with the lighter proteins traveling further down a gel and the heavier ones staying on the top. Since DNA is negatively charged, the more nucleotides in a sample (meaning the more DNA) the slower it will migrate to the end of the gel. These proteins are seen as bands on the gel - however, to truly visualize them the gel must be dyed with an agent such as EtBr.

How does EtBr Work?

Ethidium Bromide is an intercalating agent - this means that it inserts itself between the nucleotides of a nucleic acid such as DNA or RNA. It has been shown that the amount of EtBr intercalating throughout a sample is proportional to its concentration.

Once the agarose gel is stained with EtBr, it is run and imaged. During imaging, the gel is hit with UV light to visualize the bands. Fluorescence occurs because EtBr is an aromatic compound, meaning it contains many double bonds. When EtBr is hit with UV light, these double bonds absorb energy from the visible light at a certain wavelength and reflect light at others. The orange color we commonly associate with EtBr is the result of reflected light of a particular wavelength.

Ethidium Bromide

[1]

Predicting Collateral Cleavage Activity of Cas13a

This year, we collaborated with the Columbia University iGEM Team to help them model the collateral cleavage activity of Cas13a, an enzyme used to cleave RNA in CRISPR technology. Our team provided the system of equations and resulting graphs.

What is a CRISPR?

CRISPRs, or Clustered Regularly Interspaced Short Palindromic Repeats, are DNA sequences commonly found in bacteria and archaea that serve as a defense mechanism. They originate from pathogens that previously infected the host are are used to detect said pathogens when they try to re-infect the host.

A Nuclease Defends - Its Mechanism of Action

When pathogens that have previously infected the host try to re-invade, host nucleases use CRISPR sequences to detect the RNA sequences of the pathogen. A nuclease is an enzyme the cleaves nucleic acids in DNA or RNA. In CRISPR derived technology, the nuclease is lead by a guid RNA (gRNA) - a sequence of nucleotides complementary to a target strand area - to the CRISPR originating from the pathogen, and cleaves it. Here, Cas13a is the nuclease.

Cas9, a nuclease, cleaving RNA in CRISPR technology
[2]

Exchanging Ideas

Credits to Team HD Resolution for the Picture

Thanks to the HD Resolution Team in NYC, USA, we collaborated to host an event to present our projects to each other. They learned about the EtBr Spot Protocol and the light operon and we learned about their goal to cure Huntington's Disease. It was a great experience!

Citations

[1]Info on EtBr

[1]more EtBr info

[2] more CRISPR info

Collaborations

Sharing and collaboration are core values of iGEM. We encourage you to reach out and work with other teams on difficult problems that you can more easily solve together.

Silver Medal Criterion #2

Complete this page if you intend to compete for the silver medal criterion #2 on collaboration. Please see the 2018 Medals Page for more information.

Which other teams can we work with?

You can work with any other team in the competition, including software, hardware, high school and other tracks. You can also work with non-iGEM research groups, but they do not count towards the iGEM team collaboration silver medal criterion.

In order to meet the silver medal criteria on helping another team, you must complete this page and detail the nature of your collaboration with another iGEM team.

Here are some suggestions for projects you could work on with other teams:

• Improve the function of another team's BioBrick Part or Device
• Characterize another team's part
• Debug a construct
• Model or simulate another team's system
• Test another team's software
• Help build and test another team's hardware project
• Mentor a high-school team