paper — Posts — The Bailey Lab

Solving a targeting puzzle: Type III-B DNA cleavage

Type III CRISPR systems are unusual in part because they have multiple mechanisms for cleaving nucleic acids, and target both RNA and DNA, but the latter only in a transcription-dependent matter. A 2016 paper from the Bailey lab in Genes and Development filled in key pieces of the puzzle about Type III systems, helping to clarify two major questions: What are the specific RNA and DNA targets of Type III complex? And what mechanisms control and coordinate the RNA and DNA cleavage activities?

Sarah StuderJanuary 11, 2022paper, type iii paper, type iii, Solving a targeting puzzle, cleavage mechanisms

Viewing a Cascade

In 2014, three labs completed structures of different versions of the Cascade complex, in three papers published at the same time – including one led by Sabin Mulepati, a then-PhD student in the Bailey lab. Sabin used x-ray crystallography to determine the structure of Cascade bound to a single strand of target DNA that matched the Cascade crRNA, to a resolution of 3 angstroms.

Sarah StuderOctober 4, 2021paper, type i paper, type i, cascade structure, complex target interactions

A look at a Cas3 HD domain

In the news you might only hear about CRISPR-Cas9, but there are actually several types of CRISPR systems – and the most common are Type I systems, defined by the cas3 gene. In 2011, Sabin Mulepati, then a PhD student, and Scott Bailey were used x-ray crystallography and biochemical analysis to characterize the HD domain of the Thermus thermophilus Cas3 – read on to learn what they found out.

Sarah StuderMarch 24, 2021paper, type i paper, type i, cleavage mechanisms

CRISPR spacers - asymmetry and orientation

CRISPR array spacers need to be in the correct orientation for the CRISPR system to work. In a new paper, our lab showed that in E. coli, asymmetrical trimming of prespacer overhangs by certain exonucleases helps the system insert spacers correctly.

Sarah StuderJanuary 29, 2020paper, type i paper, acquisition paper, type i, asymmetry and orientation

What makes a match? For CRISPR type III-B, it depends on location

CRISPR is used by some bacteria to target and destroy DNA and RNA from invading viruses and other sources - but how do they keep from damaging their own DNA?

A recent paper from our lab shows how one type of CRISPR system distinguishes between its own DNA and others.

Sarah StuderOctober 30, 2019paper, type iii paper, type iii, what makes a match, complex target interactions