Cloning thousands of genes for massive protein libraries – Phys.Org

Posted: June 26, 2017 at 4:46 pm

June 26, 2017 New DNA-based LASSO molecule probe can bind target genome regions for functional cloning and analysis. Credit: Jennifer E. Fairman/Johns Hopkins University

Discovering the function of a gene requires cloning a DNA sequence and expressing it. Until now, this was performed on a one-gene-at-a-time basis, causing a bottleneck. Scientists at Rutgers University-New Brunswick in collaboration with Johns Hopkins University and Harvard Medical School have invented a technology to clone thousands of genes simultaneously and create massive libraries of proteins from DNA samples, potentially ushering in a new era of functional genomics.

"We think that the rapid, affordable, and high-throughput cloning of proteins and other genetic elements will greatly accelerate biological research to discover functions of molecules encoded by genomes and match the pace at which new genome sequencing data is coming out," said Biju Parekkadan, an associate professor in the Department of Biomedical Engineering at Rutgers University-New Brunswick.

In a study published online today in the journal Nature Biomedical Engineering, the researchers showed that their technologyLASSO (long-adapter single-strand oligonucleotide) probescan capture and clone thousands of long DNA fragments at once.

As a proof-of-concept, the researchers cloned more than 3,000 DNA fragments from E. coli bacteria, commonly used as a model organism with a catalogued genome sequence available.

"We captured about 95 percent of the gene targets we set out to capture, many of which were very large in DNA length, which has been challenging in the past," Parekkadan said. "I think there will certainly be more improvements over time."

They can now take a genome sequence (or many of them) and make a protein library for screening with unprecedented speed, cost-effectiveness and precision, allowing rapid discovery of potentially beneficial biomolecules from a genome.

In conducting their research, they coincidentally solved a longstanding problem in the genome sequencing field. When it comes to genetic sequencing of individual genomes, today's gold standard is to sequence small pieces of DNA one by one and overlay them to map out the full genome code. But short reads can be hard to interpret during the overlaying process and there hasn't been a way to sequence long fragments of DNA in a targeted and more efficient way. LASSO probes can do just this, capturing DNA targets of more than 1,000 base pairs in length where the current format captures about 100 base pairs.

The team also reported the capture and cloning of the first protein library, or suite of proteins, from a human microbiome sample. Shedding light on the human microbiome at a molecular level is a first step toward improving precision medicine efforts that affect the microbial communities that colonize our gut, skin and lungs, Parekkadan added. Precision medicine requires a deep and functional understanding, at a molecular level, of the drivers of healthy and disease-forming microbiota.

Today, the pharmaceutical industry screens synthetic chemical libraries of thousands of molecules to find one that may have a medicinal effect, said Parekkadan, who joined Rutgers' School of Engineering in January.

"Our vision is to apply the same approach but rapidly screen non-synthetic, biological or 'natural' molecules cloned from human or other genomes, including those of plants, animals and microbes," he said. "This could transform pharmaceutical drug discovery into biopharmaceutical drug discovery with much more effort."

The next phase, which is underway, is to improve the cloning process, build libraries and discover therapeutic proteins found in our genomes, Parekkadan said.

Explore further: Technical advances in reading long DNA sequences have ramifications in understanding primate evolution, human disease

More information: Long-adapter single-strand oligonucleotide probes for the massively multiplexed cloning of kilobase genome regions, Nature Biomedical Engineering (2017). DOI: 10.1038/s41551-017-0092

Technical advances in reading long DNA sequences have ramifications in understanding primate evolution and human disease.

The most popular varieties of teaincluding black tea, green tea, Oolong tea, white tea, and chaiall come from the leaves of the evergreen shrub Camellia sinensis, otherwise known as the tea tree. Despite tea's immense ...

(Phys.org)For the first time, researchers sequenced DNA molecules without the need for the standard pre-sequencing workflow known as library preparation.

An international team of computer scientists developed a method that greatly improves researchers' ability to sequence the DNA of organisms that can't be cultured in the lab, such as microbes living in the human gut or bacteria ...

A new approach to studying microbes in the wild will allow scientists to sequence the genomes of individual species from complex mixtures. It marks a big advance for understanding the enormous diversity of microbial communities ...

With the rapid rise of next-generation sequencing technologies, disparate fields from cancer research to evolutionary biology have seen a drastic shift in the way DNA sequence data is obtained. It is now possible to sequence ...

In his classic comedy routine, "A Place for your Stuff," George Carlin argues that the whole point of life is to find an appropriately sized space for the things you own. What holds for people is also true for bacteria.

Since at least the 1920s, anecdotes and some studies have suggested that chimpanzees are "super strong" compared to humans, implying that their muscle fibers, the cells that make up muscles, are superior to humans.

Mammals possess several lines of defense against microbes. One of them is activated when receptors called Fprs, which are present on immune cells, bind to specific molecules that are linked to pathogens. Researchers at the ...

When Mark Martindale decided to trace the evolutionary origin of muscle cells, like the ones that form our hearts, he looked in an unlikely place: the genes of animals without hearts or muscles.

Researchers at the RIKEN Center for Sustainable Resource Science (CSRS) have discovered a new, yet simple, way to increase drought tolerance in a wide range of plants. Published in Nature Plants, the study reports a newly ...

Over two million years ago, a third of the largest marine animals like sharks, whales, sea birds and sea turtles disappeared. This previously unknown extinction event not only had a consid-erable impact on the earth's historical ...

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Go here to read the rest:
Cloning thousands of genes for massive protein libraries - Phys.Org

Related Posts