Genetic Engineering & Biotechnology News

AUG 2017

Genetic Engineering & Biotechnology News (GEN) is the world's most widely read biotech publication. It provides the R&D community with critical information on the tools, technologies, and trends that drive the biotech industry.

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Page 17 of 37

16 | AUGUST 2017 | | Genetic Engineering & Biotechnology News available yet, but the BioXp 3200 system, a benchtop DNA printer, is already being marketed through the SGI subsidiary SGI- DNA. Whereas the DBC starts with DNA sequence information, the BioXp 3200 in- strument starts with oligonucleotide pools that are obtained from a vendor and then pooled and sent to customers. More New Tools "We are focusing on developing new tools for detecting and analyzing different types of DNA and RNA sequences," says Ken Halvorsen, Ph.D., principal investigator at The RNA Institute, University at Albany, State University of New York. A major effort in Dr. Halvorsen's group is focusing on study- ing DNA nanoswitches, which are molecular structures that comprise a linear DNA du- plex and an inducible loop. Upon exposure to external target mol- ecules, DNA nanoswitches undergo revers- ible topological changes that can provide information about molecular association and dissociation reactions. The nanoswitch starts out as a linear piece of DNA. When the nanoswitch interacts with a target oli- gonucleotide, a bulge or loop structure is generated. "That is the main outcome of the switch function," explains Dr. Halvorsen. "There are several ways to determine whether a molecule that a researcher is looking for is present." One strategy is to perform agarose gel electrophoresis, which can separate a struc- ture with a loop from a structure without a loop based on the differential migration patterns of the two. Another strategy is to detect the presence of a loop, at the single- molecule level, and then measure its length. The second strategy, notes Dr. Halvorsen, is one of the main DNA-related nanotechnolo- gies that has been used in his laboratory. In collaboration with Alan Chen, Ph.D., and Mehmet Yigit, Ph.D., both chemists at the University of Albany, Dr. Halvorsen and colleagues modeled the molecular dynam- ics of an experimentally observed phenom- enon: the preferential affinity of graphene oxide to single-stranded DNA over double- stranded DNA. Graphene oxide, the water- soluble form of graphene, can be used for DNA and RNA detection and has shown promise for applications including environ- mental monitoring and biosensor develop- ment. "We wanted to shed light on some of the basic principles of the thermodynam- ics of the interaction between graphene surfaces and oligonucleotides," says Dr. Halvorsen. The molecular models that were devel- oped by Dr. Halvorsen and colleagues may be used to characterize the adsorption of oligonucleotides to graphene surfaces. By revealing details of the complex interaction between graphene surfaces and nucleic acids, these models provide a framework for the ra- tional design of graphene-based biosensors. "Rather than synthesize individual se- quences one at a time via a solid support, as is done in conventional DNA synthesis, we have a product called OligoMix ® , which is generated on a microfluidic chip," says Chris Hebel, Ph.D., vice president of business de- velopment at LC Sciences. OligoMix consists of pooled oligonucle- otids, which are generated with a technol- ogy that has also been used to synthesize mi- croarrays in gene-expression applications. "We discovered that these oligonucleotides, if they are cleaved off the array into the mix, have quite a few applications in addition to the applications of the oligonucleotide ar- rays," asserts Dr. Hebel. OligoMix contains thousands of single-stranded oligonucle- otides per tube. The oligonucleotides can be up to 150-mers, and they can be prepared with a variety of 5'-, 3'-, or internal modi- fications. The approach used to prepare the Oligo- Mix is based on three different technologies. The first technology is the microfluidic chip The Science of Precision Health Simoa TM assays can detect critical biomarkers with 1000X increase in sensitivity. Researchers now have access to new classes of blood-based biomarkers for early disease detection, progression and response to treatment. Learn more at Undetectable is not in our vocabulary. Discover what's new from the leading journal on post-genomic medicine and integrative biology Sign Up for TOC Alerts Discover what's new from the leading journal on post-genomic medicine and integrative biology Sign Up for TOC Alerts Editor-in-Chief: Vural Özdemir, MD, PhD, DABCP DNA Synthesis Continued from page 14 OMICS

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