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Rapid intercalator removal from size-selected DNA for next generation sequencing

Award Information
Agency: Department of Health and Human Services
Branch: National Institutes of Health
Contract: 1R41HG006912-01
Agency Tracking Number: R41HG006912
Amount: $99,647.00
Phase: Phase I
Program: STTR
Solicitation Topic Code: NHGRI
Solicitation Number: PA11-097
Solicitation Year: 2012
Award Year: 2012
Award Start Date (Proposal Award Date): N/A
Award End Date (Contract End Date): N/A
Small Business Information
United States
DUNS: 611509451
HUBZone Owned: No
Woman Owned: No
Socially and Economically Disadvantaged: No
Principal Investigator
 (585) 273-4725
Business Contact
Phone: (585) 273-4725
Research Institution
UNIVERSITY OF ROCHESTER 518 Hylan Bldg., Box 270140 Office of Research AND Project Administration
United States

 () -
 Nonprofit College or University

DESCRIPTION (provided by applicant): Information from next generation sequencing is widely used in translational studies and promises to be a cornerstone of personalized medicine where therapeutic courses are linked to an individual's genetic makeup. Extraction of DNA from gels following electrophoresis to obtain size-selected DNA fragments is a labor intensive part of library preparation present in the protocols of all of the major next generation sequencing platforms. Recently, Sage Science introduceda disruptive product for DNA size selection that electrically switches the desired DNA fragments out of the gel and obviates the need for physically extracting the DNA. Due to its speed and labor saving protocol, the Sage Science Pippin Prep is beingquickly adopted by the rapidly growing next generation sequencing market. Unfortunately, with the Pippin Prep it remains necessary to do a relatively labor-intensive purification to remove the intercalating dyes used to identify the bands because they interfere with subsequent processes in next generation sequencing library preparation. Diffinity Genomics proposes to develop a single-step purification process based on a functional pipette tip that will eliminate intercalating dyes in less than 60 seconds while retaining the desired DNA. Diffinity Genomics has licensed novel materials technology developed in the PI's lab at the University of Rochester that can be used for fast, inexpensive and simple biomolecular separations needed to purify nucleic acid reactions. Particle surfaces are specially configured to selectively adsorb or repel various solution components making it possible to retain desired components in solution while removing unwanted impurities. Diffinity has utilized that differential adsorption technology to launch a fast PCR purification product (RapidTipTM) that enables single-step PCR cleanup in less than a minute simply by aspirating the PCR product into a functional pipette tip and dispensing purified DNA reaction solution. The work in the present proposal is to develop particles with surfaces that selectively bind the intercalating dyes used by Sage Science and to make the particles easily dispersible in water to facilitate rapid mixing and collection of impurities. We will also ascertain whether the size-selected DNA obtained with the Sage Science instrument and Diffinity purification is suitable for next generation sequencing library preparation. PUBLIC HEALTH RELEVANCE: Next generation sequencing of DNA is growing rapidly since it provides genetic information important to medical research and diagnosis. Size selection of DNA using gel electrophoresis is part of next generation sequencing protocols and a new product from Sage Science is streamlining that process. We propose a companion product that will reduce the time, cost and material waste associated with purifying the size-selected DNA obtained from the Sage Science process.

* Information listed above is at the time of submission. *

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