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Computational Enzymology to Study Diverse Catalytic Strategies of RNA

Award Number: R01GM062248
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 06/01/2001
PERIOD OF PERFORMANCE END DATE: 01/31/2027

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Computational Enzymology to Study Diverse Catalytic Strategies of RNA - Computational Enzymology to Study Diverse Catalytic Strategies of RNA PI: Darrin M. York, Rutgers University, Piscataway, NJ 08854-8087 USA. RNA enzymes (ribozymes) are fundamental in biology, and have important applications in chemistry, biotech- nology and medicine. The scientiﬁc community is still in early stages of discovery, and the full breadth of poten- tially transformative RNA and related nucleic acid based technology and therapeutics have yet to be realized. A critical barrier to progress toward this realization is the lack of a predictive understanding of ribozyme mechanisms that can be used to guide design. This proposal addresses this critical barrier by the creation of new enabling technology to study RNA enzymes (Aim 1) that will be applied to small self-cleaving (nucleolytic) ribozymes (Aim 2), and artiﬁcially engineered self-alkylating and methyltransferase ribozymes and a naturally occurring group I intron ribozyme (Aim 3). Predictive insight gained from these studies will unveil general principles crucial for our understanding of RNA catalysis and the rational design of new ribozyme-based biomedical technology. Aim 1 will create advanced tools for computational RNA enzymology, including 1) new fast/accurate quan- tum+machine learning force ﬁelds for RNA catalysis, 2) integrated software for inclusion of nuclear quantum effects, and 3) robust methods for determination of reaction paths and free energy surfaces (including corrections to expensive high-level ab initio surfaces). These methods are signiﬁcant as enabling technology to study mech- anisms of RNA catalysis. The goal of this aim is develop innovative technology designed to meet the needs of the driving ribozyme applications in Aims 2 and 3, as well as many applications outside the scope of the proposal. Aim 2 will apply our computational enzymology tools to study the catalytic mechanisms of small nucleolytic ribozymes (Psr, HHr and HDVr) and a related artiﬁcially engineered DNAzyme (8-17dz). These systems are important as tools for chemical and molecular biology, and as tractable models for RNA/DNA catalysis. The goal of this aim is to apply and further develop general principles for RNA-cleaving nucleic acid enzyme design, building on our L-platform/L-scaffold framework for naturally occurring “G+A” and “G+M” ribozyme classes. Aim 3 will explore mechanisms of artiﬁcially engineered self-alkylating ribozyme (SAR) and methyl transferase ribozyme (MTR1), and the naturally occurring Tetrahymena group I intron (THr) ribozyme. These systems have far-reaching implications for biotechnology and medicine. The goal of this aim is to examine the extent to which design principles can be extended and transferred to these systems to provide deeper insight into the diverse array of catalytic strategies available to nucleic acid enzymes. Working together, these aims will accomplish the overarching goal to achieve a predictive understanding of ribozyme mechanisms that can be used to guide the design of new technology and therapeutics.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2025 ( Subtotal = $347,341 )
2025	2025	RUTGERS, THE STATE UNIVERSITY	3 RUTGERS PLZ	NEW BRUNSWICK	NJ	08901	MIDDLESEX	USA	Biomedical Research and Research Training	001	25	8/5/2025	NON-COMPETING CONTINUATION	$34,734
2025	2025	RUTGERS, THE STATE UNIVERSITY	3 RUTGERS PLZ	NEW BRUNSWICK	NJ	08901	MIDDLESEX	USA	Biomedical Research and Research Training	000	25	3/4/2025	NON-COMPETING CONTINUATION	$312,607
														Subtotal = $347,341

Issue Date FY: 2024 ( Subtotal = $347,341 )
2024	2024	RUTGERS, THE STATE UNIVERSITY	3 RUTGERS PLZ	NEW BRUNSWICK	NJ	08901	MIDDLESEX	USA	Biomedical Research and Research Training	000	24	1/10/2024	NON-COMPETING CONTINUATION	$312,607
2024	2024	RUTGERS, THE STATE UNIVERSITY	3 RUTGERS PLZ	NEW BRUNSWICK	NJ	08901	MIDDLESEX	USA	Biomedical Research and Research Training	001	24	6/17/2024	NON-COMPETING CONTINUATION	$34,734
														Subtotal = $347,341

Issue Date FY: 2023 ( Subtotal = $345,293 )
2023	2023	RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY	3 RUTGERS PLZA	NEW BRUNSWICK	NJ	08901	MIDDLESEX	USA	Biomedical Research and Research Training	001	23	4/26/2023	COMPETING CONTINUATION	$345,293
2023	2021	RUTGERS, THE STATE UNIVERSITY	3 RUTGERS PLZ	NEW BRUNSWICK	NJ	08901	MIDDLESEX	USA	Biomedical Research and Research Training	000	22	4/3/2023	NON-COMPETING CONTINUATION	$0
														Subtotal = $345,293

Issue Date FY: 2021 ( Subtotal = $330,631 )
2021	2021	RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY	3 RUTGERS PLZA	NEW BRUNSWICK	NJ	08901	MIDDLESEX	USA	Biomedical Research and Research Training	000	22	8/22/2021	NON-COMPETING CONTINUATION	$330,631
														Subtotal = $330,631

Issue Date FY: 2020 ( Subtotal = $330,693 )
2020	2020	RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY	3 RUTGERS PLZA	NEW BRUNSWICK	NJ	08901	MIDDLESEX	USA	Biomedical Research and Research Training	000	21	8/18/2020	NON-COMPETING CONTINUATION	$330,693
														Subtotal = $330,693

Issue Date FY: 2019 ( Subtotal = $330,753 )
2019	2019	RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY	3 RUTGERS PLZA	NEW BRUNSWICK	NJ	08901	MIDDLESEX	USA	Biomedical Research and Research Training	001	20	9/10/2019	NON-COMPETING CONTINUATION	$330,753
2019	2017	RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY	3 RUTGERS PLZA	NEW BRUNSWICK	NJ	08901	MIDDLESEX	USA	Biomedical Research and Research Training	000	18	9/5/2019	NON-COMPETING CONTINUATION	$0
														Subtotal = $330,753

Issue Date FY: 2018 ( Subtotal = $330,812 )
2018	2018	RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY	3 RUTGERS PLZA	NEW BRUNSWICK	NJ	08901	MIDDLESEX	USA	Biomedical Research and Research Training	001	19	9/20/2018	COMPETING CONTINUATION	$330,812
2018	2017	RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY	3 RUTGERS PLZA	NEW BRUNSWICK	NJ	08901	MIDDLESEX	USA	Biomedical Research and Research Training	000	18	9/17/2018	NON-COMPETING CONTINUATION	$0
														Subtotal = $330,812

Issue Date FY: 2017 ( Subtotal = $321,533 )
2017	2017	RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY	3 RUTGERS PLZA	NEW BRUNSWICK	NJ	08901	MIDDLESEX	USA	Biomedical Research and Research Training	000	18	7/20/2017	NON-COMPETING CONTINUATION	$321,533
														Subtotal = $321,533

Issue Date FY: 2016 ( Subtotal = $321,533 )
2016	2016	RUTGERS THE STATE UNIVERSITY OF NEW JERSEY	3 RUTGERS PLAZA	NEW BRUNSWICK	NJ	08901	MIDDLESEX	USA	Biomedical Research and Research Training	000	17	8/1/2016	NON-COMPETING CONTINUATION	$321,533
														Subtotal = $321,533

Issue Date FY: 2015 ( Subtotal = $321,533 )
2015	2015	RUTGERS THE STATE UNIVERSITY OF NEW JERSEY	3 RUTGERS PLAZA	NEW BRUNSWICK	NJ	08901	MIDDLESEX	USA	Biomedical Research and Research Training	000	16	7/31/2015	NON-COMPETING CONTINUATION	$321,533
														Subtotal = $321,533

Issue Date FY: 2014 ( Subtotal = $321,533 )
2014	2014	RUTGERS THE STATE UNIVERSITY OF NEW JERSEY	3 RUTGERS PLAZA	NEW BRUNSWICK	NJ	08901	MIDDLESEX	USA	Biomedical Research and Research Training	000	15	7/28/2014	COMPETING CONTINUATION	$321,533
														Subtotal = $321,533

Issue Date FY: 2013 ( Subtotal = $301,718 )
2013	2013	RUTGERS THE STATE UNIVERSITY OF NEW JERSEY	3 RUTGERS PLAZA	NEW BRUNSWICK	NJ	08901	MIDDLESEX	USA	Biomedical Research and Research Training	000	14	7/29/2013	NON-COMPETING CONTINUATION	$301,718
														Subtotal = $301,718

Issue Date FY: 2012 ( Subtotal = $312,098 )
2012	2012	RUTGERS THE STATE UNIVERSITY OF NEW JERSEY	3 RUTGERS PLAZA	NEW BRUNSWICK	NJ	08901	MIDDLESEX	USA	Biomedical Research and Research Training	000	13	7/30/2012	NON-COMPETING CONTINUATION	$312,098
														Subtotal = $312,098

Issue Date FY: 2011 ( Subtotal = $244,116 )
2011	2011	RUTGERS THE STATE UNIVERSITY OF NEW JERSEY	3 RUTGERS PLAZA	NEW BRUNSWICK	NJ	08901	MIDDLESEX	USA	Biomedical Research and Research Training	002	12	8/5/2011	NON-COMPETING CONTINUATION	$263,425
2011	2010	RUTGERS THE STATE UNIVERSITY OF NEW JERSEY	3 RUTGERS PLAZA	NEW BRUNSWICK	NJ	08901	MIDDLESEX	USA	Biomedical Research and Research Training	001	11	6/13/2011	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$268,597
2011	2010	UNIVERSITY OF MINNESOTA	UNIV GATEWAY#450/200 OAK ST SE	MINNEAPOLIS	MN	55455	HENNEPIN	USA	Biomedical Research and Research Training	000	10	6/9/2011	COMPETING CONTINUATION	-$287,906
														Subtotal = $244,116

Issue Date FY: 2010 ( Subtotal = $287,906 )
2010	2010	UNIVERSITY OF MINNESOTA	UNIV GATEWAY#450/200 OAK ST SE	MINNEAPOLIS	MN	55455	HENNEPIN	USA	Biomedical Research and Research Training	001	10	8/30/2010	COMPETING CONTINUATION	$287,906
2010	2009	UNIVERSITY OF MINNESOTA	UNIV GATEWAY#450/200 OAK ST SE	MINNEAPOLIS	MN	55455	HENNEPIN	USA	Biomedical Research and Research Training	000	9	8/30/2010	NON-COMPETING CONTINUATION	$0
														Subtotal = $287,906

Issue Date FY: 2009 ( Subtotal = $237,491 )
2009	2009	UNIVERSITY OF MINNESOTA	UNIV GATEWAY#450/200 OAK ST SE	MINNEAPOLIS	MN	55455	HENNEPIN	USA	Biomedical Research and Research Training	000	9	6/2/2009	NON-COMPETING CONTINUATION	$237,491
														Subtotal = $237,491

Issue Date FY: 2008 ( Subtotal = $237,690 )
2008	2008	UNIVERSITY OF MINNESOTA	UNIV GATEWAY#450/200 OAK ST SE	MINNEAPOLIS	MN	55455	HENNEPIN	USA	Biomedical Research and Research Training	000	8	6/2/2008	NON-COMPETING CONTINUATION	$237,690
														Subtotal = $237,690

Issue Date FY: 2007 ( Subtotal = $237,885 )
2007	2007	UNIVERSITY OF MINNESOTA	UNIV GATEWAY#450/200 OAK ST SE	MINNEAPOLIS	MN	55455	HENNEPIN	USA	Biomedical Research and Research Training	000	7	5/7/2007	NON-COMPETING CONTINUATION	$237,885
														Subtotal = $237,885

Issue Date FY: 2006 ( Subtotal = $245,280 )
2006	2006	UNIVERSITY OF MINNESOTA	UNIV GATEWAY#450/200 OAK ST SE	MINNEAPOLIS	MN	55455	HENNEPIN	USA	Biomedical Research and Research Training	000	6	5/30/2006	COMPETING CONTINUATION	$245,280
														Subtotal = $245,280

Issue Date FY: 2005 ( Subtotal = $211,337 )
2005	2005	UNIVERSITY OF MINNESOTA	UNIV GATEWAY#450/200 OAK ST SE	MINNEAPOLIS	MN	55455	HENNEPIN	USA	Biomedical Research and Research Training	000	5	5/23/2005	NON-COMPETING CONTINUATION	$211,337
														Subtotal = $211,337

Issue Date FY: 2004 ( Subtotal = $211,437 )
2004	2004	UNIVERSITY OF MINNESOTA	UNIV GATEWAY#450/200 OAK ST SE	MINNEAPOLIS	MN	55455	HENNEPIN	USA	Biomedical Research and Research Training	000	4	5/6/2004	NON-COMPETING CONTINUATION	$211,437
														Subtotal = $211,437

Grand Total All Awards = $6,793,117

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Computational Enzymology to Study Diverse Catalytic Strategies of RNA

Award Number: R01GM062248

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 06/01/2001

PERIOD OF PERFORMANCE END DATE: 01/31/2027

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