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7-deazaguanines in DNA: mechanism and structure of complex genome modification

Award Number: R01GM146075
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: 08/15/2022
PERIOD OF PERFORMANCE END DATE: 07/31/2026

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7-deazaguanines in DNA: mechanism and structure of complex genome modification - SUMMARY. Enzymatically-directed nucleotide modification is a key component of nucleic acid processing and is used by all organisms to address a multitude of fundamental needs in information transfer systems, including protection of DNA, translational fidelity, RNA stabilization, and epigenetic regulation. In a remarkable example of the cross-talk between RNA and DNA processing, we recently discovered that one of the most complex modification systems known to occur in RNA, that responsible for the 7-deazaguanine modifications queuosine (Q) and archaeosine (G+), is also utilized by diverse organisms for the modification of DNA. Indeed, in Bacteria a set of roughly 10 proteins comprise an elaborate restriction-modification (RM) system based on the formation of 2’-deoxy-7-cyano- and 2’-deoxy-7-amido-7-deazaguanosine (dPreQ0 and dADG, respectively) in DNA, and these nucleosides, as well as dG+ and 2’-deoxy-7- aminomethyl-7-deazaguanosine (dPreQ1), have also been found in the DNA of phage and archaeal viruses. Having identified the relevant proteins involved in the formation of 7- deazaguanine based DNA modifications, we are now proposing to elucidate the molecular basis for their function. The research described in specific aims 1 & 2 address the modification machinery in bacteria, the proteins DpdA, DpdB, and DpdC, which together are responsible for the formation of dPreQ0 and dADG, and serve as a model for 7-deazaguanine based modification in DNA. In specific aim 3 we take a broader look at the DpdA family and consider systems that lack DpdB and contain DpdAC fusions, as well as a phage DpdA in order to better understand the need for the cryptic ATPase activity of DpdB in bacterial modification, and the structural basis of sequence specificity in the bacterial and viral systems.


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 = $397,426 )
2025	2025	PORTLAND STATE UNIVERSITY	1600 SW 4TH AVE	PORTLAND	OR	97201	MULTNOMAH	USA	Biomedical Research and Research Training	000	4	8/1/2025	NON-COMPETING CONTINUATION	$397,426
														Subtotal = $397,426

Issue Date FY: 2024 ( Subtotal = $397,265 )
2024	2024	PORTLAND STATE UNIVERSITY	1600 SW 4TH AVE	PORTLAND	OR	97201	MULTNOMAH	USA	Biomedical Research and Research Training	000	3	8/29/2024	NON-COMPETING CONTINUATION	$397,265
														Subtotal = $397,265

Issue Date FY: 2023 ( Subtotal = $409,455 )
2023	2023	PORTLAND STATE UNIVERSITY	1600 SW 4TH AVE	PORTLAND	OR	97201	MULTNOMAH	USA	Biomedical Research and Research Training	001	2	9/13/2023	NON-COMPETING CONTINUATION	$397,110
2023	2023	PORTLAND STATE UNIVERSITY	1600 SW 4TH AVE	PORTLAND	OR	97201	MULTNOMAH	USA	Biomedical Research and Research Training	000	1	5/26/2023	SUPPLEMENT FOR EXPANSION	$12,345
														Subtotal = $409,455

Issue Date FY: 2022 ( Subtotal = $433,335 )
2022	2022	PORTLAND STATE UNIVERSITY	1600 SW 4TH AVE	PORTLAND	OR	97201	MULTNOMAH	USA	Biomedical Research and Research Training	000	1	8/12/2022	NEW	$433,335
														Subtotal = $433,335

Grand Total All Awards = $1,637,481

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7-deazaguanines in DNA: mechanism and structure of complex genome modification

Award Number: R01GM146075

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: 08/15/2022

PERIOD OF PERFORMANCE END DATE: 07/31/2026

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