Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations.

dc.contributor.author

Shi, Honglue

dc.contributor.author

Clay, Mary C

dc.contributor.author

Rangadurai, Atul

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Sathyamoorthy, Bharathwaj

dc.contributor.author

Case, David A

dc.contributor.author

Al-Hashimi, Hashim M

dc.date.accessioned

2018-09-18T03:01:05Z

dc.date.available

2018-09-18T03:01:05Z

dc.date.issued

2018-04-19

dc.date.updated

2018-09-18T03:01:04Z

dc.description.abstract

NMR relaxation dispersion studies indicate that in canonical duplex DNA, Watson-Crick base pairs (bps) exist in dynamic equilibrium with short-lived low abundance excited state Hoogsteen bps. N1-methylated adenine (m1A) and guanine (m1G) are naturally occurring forms of damage that stabilize Hoogsteen bps in duplex DNA. NMR dynamic ensembles of DNA duplexes with m1A-T Hoogsteen bps reveal significant changes in sugar pucker and backbone angles in and around the Hoogsteen bp, as well as kinking of the duplex towards the major groove. Whether these structural changes also occur upon forming excited state Hoogsteen bps in unmodified duplexes remains to be established because prior relaxation dispersion probes provided limited information regarding the sugar-backbone conformation. Here, we demonstrate measurements of C3' and C4' spin relaxation in the rotating frame (R1ρ) in uniformly 13C/15N labeled DNA as sensitive probes of the sugar-backbone conformation in DNA excited states. The chemical shifts, combined with structure-based predictions using an automated fragmentation quantum mechanics/molecular mechanics method, show that the dynamic ensemble of DNA duplexes containing m1A-T Hoogsteen bps accurately model the excited state Hoogsteen conformation in two different sequence contexts. Formation of excited state A-T Hoogsteen bps is accompanied by changes in sugar-backbone conformation that allow the flipped syn adenine to form hydrogen-bonds with its partner thymine and this in turn results in overall kinking of the DNA toward the major groove. Results support the assignment of Hoogsteen bps as the excited state observed in canonical duplex DNA, provide an atomic view of DNA dynamics linked to formation of Hoogsteen bps, and lay the groundwork for a potentially general strategy for solving structures of nucleic acid excited states.

dc.identifier.issn

0925-2738

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1573-5001

dc.identifier.uri

https://hdl.handle.net/10161/17417

dc.language

eng

dc.publisher

Springer Science and Business Media LLC

dc.relation.ispartof

Journal of biomolecular NMR

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10.1007/s10858-018-0177-2

dc.subject

DNA bending

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DNA dynamics

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Major groove kinking

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Nucleic acids

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Rotating frame spin relaxation

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Sugar pucker

dc.title

Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations.

dc.type

Journal article

pubs.begin-page

229

pubs.end-page

244

pubs.issue

4

pubs.organisational-group

School of Medicine

pubs.organisational-group

Duke

pubs.organisational-group

Biochemistry

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Basic Science Departments

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Student

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Chemistry

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Trinity College of Arts & Sciences

pubs.publication-status

Published

pubs.volume

70

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