Time-Resolved Fluorescence Detection of Nicked DNA via Site-Specific Stacking of Sulfo-Cy3: The Role of Charge, Polarity, Linker, and Sequence Context.

Raul Berrocal-Martin, Henry G Sansom, Katalin Orosz, Max B Paterson, Brian O Smith, Steven W Magennis

Abstract read

In one paragraph

Article in The journal of physical chemistry. B, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Raul Berrocal-MartinSchool of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K.

Henry G SansomSchool of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K.

Katalin OroszSchool of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K.

Max B PatersonSchool of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K.

Brian O SmithSchool of Molecular Biosciences, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K.ORCID 0000-0003-3363-4168

Steven W MagennisSchool of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K.ORCID 0000-0002-4327-8366

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Nicked DNA can result from damage or cellular processing and is also prevalent in DNA nanostructures, so sensitive methods to probe the generation and location of nicks are desirable. It was found recently that sulfo-Cy3 (sCy3), a disulfonated version of Cy3, could stack in a nick of double-stranded DNA (dsDNA) when attached to a thymidine on the 3' end of one strand, resulting in an increase in fluorescence brightness. Here, we have performed a systematic time-resolved fluorescence study of the stacking of sCy3 on nicked DNA. We have varied the labeling polarity (5' vs 3'), linker (dT vs phosphate), labeled nucleotide (A, C, T, or G), DNA structure (nicked dsDNA, dsDNA, single-stranded DNA, and dsDNA with a single-strand overhang), and NaCl concentration. We also studied the effect of switching the negatively charged sCy3 to the positively charged Cy3. We have shown that the site-specific stacking and fluorescence modulation of sCy3 on nicked DNA is a general phenomenon that could find application in time-resolved assays of DNA processes such as annealing, strand displacement, and enzymatic nicking.

Indexed as

CarbocyaninesDNAFluorescent DyesBase SequenceDNA, Single-StrandedFluorescenceSpectrometry, FluorescenceTime FactorsCarbocyaninescyanine dye 3DNADNA, Single-StrandedFluorescent Dyes

Identifiers

PMID41150832

DOI10.1021/acs.jpcb.5c03845

PMCPMC12621249

What Socratic holds

Textmetadata

LicenceCC BY

Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.