Stacking-induced fluorescence increase reveals allosteric interactions through DNA.


:From gene expression to nanotechnology, understanding and controlling DNA requires a detailed knowledge of its higher order structure and dynamics. Here we take advantage of the environment-sensitive photoisomerization of cyanine dyes to probe local and global changes in DNA structure. We report that a covalently attached Cy3 dye undergoes strong enhancement of fluorescence intensity and lifetime when stacked in a nick, gap or overhang region in duplex DNA. This is used to probe hybridization dynamics of a DNA hairpin down to the single-molecule level. We also show that varying the position of a single abasic site up to 20 base pairs away modulates the dye-DNA interaction, indicative of through-backbone allosteric interactions. The phenomenon of stacking-induced fluorescence increase (SIFI) should find widespread use in the study of the structure, dynamics and reactivity of nucleic acids.


Nucleic Acids Res


Nucleic acids research


Morten MJ,Lopez SG,Steinmark IE,Rafferty A,Magennis SW




Has Abstract


2018-11-30 00:00:00














  • Efficient extension of a misaligned tRNA-primer during replication of the HIV-1 retrovirus.

    abstract::The human immunodeficiency virus (HIV) and other retroviruses show extensive genomic variation, which is primarily due to error-prone replication by the viral reverse transcriptase (RT) enzymes. RT errors include misincorporation with subsequent extension of the mismatched terminal base, and extension of realigned pri...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Das AT,Berkhout B

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  • Genome wide interactions of wild-type and activator bypass forms of σ54.

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Schaefer J,Engl C,Zhang N,Lawton E,Buck M

    更新日期:2015-09-03 00:00:00

  • Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: library construction methods for directed evolution.

    abstract::Directed molecular evolution and combinatorial methodologies are playing an increasingly important role in the field of protein engineering. The general approach of generating a library of partially randomized genes, expressing the gene library to generate the proteins the library encodes and then screening the protei...

    journal_title:Nucleic acids research

    pub_type: 杂志文章,评审


    authors: Neylon C

    更新日期:2004-02-27 00:00:00

  • Protection of (dA.dT) cluster regions in the DNAase I cleavage of DNA by specific interaction with netropsin.

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zimmer C,Luck G,Nüske R

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Altenhoff AM,Schneider A,Gonnet GH,Dessimoz C

    更新日期:2011-01-01 00:00:00

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    pub_type: 杂志文章


    authors: Angellotti MC,Bhuiyan SB,Chen G,Wan XF

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    pub_type: 杂志文章


    authors: Gunsalus RP,Kalman LV,Stewart RR

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Baker SM,Margison GP,Strike P

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    pub_type: 杂志文章


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    pub_type: 杂志文章


    authors: Bahlawane C,Dian C,Muller C,Round A,Fauquant C,Schauer K,de Reuse H,Terradot L,Michaud-Soret I

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    pub_type: 杂志文章


    authors: Saito H,Uehara H,Kusano T,Oishi M

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    pub_type: 杂志文章


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    authors: Waldispühl J,Devadas S,Berger B,Clote P

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    pub_type: 杂志文章


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    pub_type: 杂志文章


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    pub_type: 杂志文章


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    authors: Martin J,Abubucker S,Wylie T,Yin Y,Wang Z,Mitreva M

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    pub_type: 杂志文章


    authors: Potter BV,Eckstein F,Uznański B

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  • The processing of wild type and mutant forms of rat nuclear pre-tRNA(Lys) by the homologous RNase P.

    abstract::The 5' processing of rat pre-tRNA(Lys) and a series of mutant derivatives by rat cytosolic RNase P was examined. In standard, non-kinetic assays, mutant precursors synthesized in vitro with 5' leader sequences of 10, 17, 24, 25, and 46 nucleotides were processed to approximately equal levels and yielded precisely clea...

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    pub_type: 杂志文章


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    journal_title:Nucleic acids research

    pub_type: 杂志文章


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  • MGD: the Mouse Genome Database.

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


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  • Phosphorylation/dephosphorylation of the repressor MDBP-2-H1 selectively affects the level of transcription from a methylated promoter in vitro.

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bruhat A,Jost JP

    更新日期:1996-05-15 00:00:00

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Roy AA,Dhawanjewar AS,Sharma P,Singh G,Madhusudhan MS

    更新日期:2019-07-02 00:00:00

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Homann M,Tabler M,Tzortzakaki S,Sczakiel G

    更新日期:1994-09-25 00:00:00

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    pub_type: 杂志文章


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    更新日期:2008-06-01 00:00:00

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    pub_type: 杂志文章


    authors: Howe DG,Ramachandran S,Bradford YM,Fashena D,Toro S,Eagle A,Frazer K,Kalita P,Mani P,Martin R,Moxon ST,Paddock H,Pich C,Ruzicka L,Schaper K,Shao X,Singer A,Van Slyke CE,Westerfield M

    更新日期:2021-01-08 00:00:00

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Turner PC,Bagenal EB,Vlad MT,Woodland HR

    更新日期:1988-04-25 00:00:00

  • Mouse genome database 2016.

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bult CJ,Eppig JT,Blake JA,Kadin JA,Richardson JE,Mouse Genome Database Group.

    更新日期:2016-01-04 00:00:00