Strand-invading linear probe combined with unmodified PNA

Asanuma, Hiroyuki; Niwa, Rie; Akahane, Mariko; Murayama, Keiji; Kashida, Hiromu

doi:10.1016/j.bmc.2016.06.055

Cited by 10 publications

(5 citation statements)

References 38 publications

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“…Thus, the mechanistic principles of MP γPNA:Invader chimeras resemble those of heteroduplexes between intercalator-modified oligonucleotides and RNA, PNA or locked nucleic acid (LNA) strands. [20][21][22] The chimeric MP γPNA:Invader probes resulted in more efficient and specific dsDNA-recognition than singlestranded MP γPNA probes. 45 In the present study we evaluated the dsDNA-recognition properties of SγPNA, Invader, and chimeric SγPNA:Invader probes, using DNA hairpin and chromosomal DNA targets with low levels of self-complementarity (Fig.…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…These challenges spurred the development of strand-invading strategies, i.e., probes capable of unzipping the Watson-Crick base-pairs of dsDNA targets and forming new, more stable Watson-Crick base-pairs between probe strands and the complementary DNA (cDNA) regions. Examples include various modified single-stranded PNAs, [8][9][10][11][12][13] as well as doublestranded probes like pseudo-complementary PNAs, [14][15][16][17][18] Invader probes, 19 heteroduplexes between intercalator-modified oligonucleotides and RNA, PNA or locked nucleic acid (LNA) strands, [20][21][22] and related approaches. [23][24][25][26] Some of these strand-invading strategies are discussed in more detail below.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Serine-γPNA, Invader probes, and chimeras thereof: three probe chemistries that enable sequence-unrestricted recognition of double-stranded DNA

et al. 2022

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Serine-γPNA, Invader probes, and chimeras thereof: three probe chemistries that enable sequence-unrestricted recognition of double-stranded DNA

et al. 2022

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“…, probes capable of unzipping the Watson–Crick base-pairs of dsDNA targets and forming new, more stable Watson–Crick base-pairs between individual probe strands and complementary DNA (cDNA). Representative examples include modified PNA, 10–12 Zorro LNAs (locked nucleic acids), 13 and easily denaturing double-stranded probes such as pseudo-complementary (pc) DNA, 14 pcPNA, 15–17 heteroduplexes between intercalator-modified oligonucleotides and RNA, LNA or PNA strands, 18–20 and related approaches. 21–23…”

Section: Introductionmentioning

confidence: 99%

Nicked Invader probes: multistranded and sequence-unrestricted recognition of double-stranded DNA

2022

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“…A key advantage of strand-invading strategies is the prospect of the sequenceunrestricted recognition of dsDNA. Progress towards this end has been realized with various modified single-stranded PNAs [7][8][9][10][11][12], double-stranded probes such as pseudocomplementary (pc) PNAs [13][14][15], and related approaches [16][17][18][19][20][21][22][23].…”

Section: Introductionmentioning

confidence: 99%

Factors Impacting Invader-Mediated Recognition of Double-Stranded DNA

et al. 2022

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The development of chemically modified oligonucleotides enabling robust, sequence-unrestricted recognition of complementary chromosomal DNA regions has been an aspirational goal for scientists for many decades. While several groove-binding or strand-invading probes have been developed towards this end, most enable recognition of DNA only under limited conditions (e.g., homopurine or short mixed-sequence targets, low ionic strength, fully modified probe strands). Invader probes, i.e., DNA duplexes modified with +1 interstrand zippers of intercalator-functionalized nucleotides, are predisposed to recognize DNA targets due to their labile nature and high affinity towards complementary DNA. Here, we set out to gain further insight into the design parameters that impact the thermal denaturation properties and binding affinities of Invader probes. Towards this end, ten Invader probes were designed, and their biophysical properties and binding to model DNA hairpins and chromosomal DNA targets were studied. A Spearman’s rank-order correlation analysis of various parameters was then performed. Densely modified Invader probes were found to result in efficient recognition of chromosomal DNA targets with excellent binding specificity in the context of denaturing or non-denaturing fluorescence in situ hybridization (FISH) experiments. The insight gained from the initial phase of this study informed subsequent probe optimization, which yielded constructs displaying improved recognition of chromosomal DNA targets. The findings from this study will facilitate the design of efficient Invader probes for applications in the life sciences.

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Strand-invading linear probe combined with unmodified PNA

Cited by 10 publications

References 38 publications

Serine-γPNA, Invader probes, and chimeras thereof: three probe chemistries that enable sequence-unrestricted recognition of double-stranded DNA

Serine-γPNA, Invader probes, and chimeras thereof: three probe chemistries that enable sequence-unrestricted recognition of double-stranded DNA

Nicked Invader probes: multistranded and sequence-unrestricted recognition of double-stranded DNA

Factors Impacting Invader-Mediated Recognition of Double-Stranded DNA

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