Literature DB >> 26314212

Bulged Invader probes: activated duplexes for mixed-sequence dsDNA recognition with improved thermodynamic and kinetic profiles.

Dale C Guenther1, Saswata Karmakar, Patrick J Hrdlicka.   

Abstract

Double-stranded oligonucleotides with +1 interstrand zipper arrangements of intercalator-functionalized nucleotides are energetically activated for recognition of mixed-sequence double-stranded DNA. Incorporation of nonyl (C9) bulges at specific positions of these probes, results in more highly affine (>5-fold), faster (>4-fold) and more persistent dsDNA recognition relative to conventional Invader probes.

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Year:  2015        PMID： 26314212      PMCID： PMC4589525          DOI： 10.1039/c5cc06264k

Source DB:  PubMed          Journal:  Chem Commun (Camb)        ISSN： 1359-7345            Impact factor:   6.222


  22 in total

1.  Sequence-universal recognition of duplex DNA by oligonucleotides via pseudocomplementarity and helix invasion.

Authors:  Irina V Smolina; Vadim V Demidov
Journal:  Chem Biol       Date:  2003-07

2.  Invader LNA: efficient targeting of short double stranded DNA.

Authors:  Sujay P Sau; T Santhosh Kumar; Patrick J Hrdlicka
Journal:  Org Biomol Chem       Date:  2010-03-04       Impact factor: 3.876

Review 3.  Triplex-forming oligonucleotides - sequence-specific DNA ligands as tools for gene inhibition and for modulation of DNA-associated functions.

Authors:  Robert Besch; Carine Giovannangeli; Klaus Degitz
Journal:  Curr Drug Targets       Date:  2004-11       Impact factor: 3.465

4.  DNA meter: Energy tunable, quantitative hybridization assay.

Authors:  William Braunlin; Jens Völker; G Eric Plum; Kenneth J Breslauer
Journal:  Biopolymers       Date:  2013-06       Impact factor: 2.505

5.  Recognition of mixed-sequence DNA duplexes: design guidelines for invaders based on 2'-O-(pyren-1-yl)methyl-RNA monomers.

Authors:  Saswata Karmakar; Dale C Guenther; Patrick J Hrdlicka
Journal:  J Org Chem       Date:  2013-11-20       Impact factor: 4.354

6.  Conditionally fluorescent molecular probes for detecting single base changes in double-stranded DNA.

Authors:  Sherry Xi Chen; David Yu Zhang; Georg Seelig
Journal:  Nat Chem       Date:  2013-07-28       Impact factor: 24.427

Review 7.  Programmable DNA-binding small molecules.

Authors:  Meghan S Blackledge; Christian Melander
Journal:  Bioorg Med Chem       Date:  2013-04-18       Impact factor: 3.641

Review 8.  ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering.

Authors:  Thomas Gaj; Charles A Gersbach; Carlos F Barbas
Journal:  Trends Biotechnol       Date:  2013-05-09       Impact factor: 19.536

9.  Identification and characterization of second-generation invader locked nucleic acids (LNAs) for mixed-sequence recognition of double-stranded DNA.

Authors:  Sujay P Sau; Andreas S Madsen; Peter Podbevsek; Nicolai K Andersen; T Santhosh Kumar; Sanne Andersen; Rie L Rathje; Brooke A Anderson; Dale C Guenther; Saswata Karmakar; Pawan Kumar; Janez Plavec; Jesper Wengel; Patrick J Hrdlicka
Journal:  J Org Chem       Date:  2013-09-25       Impact factor: 4.354

10.  Pseudo-complementary PNA actuators as reversible switches in dynamic DNA nanotechnology.

Authors:  Damian Ackermann; Michael Famulok
Journal:  Nucleic Acids Res       Date:  2013-02-26       Impact factor: 16.971
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  7 in total

1.  Impact of non-nucleotidic bulges on recognition of mixed-sequence dsDNA by pyrene-functionalized Invader probes.

Authors:  Dale C Guenther; Raymond G Emehiser; Allison Inskeep; Saswata Karmakar; Patrick J Hrdlicka
Journal:  Org Biomol Chem       Date:  2020-06-24       Impact factor: 3.876

2.  Recognition of mixed-sequence DNA using double-stranded probes with interstrand zipper arrangements of O2'-triphenylene- and coronene-functionalized RNA monomers.

Authors:  Saswata Karmakar; Dale C Guenther; Bradley C Gibbons; Patrick J Hrdlicka
Journal:  Org Biomol Chem       Date:  2017-11-15       Impact factor: 3.876

3.  Recognition of double-stranded DNA using LNA-modified toehold Invader probes.

Authors:  Shiva P Adhikari; Philip Vukelich; Dale C Guenther; Saswata Karmakar; Patrick J Hrdlicka
Journal:  Org Biomol Chem       Date:  2021-11-03       Impact factor: 3.876

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

Authors:  Shiva P Adhikari; Saswata Karmakar; Patrick J Hrdlicka
Journal:  Org Biomol Chem       Date:  2022-02-02       Impact factor: 3.876

Review 5.  Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides.

Authors:  Olga A Krasheninina; Darya S Novopashina; Evgeny K Apartsin; Alya G Venyaminova
Journal:  Molecules       Date:  2017-11-30       Impact factor: 4.411

6.  Merging Two Strategies for Mixed-Sequence Recognition of Double-Stranded DNA: Pseudocomplementary Invader Probes.

Authors:  Brooke A Anderson; Patrick J Hrdlicka
Journal:  J Org Chem       Date:  2016-03-30       Impact factor: 4.354

7.  Thrombin binding aptamer G-quadruplex stabilized by pyrene-modified nucleotides.

Authors:  Matic Kovačič; Peter Podbevšek; Hisae Tateishi-Karimata; Shuntaro Takahashi; Naoki Sugimoto; Janez Plavec
Journal:  Nucleic Acids Res       Date:  2020-04-17       Impact factor: 16.971
  7 in total

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