Literature DB >> 24038876

Invaders: Recognition of Double-Stranded DNA by Using Duplexes Modified with Interstrand Zippers of 2'-O-(Pyren-1-yl)methyl-ribonucleotides.

Bradley A Didion1, Saswata Karmakar, Dale C Guenther, Sujay P Sau, John P Verstegen, Patrick J Hrdlicka.   

Abstract

The invasion has begun: Invaders are shown to recognize DNA hairpins in cell-free assays and chromosomal DNA during non-denaturing fluorescence in situ hybridization (nd-FISH) experiments. As Invaders are devoid of inherent sequence limitations, many previously inaccessible DNA targets could become accessible to exogenous control with important ramifications for karyotyping, in vivo imaging, and gene regulation.
Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Entities:  

Keywords:  DNA recognition; FISH; fluorescent probes; nucleic acid hybridization; oligonucleotides

Year:  2013        PMID： 24038876      PMCID： PMC3838861          DOI： 10.1002/cbic.201300414

Source DB:  PubMed          Journal:  Chembiochem        ISSN： 1439-4227            Impact factor:   3.164


  43 in total

Review 1.  Targeting DNA secondary structures.

Authors:  R M Wadkins
Journal:  Curr Med Chem       Date:  2000-01       Impact factor: 4.530

2.  Inhibiting transcription of chromosomal DNA with antigene peptide nucleic acids.

Authors:  Bethany A Janowski; Kunihiro Kaihatsu; Kenneth E Huffman; Jacob C Schwartz; Rosalyn Ram; Daniel Hardy; Carole R Mendelson; David R Corey
Journal:  Nat Chem Biol       Date:  2005-07-31       Impact factor: 15.040

3.  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 4.  Triplex technology in studies of DNA damage, DNA repair, and mutagenesis.

Authors:  Anirban Mukherjee; Karen M Vasquez
Journal:  Biochimie       Date:  2011-04-11       Impact factor: 4.079

5.  COMBinatorial Oligo FISH: directed labeling of specific genome domains in differentially fixed cell material and live cells.

Authors:  Eberhard Schmitt; Jutta Schwarz-Finsterle; Stefan Stein; Carmen Boxler; Patrick Müller; Andriy Mokhir; Roland Krämer; Christoph Cremer; Michael Hausmann
Journal:  Methods Mol Biol       Date:  2010

6.  Strand invasion of mixed-sequence, double-helical B-DNA by γ-peptide nucleic acids containing G-clamp nucleobases under physiological conditions.

Authors:  Srinivas Rapireddy; Raman Bahal; Danith H Ly
Journal:  Biochemistry       Date:  2011-04-25       Impact factor: 3.162

7.  Oligonucleotides containing 2-aminoadenine and 2-thiothymine act as selectively binding complementary agents.

Authors:  I V Kutyavin; R L Rhinehart; E A Lukhtanov; V V Gorn; R B Meyer; H B Gamper
Journal:  Biochemistry       Date:  1996-08-27       Impact factor: 3.162

8.  Pyrene aromatic arrays on RNA duplexes as helical templates.

Authors:  Mitsunobu Nakamura; Yukinori Shimomura; Yukinori Ohtoshi; Kazuhiro Sasa; Haruhisa Hayashi; Hidehiko Nakano; Kazushige Yamana
Journal:  Org Biomol Chem       Date:  2007-05-18       Impact factor: 3.876

9.  Four base recognition by triplex-forming oligonucleotides at physiological pH.

Authors:  David A Rusling; Vicki E C Powers; Rohan T Ranasinghe; Yang Wang; Sadie D Osborne; Tom Brown; Keith R Fox
Journal:  Nucleic Acids Res       Date:  2005-05-23       Impact factor: 16.971

10.  Chiral introduction of positive charges to PNA for double-duplex invasion to versatile sequences.

Authors:  Takumi Ishizuka; Junya Yoshida; Yoji Yamamoto; Jun Sumaoka; Tullia Tedeschi; Roberto Corradini; Stefano Sforza; Makoto Komiyama
Journal:  Nucleic Acids Res       Date:  2008-01-18       Impact factor: 16.971
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  10 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 double-stranded DNA using energetically activated duplexes with interstrand zippers of 1-, 2- or 4-pyrenyl-functionalized O2'-alkylated RNA monomers.

Authors:  Saswata Karmakar; Andreas S Madsen; Dale C Guenther; Bradley C Gibbons; Patrick J Hrdlicka
Journal:  Org Biomol Chem       Date:  2014-08-21       Impact factor: 3.876

3.  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

4.  Sandwich assay for mixed-sequence recognition of double-stranded DNA: invader-based detection of targets specific to foodborne pathogens.

Authors:  Benjamin Denn; Saswata Karmakar; Dale C Guenther; Patrick J Hrdlicka
Journal:  Chem Commun (Camb)       Date:  2013-10-28       Impact factor: 6.222

5.  Synthesis and characterization of oligodeoxyribonucleotides modified with 2'-amino-α-L-LNA adenine monomers: high-affinity targeting of single-stranded DNA.

Authors:  Nicolai K Andersen; Brooke A Anderson; Jesper Wengel; Patrick J Hrdlicka
Journal:  J Org Chem       Date:  2013-12-11       Impact factor: 4.354

6.  Next-generation bis-locked nucleic acids with stacking linker and 2'-glycylamino-LNA show enhanced DNA invasion into supercoiled duplexes.

Authors:  Sylvain Geny; Pedro M D Moreno; Tomasz Krzywkowski; Olof Gissberg; Nicolai K Andersen; Abdirisaq J Isse; Amro M El-Madani; Chenguang Lou; Y Vladimir Pabon; Brooke A Anderson; Eman M Zaghloul; Rula Zain; Patrick J Hrdlicka; Per T Jørgensen; Mats Nilsson; Karin E Lundin; Erik B Pedersen; Jesper Wengel; C I Edvard Smith
Journal:  Nucleic Acids Res       Date:  2016-02-08       Impact factor: 16.971

Review 7.  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

8.  Invader probes: Harnessing the energy of intercalation to facilitate recognition of chromosomal DNA for diagnostic applications.

Authors:  Dale C Guenther; Grace H Anderson; Saswata Karmakar; Brooke A Anderson; Bradley A Didion; Wei Guo; John P Verstegen; Patrick J Hrdlicka
Journal:  Chem Sci       Date:  2015-08-01       Impact factor: 9.825

9.  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

10.  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
  10 in total

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