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Makoto Komiyama
Research Center for Advanced Science and Technology, University of Tokyo, Japan

Faculty Member: Chemical Biology > Biomimetic Chemistry [ since 29 June 2001 ]
[ Evaluations ]
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Evaluations

Solution Structure of a Unique G-Quadruplex Scaffold Adopted by a Guanosine-Rich Human Intronic Sequence.
Kuryavyi V, Patel DJ
Structure 2010 Jan 13 18(1):73-82 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Yan Xu and Makoto Komiyama
Evaluated 16 Feb 2010

In Vitro Recombination Mediated by G-Quadruplex.
Boán F, Gómez-Márquez J
Chembiochem 2009 Dec 14 [abstract on PubMed] [related articles] [full text]
Selected by | Yan Xu and Makoto Komiyama
Evaluated 12 Jan 2010

Giardia Telomeric Sequence d(TAGGG)(4) Forms Two Intramolecular G-Quadruplexes in K(+) Solution: Effect of Loop Length and Sequence on the Folding Topology.
Hu L, Lim KW, Bouaziz S, Phan AT
J Am Chem Soc 2009 Oct 29 [abstract on PubMed] [related articles] [full text]
Selected by | Yan Xu and Makoto Komiyama
Evaluated 6 Nov 2009

Molecular crowding creates an essential environment for the formation of stable G-quadruplexes in long double-stranded DNA.
Zheng KW, Chen Z, Hao YH, Tan Z
Nucleic Acids Res 2009 Oct 25 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Yan Xu and Makoto Komiyama
Evaluated 4 Nov 2009

Formation of a unique end-to-end stacked pair of G-quadruplexes in the hTERT core promoter with implications for inhibition of telomerase by G-quadruplex-interactive ligands.
Palumbo SL, Ebbinghaus SW, Hurley LH
J Am Chem Soc 2009 Aug 12 131(31):10878-91 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Yan Xu and Makoto Komiyama
Evaluated 16 Sep 2009

An alternative DNA structure is necessary for pilin antigenic variation in Neisseria gonorrhoeae.
Cahoon LA, Seifert HS
Science 2009 Aug 7 325(5941):764-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Yan Xu and Makoto Komiyama
Evaluated 11 Aug 2009

G-quadruplex nucleic acids as therapeutic targets.
Balasubramanian S, Neidle S
Curr Opin Chem Biol 2009 Jun 8 [abstract on PubMed] [related articles] [full text]
Selected by | Yan Xu and Makoto Komiyama
Evaluated 15 Jun 2009

The structures of quadruplex nucleic acids and their drug complexes.
Neidle S
Curr Opin Struct Biol 2009 May 30 [abstract on PubMed] [related articles] [full text]
Selected by | Yan Xu and Makoto Komiyama
Evaluated 4 Jun 2009

Direct detection of abortive RNA transcripts in vivo.
Goldman SR, Ebright RH, Nickels BE
Science 2009 May 15 324(5929):927-8 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Yan Xu and Makoto Komiyama / Katsu Murakami
Evaluated 19 May 2009

Metabolic Labeling of Sialic Acids in Living Animals with Alkynyl Sugars.
Chang PV, Chen X, …, Bertozzi CR, Wu P
Angew Chem Int Ed Engl 2009 Apr 22 [abstract on PubMed] [related articles] [full text]
Selected by | Yan Xu and Makoto Komiyama
Evaluated 1 May 2009

Local DNA topography correlates with functional noncoding regions of the human genome.
Parker SC, Hansen L, …, Tullius TD, Margulies EH
Science 2009 Apr 17 324(5925):389-92 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Yan Xu and Makoto Komiyama / Megana Prasad and Andrew S McCallion / Jim Maher
Evaluated 31 Mar 2009

Self-sustained replication of an RNA enzyme.
Lincoln TA, Joyce GF
Science 2009 Feb 27 323(5918):1229-32 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Robert Batey / Yan Xu and Makoto Komiyama / Andy Maule / Russ Hille
Evaluated 11 Mar 2009

Spliceosomal cleavage generates the 3' end of telomerase RNA.
Box JA, Bunch JT, Tang W, Baumann P
Nature 2008 Dec 18 456(7224):910-4 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Yan Xu and Makoto Komiyama / Nick Rhind
Evaluated 2 Jan 2009

RNA toxicity is a component of ataxin-3 degeneration in Drosophila.
Li LB, Yu Z, Teng X, Bonini NM
Nature 2008 Jun 19 453(7198):1107-11 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Yan Xu and Makoto Komiyama
Evaluated 8 Dec 2008

Telomerase recruitment by the telomere end binding protein-beta facilitates G-quadruplex DNA unfolding in ciliates.
Paeschke K, Juranek S, …, Rhodes D, Lipps HJ
Nat Struct Mol Biol 2008 Jun 15(6):598-604 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Yan Xu and Makoto Komiyama
Evaluated 27 Nov 2008

G-Quadruplex formation interferes with P1 helix formation in the RNA component of telomerase hTERC.
Gros J, Guédin A, Mergny JL, Lacroix L
Chembiochem 2008 Sep 1 9(13):2075-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Yan Xu and Makoto Komiyama
Evaluated 20 Oct 2008

Effect of O6-methylguanine on the stability of G-quadruplex DNA.
Mekmaysy CS, Petraccone L, …, Trent JO, Chaires JB
J Am Chem Soc 2008 May 28 130(21):6710-1 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Yan Xu and Makoto Komiyama
Evaluated 15 Jul 2008

Developmentally regulated transcription of mammalian telomeres by DNA-dependent RNA polymerase II.
Schoeftner S, Blasco MA
Nat Cell Biol 2008 Feb 10(2):228-36 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Makoto Komiyama
Evaluated 29 Apr 2008

An RNA G-quadruplex in the 5' UTR of the NRAS proto-oncogene modulates translation.
Kumari S, Bugaut A, Huppert JL, Balasubramanian S
Nat Chem Biol 2007 Apr 3(4):218-21 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Ben Davis / Eric Westhof / Sabine Müller / Makoto Komiyama
Evaluated 29 Apr 2008

Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends.
Azzalin CM, Reichenbach P, …, Giulotto E, Lingner J
Science 2007 Nov 2 318(5851):798-801 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Makoto Komiyama
Evaluated 18 Mar 2008

Positioning scission of single DNA molecules with nonspecific endonuclease based on nanomanipulation.
Li B, Zhang Y, …, Li MQ, Hu J
J Am Chem Soc 2007 May 30 129(21):6668-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Makoto Komiyama
Evaluated 31 Aug 2007

The new models of the human telomere d[AGGG(TTAGGG)3] in K+ solution.
Xu Y, Noguchi Y, Sugiyama H
Bioorg Med Chem 2006 Aug 15 14(16):5584-91 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Makoto Komiyama
Evaluated 23 Apr 2007

Cationic oligonucleotide-peptide conjugates with aggregating properties enter efficiently into cells while maintaining hybridization properties and enzymatic recognition.
Fraley AW, Pons B, …, Behr JP, Zuber G
J Am Chem Soc 2006 Aug 23 128(33):10763-71 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Makoto Komiyama
Evaluated 6 Sep 2006

Sequencing genomes from single cells by polymerase cloning.
Zhang K, Martiny AC, …, Chisholm SW, Church GM
Nat Biotechnol 2006 Jun 24(6):680-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Makoto Komiyama
Evaluated 20 Jun 2006

A mismatch-selective bifunctional rhodium-Oregon Green conjugate: a fluorescent probe for mismatched DNA.
Zeglis BM, Barton JK
J Am Chem Soc 2006 May 3 128(17):5654-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Makoto Komiyama
Evaluated 12 Jun 2006

Template-directed DNA photoligation in rapid and selective detection of RNA point mutations.
Yoshimura Y, Noguchi Y, Sato H, Fujimoto K
Chembiochem 2006 Apr 7(4):598-601 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Makoto Komiyama
Evaluated 19 Apr 2006

The incorporation of a photoisomerizable amino acid into proteins in E. coli.
Bose M, Groff D, …, Brustad E, Schultz PG
J Am Chem Soc 2006 Jan 18 128(2):388-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Makoto Komiyama
Evaluated 18 Jan 2006

Cell-free cloning using phi29 DNA polymerase.
Hutchison CA, Smith HO, Pfannkoch C, Venter JC
Proc Natl Acad Sci U S A 2005 Nov 29 102(48):17332-6 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Makoto Komiyama
Evaluated 5 Dec 2005

Methyltransferase-directed DNA strand scission.
Comstock LR, Rajski SR
J Am Chem Soc 2005 Oct 19 127(41):14136-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Makoto Komiyama
Evaluated 7 Nov 2005

DNA sequence-enabled reassembly of the green fluorescent protein.
Stains CI, Porter JR, …, Segal DJ, Ghosh I
J Am Chem Soc 2005 Aug 10 127(31):10782-3 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Makoto Komiyama / Larry McLaughlin
Evaluated 10 Aug 2005

Highly efficient endogenous human gene correction using designed zinc-finger nucleases.
Urnov FD, Miller JC, …, Gregory PD, Holmes MC
Nature 2005 Jun 2 435(7042):646-51 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard / John Cambier / Makoto Komiyama / Daniel Reines / Charles Coutelle
Evaluated 10 Jun 2005

Helix-forming properties of size-expanded DNA, an alternative four-base genetic form.
Liu H, Gao J, Kool ET
J Am Chem Soc 2005 Feb 9 127(5):1396-402 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Makoto Komiyama
Evaluated 2 Mar 2005

Site-selective RNA cleavage by DNA bearing a base pair-mimic nucleoside.
Nakano S, Uotani Y, …, Fujii M, Sugimoto N
J Am Chem Soc 2005 Jan 19 127(2):518-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Makoto Komiyama
Evaluated 20 Jan 2005

Sequence-selective and hydrolytic cleavage of DNA by zinc finger mutants.
Nomura A, Sugiura Y
J Am Chem Soc 2004 Dec 1 126(47):15374-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Makoto Komiyama
Evaluated 2 Dec 2004

The site-specific incorporation of p-iodo-L-phenylalanine into proteins for structure determination.
Xie J, Wang L, …, Spraggon G, Schultz PG
Nat Biotechnol 2004 Oct 22(10):1297-301 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Fred Dyda / David Waugh / Makoto Komiyama / Mark Nelson
Evaluated 25 Nov 2004

5'-end SAGE for the analysis of transcriptional start sites.
Hashimoto S, Suzuki Y, …, Sugano S, Matsushima K
Nat Biotechnol 2004 Sep 22(9):1146-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | John McPherson / Makoto Komiyama
Evaluated 17 Sep 2004

Circle-to-circle amplification for precise and sensitive DNA analysis.
Dahl F, Banér J, …, Landegren U, Nilsson M
Proc Natl Acad Sci U S A 2004 Mar 15 [abstract on PubMed] [related articles]
Selected by | Makoto Komiyama
Evaluated 2 Apr 2004

Sequence selective hydrolysis of linear DNA using conjugates of Zr(IV) complexes and peptide nucleic acids.
Zelder FH, Mokhir AA, Krämer R
Inorg Chem 2003 Dec 29 42(26):8618-20 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Makoto Komiyama
Evaluated 23 Feb 2004

LNAzymes: incorporation of LNA-type monomers into DNAzymes markedly increases RNA cleavage.
Vester B, Lundberg LB, …, Douthwaite S, Wengel J
J Am Chem Soc 2002 Nov 20 124(46):13682-3 [abstract on PubMed] [related articles] [order article]
Selected by | Makoto Komiyama
Evaluated 23 Jan 2003

A continuous kinetic assay for RNA-cleaving deoxyribozymes, exploiting ethidium bromide as an extrinsic fluorescent probe.
Ferrari D, Peracchi A
Nucleic Acids Res 2002 Oct 15 30(20):e112 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Makoto Komiyama
Evaluated 2 Jan 2003

A monomeric red fluorescent protein.
Campbell RE, Tour O, …, Zacharias DA, Tsien RY
Proc Natl Acad Sci U S A 2002 Jun 11 99(12):7877-82 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Ed Manser / Suresh Subramani / Atsushi Miyawaki / Makoto Komiyama
Evaluated 9 Oct 2002

Amplification of screening sensitivity through selective destruction: theory and screening of a library of carbonic anhydrase inhibitors.
Cheeseman JD, Corbett AD, …, Gleason JL, Kazlauskas RJ
J Am Chem Soc 2002 May 22 124(20):5692-701 [abstract on PubMed] [related articles] [order article]
Selected by | Morten Meldal / Makoto Komiyama / Dennis Hall / Anthony Czarnik
Evaluated 25 Jun 2002

Directed evolution of novel polymerase activities: mutation of a DNA polymerase into an efficient RNA polymerase.
Xia G, Chen L, …, Schultz PG, Romesberg FE
Proc Natl Acad Sci U S A 2002 May 14 99(10):6597-602 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Makoto Komiyama / Niles Lehman
Evaluated 31 May 2002

Characterization of an RNA active site: interactions between a Diels-Alderase ribozyme and its substrates and products.
Stuhlmann F, Jäschke A
J Am Chem Soc 2002 Apr 3 124(13):3238-44 [abstract on PubMed] [related articles] [order article]
Selected by | Makoto Komiyama
Evaluated 13 May 2002

Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules.
Han M, Gao X, Su JZ, Nie S
Nat Biotechnol 2001 Jul 19(7):631-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Makoto Komiyama
Evaluated 19 Apr 2002

Significantly higher activity of a cytoplasmic hammerhead ribozyme than a corresponding nuclear counterpart: engineered tRNAs with an extended 3' end can be exported efficiently and specifically to the cytoplasm in mammalian cells.
Kuwabara T, Warashina M, …, Nakayama K, Taira K
Nucleic Acids Res 2001 Jul 1 29(13):2780-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Makoto Komiyama
Evaluated 7 Jan 2002

Single-molecule observation of protein-protein interactions in the chaperonin system.
Taguchi H, Ueno T, …, Yoshida M, Funatsu T
Nat Biotechnol 2001 Sep 19(9):861-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | W. E. Moerner / Makoto Komiyama / Kunihiro Kuwajima
Evaluated 19 Oct 2001

Activation of human gamma-globin gene expression via triplex-forming oligonucleotide (TFO)-directed mutations in the gamma-globin gene 5' flanking region.
Xu XS, Glazer PM, Wang G
Gene 2000 Jan 25 242(1-2):219-28 [abstract on PubMed] [related articles] [order article]
Selected by | Makoto Komiyama
Evaluated 19 Oct 2001

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