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Niles Lehman
Department of Chemistry, Portland State University, Portland, United States of America

Faculty Member: CHEMICAL BIOLOGY > Directed molecular evolution [ since 4 July 2001 ]
[ Sponsorship ] [ Biography ] [ Homepage ] [ Evaluations ]
Sponsorship

Niles Lehman sponsors free access to F1000 for Universidad Simon Bolivar, Baruta, Venezuela. Supporting F1000's initiative to make itself available to scientists in all countries, including free access to developing countries (more details).

Biography

B.S. Chemistry, University of California 1984
M.A. Biochemistry, University of California, 1986
Ph.D. Biology, University of California, Los Angeles, 1990

Home page

http://chem.pdx.edu/

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Evaluations

From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal.
Smit S, Rother K, Heringa J, Knight R
RNA 2008 Mar 14(3):410-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman with Aaron S. Burton
Evaluated 24 Jun 2008

Degeneracy of the genetic code and stability of the base pair at the second position of the anticodon.
Lehmann J, Libchaber A
RNA 2008 Jul 14(7):1264-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 24 Jun 2008

Computational identification of obligatorily autocatalytic replicators embedded in metabolic networks.
Kun A, Papp B, Szathmáry E
Genome Biol 2008 Mar 10 9(3):R51 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 28 Apr 2008

A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism.
Regulski EE, Moy RH, …, Ruzzo WL, Breaker RR
Mol Microbiol 2008 Mar 19 0 [abstract on PubMed] [related articles] [full text]
Selected by | Niles Lehman
Evaluated 16 Apr 2008

Molecular modelling of the GIR1 branching ribozyme gives new insight into evolution of structurally related ribozymes.
Beckert B, Nielsen H, …, Westhof E, Masquida B
EMBO J 2008 Feb 20 27(4):667-78 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 25 Feb 2008

Messenger RNA-Programmed Incorporation of Multiple N-Methyl-Amino Acids into Linear and Cyclic Peptides.
Kawakami T, Murakami H, Suga H
Chem Biol 2008 Jan 15(1):32-42 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 12 Feb 2008

Riboswitch Control of Gene Expression in Plants by Splicing and Alternative 3' End Processing of mRNAs.
Wachter A, Tunc-Ozdemir M, …, Shintani DK, Breaker RR
Plant Cell 2007 Nov 19(11):3437-50 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman / Andrea Barta
Evaluated 19 Dec 2007

Ty1 reverse transcriptase does not read through the proposed 2',5'-branched retrotransposition intermediate in vitro.
Pratico ED, Silverman SK
RNA 2007 Sep 13(9):1528-36 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 9 Nov 2007

A novel lantibiotic acting on bacterial cell wall synthesis produced by the uncommon actinomycete Planomonospora sp.
Castiglione F, Cavaletti L, …, Marinelli F, Selva E
Biochemistry 2007 May 22 46(20):5884-95 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 21 Sep 2007

Enzymatic incorporation of a third nucleobase pair.
Yang Z, Sismour AM, …, Puskar NL, Benner SA
Nucleic Acids Res 2007 35(13):4238-49 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 29 Aug 2007

A recoding element that stimulates decoding of UGA codons by Sec tRNA[Ser]Sec.
Howard MT, Moyle MW, …, Carlson BA, Anderson CB
RNA 2007 Jun 13(6):912-20 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 3 Jul 2007

A single nucleotide linked to a switch in metal ion reactivity preference in the HDV ribozymes.
Perrotta AT, Been MD
Biochemistry 2007 May 1 46(17):5124-30 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 2 May 2007

Charge density of divalent metal cations determines RNA stability.
Koculi E, Hyeon C, Thirumalai D, Woodson SA
J Am Chem Soc 2007 Mar 7 129(9):2676-82 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 15 Mar 2007

An asymmetric underlying rule in the assignment of codons: possible clue to a quick early evolution of the genetic code via successive binary choices.
Delarue M
RNA 2007 Feb 13(2):161-9 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman / Eric Westhof
Evaluated 13 Feb 2007

A natural genetic code expansion cassette enables transmissible biosynthesis and genetic encoding of pyrrolysine.
Longstaff DG, Larue RC, …, Green-Church KB, Krzycki JA
Proc Natl Acad Sci U S A 2007 Jan 16 104(3):1021-6 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Michael Gelb / Niles Lehman
Evaluated 30 Jan 2007

Self-splicing of a group I intron reveals partitioning of native and misfolded RNA populations in yeast.
Jackson SA, Koduvayur S, Woodson SA
RNA 2006 Dec 12(12):2149-59 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 14 Dec 2006

Examination of the structural and functional versatility of glmS ribozymes by using in vitro selection.
Link KH, Guo L, Breaker RR
Nucleic Acids Res 2006 34(17):4968-75 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 3 Nov 2006

Extraordinary rates of transition metal ion-mediated ribozyme catalysis.
Roychowdhury-Saha M, Burke DH
RNA 2006 Oct 12(10):1846-52 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 16 Oct 2006

Folding of the adenine riboswitch.
Lemay JF, Penedo JC, …, Lilley DM, Lafontaine DA
Chem Biol 2006 Aug 13(8):857-68 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 14 Sep 2006

The P4 metal binding site in RNase P RNA affects active site metal affinity through substrate positioning.
Christian EL, Smith KM, Perera N, Harris ME
RNA 2006 Aug 12(8):1463-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 10 Aug 2006

Aptamers selected for higher-affinity binding are not more specific for the target ligand.
Carothers JM, Oestreich SC, Szostak JW
J Am Chem Soc 2006 Jun 21 128(24):7929-37 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Scott K. Silverman / Milan Stojanovic / Niles Lehman
Evaluated 19 Jul 2006

Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions.
Roth A, Nahvi A, …, Jona I, Breaker RR
RNA 2006 Apr 12(4):607-19 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman / Kathleen Hall / David M.J. Lilley
Evaluated 11 Apr 2006

Antigenomic delta ribozyme variants with mutations in the catalytic core obtained by the in vitro selection method.
¿egiewicz M, Wich¿acz A, Brzezicha B, Ciesio¿ka J
Nucleic Acids Res 2006 34(4):1270-80 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 11 Apr 2006

Evolution of programmed DNA rearrangements in a scrambled gene.
Wong LC, Landweber LF
Mol Biol Evol 2006 Apr 23(4):756-63 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 23 Feb 2006

The RNA-cleaving bipartite DNAzyme is a distinctive metalloenzyme.
Feldman AR, Leung EK, Bennet AJ, Sen D
Chembiochem 2006 Jan 7(1):98-105 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 30 Jan 2006

New catalytic structures from an existing ribozyme.
Curtis EA, Bartel DP
Nat Struct Mol Biol 2005 Nov 12(11):994-1000 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 31 Oct 2005

A ribozyme for the aldol reaction.
Fusz S, Eisenführ A, …, Heckel A, Famulok M
Chem Biol 2005 Aug 12(8):941-50 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman / Michael Yarus / Andres Jaschke
Evaluated 3 Oct 2005

tRNA creation by hairpin duplication.
Widmann J, Di Giulio M, Yarus M, Knight R
J Mol Evol 2005 Oct 61(4):524-30 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 30 Sep 2005

New ligase-derived RNA polymerase ribozymes.
Lawrence MS, Bartel DP
RNA 2005 Aug 11(8):1173-80 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 10 Aug 2005

RNA flexibility in the dimerization domain of a gamma retrovirus.
Badorrek CS, Weeks KM
Nat Chem Biol 2005 Jul 1(2):104-11 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 23 Jun 2005

The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch.
Wickiser JK, Winkler WC, Breaker RR, Crothers DM
Mol Cell 2005 Apr 1 18(1):49-60 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 16 May 2005

A more complex isoleucine aptamer with a cognate triplet.
Legiewicz M, Yarus M
J Biol Chem 2005 May 20 280(20):19815-22 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 11 Apr 2005

Newly sequenced eRF1s from ciliates: the diversity of stop codon usage and the molecular surfaces that are important for stop codon interactions.
Kim OT, Yura K, Go N, Harumoto T
Gene 2005 Feb 14 346:277-86 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 7 Mar 2005

Fast formation of the P3-P7 pseudoknot: a strategy for efficient folding of the catalytically active ribozyme.
Zhang L, Xiao M, Lu C, Zhang Y
RNA 2005 Jan 11(1):59-69 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 10 Feb 2005

The robustness of naturally and artificially selected nucleic acid secondary structures.
Meyers LA, Lee JF, Cowperthwaite M, Ellington AD
J Mol Evol 2004 Jun 58(6):681-91 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 4 Nov 2004

Folding of the Tetrahymena ribozyme by polyamines: importance of counterion valence and size.
Koculi E, Lee NK, Thirumalai D, Woodson SA
J Mol Biol 2004 Jul 30 341(1):27-36 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 4 Oct 2004

Tracing sequence diversity change of RNA-cleaving deoxyribozymes under increasing selection pressure during in vitro selection.
Schlosser K, Li Y
Biochemistry 2004 Aug 3 43(30):9695-707 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Scott K. Silverman / Niles Lehman
Evaluated 17 Sep 2004

Importance in catalysis of a magnesium ion with very low affinity for a hammerhead ribozyme.
Inoue A, Takagi Y, Taira K
Nucleic Acids Res 2004 32(14):4217-23 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 13 Sep 2004

Anticodon and wobble evolution.
Tong KL, Wong JT
Gene 2004 May 26 333:169-77 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 27 Jul 2004

Artificially ambiguous genetic code confers growth yield advantage.
Pezo V, Metzgar D, …, Schimmel P, De Crécy-Lagard V
Proc Natl Acad Sci U S A 2004 Jun 8 101(23):8593-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 18 Jun 2004

Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme.
Cruz RP, Withers JB, Li Y
Chem Biol 2004 Jan 11(1):57-67 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Scott K. Silverman / Niles Lehman
Evaluated 10 May 2004

Ligating DNA with DNA.
Sreedhara A, Li Y, Breaker RR
J Am Chem Soc 2004 Mar 24 126(11):3454-60 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 4 May 2004

Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes.
Nahvi A, Barrick JE, Breaker RR
Nucleic Acids Res 2004 32(1):143-50 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 27 Feb 2004

A deoxyribozyme that harnesses light to repair thymine dimers in DNA.
Chinnapen DJ, Sen D
Proc Natl Acad Sci U S A 2004 Jan 6 101(1):65-9 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 16 Jan 2004

Continuous in vitro evolution of ribozymes that operate under conditions of extreme pH.
Kühne H, Joyce GF
J Mol Evol 2003 Sep 57(3):292-8 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 16 Jan 2004

Selection of the simplest RNA that binds isoleucine.
Lozupone C, Changayil S, Majerfeld I, Yarus M
RNA 2003 Nov 9(11):1315-22 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman / Scott K. Silverman
Evaluated 7 Nov 2003

Active self-splicing group I introns in 23S rRNA genes of hyperthermophilic bacteria, derived from introns in eukaryotic organelles.
Nesbø CL, Doolittle WF
Proc Natl Acad Sci U S A 2003 Sep 16 100(19):10806-11 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Eugene Koonin / Niles Lehman
Evaluated 17 Oct 2003

Processivity of ribozyme-catalyzed RNA polymerization.
Lawrence MS, Bartel DP
Biochemistry 2003 Jul 29 42(29):8748-55 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 12 Aug 2003

Assemblage of signaling DNA enzymes with intriguing metal-ion specificities and pH dependences.
Liu Z, Mei SH, Brennan JD, Li Y
J Am Chem Soc 2003 Jun 25 125(25):7539-45 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 1 Aug 2003

Substrate specificity and reaction kinetics of an X-motif ribozyme.
Lazarev D, Puskarz I, Breaker RR
RNA 2003 Jun 9(6):688-97 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 18 Jun 2003

Analyzing partially randomized nucleic acid pools: straight dope on doping.
Knight R, Yarus M
Nucleic Acids Res 2003 Mar 15 31(6):e30 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 9 Apr 2003

Finding specific RNA motifs: function in a zeptomole world?
Knight R, Yarus M
RNA 2003 Feb 9(2):218-30 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 26 Feb 2003

Directed evolution of a genetic circuit.
Yokobayashi Y, Weiss R, Arnold FH
Proc Natl Acad Sci U S A 2002 Dec 24 99(26):16587-91 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Deirdre Meldrum / Niles Lehman
Evaluated 4 Feb 2003

Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression.
Winkler W, Nahvi A, Breaker RR
Nature 2002 Oct 31 419(6910):952-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | John Burke / Richard Maraia / Richard Gourse / Andrew Ellington / Niles Lehman / Gabriele Varani
Evaluated 9 Dec 2002

Evolution of Tetrahymena ribozyme mutants with increased structural stability.
Guo F, Cech TR
Nat Struct Biol 2002 Nov 9(11):855-61 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 24 Oct 2002

Designed arginine-rich RNA-binding peptides with picomolar affinity.
Austin RJ, Xia T, …, Takahashi TT, Roberts RW
J Am Chem Soc 2002 Sep 18 124(37):10966-7 [abstract on PubMed] [related articles] [order article]
Selected by | Niles Lehman
Evaluated 1 Oct 2002

Mutational analysis of HIV-1 long terminal repeats to explore the relative contribution of reverse transcriptase and RNA polymerase II to viral mutagenesis.
O'Neil PK, Sun G, …, Dougherty JP, Preston BD
J Biol Chem 2002 Oct 11 277(41):38053-61 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 27 Aug 2002

Metal ion requirements for structure and catalysis of an RNA ligase ribozyme.
Glasner ME, Bergman NH, Bartel DP
Biochemistry 2002 Jun 25 41(25):8103-12 [abstract on PubMed] [related articles] [order article]
Selected by | Niles Lehman
Evaluated 22 Jul 2002

Improving metal ion specificity during in vitro selection of catalytic DNA.
Bruesehoff PJ, Li J, Augustine AJ, Lu Y
Comb Chem High Throughput Screen 2002 Jun 5(4):327-35 [abstract on PubMed] [related articles] [order article]
Selected by | Niles Lehman
Evaluated 8 Jul 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 6 Jun 2002

Analysis of shuffled gene libraries.
Joern JM, Meinhold P, Arnold FH
J Mol Biol 2002 Feb 22 316(3):643-56 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Brent Iverson / Niles Lehman
Evaluated 10 May 2002

Rapid compaction during RNA folding.
Russell R, Millett IS, …, Herschlag D, Pollack L
Proc Natl Acad Sci U S A 2002 Apr 2 99(7):4266-71 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Scott K. Silverman / Niles Lehman
Evaluated 17 Apr 2002

Identification of an active site ligand for a group I ribozyme catalytic metal ion.
Szewczak AA, Kosek AB, Piccirilli JA, Strobel SA
Biochemistry 2002 Feb 26 41(8):2516-25 [abstract on PubMed] [related articles] [order article]
Selected by | Thorsten Dieckmann / Niles Lehman
Evaluated 17 Apr 2002

In vitro selection of a deoxyribozyme that can utilize multiple substrates.
Levy M, Ellington AD
J Mol Evol 2002 Feb 54(2):180-90 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Niles Lehman
Evaluated 25 Feb 2002

Efficient bacterial transcription of DNA nanocircle vectors with optimized single-stranded promoters.
Ohmichi T, Maki A, Kool ET
Proc Natl Acad Sci U S A 2002 Jan 8 99(1):54-9 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Niles Lehman
Evaluated 29 Jan 2002