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1

Crystal structures of the Mango-II RNA aptamer reveal heterogeneous fluorophore binding and guide engineering of variants with improved selectivity and brightness.

Trachman, Robert, Abdolahzadeh, Amir, Andreoni, Alessio, Cojocaru, Razvan, Knutson, Jay R, Ryckelynck, Michaël, Unrau, Peter John, Ferré-D’Amaré, Adrian

Journal:

Year:

2018

Language:

english

File:

PDF, 722 KB

english, 2018

2

Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch

Baird, Nathan J, Ferré-D'Amaré, Adrian R, Kulshina, Nadia

Journal:

Nature Structural and Molecular Biology

Year:

2009

Language:

english

File:

PDF, 1.01 MB

english, 2009

3

RNA-modifying enzymes

Adrian R Ferré-D’Amaré

Journal:

Current Opinion in Structural Biology

Year:

2003

Language:

english

File:

PDF, 389 KB

english, 2003

4

Long-Range Interactions in Riboswitch Control of Gene Expression

Jones, Christopher P., Ferré-D'Amaré, Adrian R.

Journal:

Annual Review of Biophysics

Year:

2017

Language:

english

File:

PDF, 2.78 MB

english, 2017

5

Co-crystal structure of the i Mango-III fluorescent RNA aptamer using an X-ray free-electron laser

Trachman, Robert J., Stagno, Jason R., Conrad, Chelsie, Jones, Christopher P., Fischer, Pontus, Meents, Alke, Wang, Yun-Xing, Ferré-D'Amaré, Adrian R.

Journal:

Acta Crystallographica Section F Structural Biology Communications

Year:

2019

Language:

english

File:

PDF, 620 KB

english, 2019

6

Tracking RNA with light: selection, structure, and design of fluorescence turn-on RNA aptamers

Trachman, Robert J., Ferré-D'Amaré, Adrian R.

Journal:

Quarterly Reviews of Biophysics

Year:

2019

File:

PDF, 1001 KB

2019

7

The hairpin ribozyme

Adrian R. Ferré-D'Amaré

Journal:

Year:

2004

Language:

english

File:

PDF, 314 KB

english, 2004

8

Pseudouridine Synthases

Tomoko Hamma, Adrian R. Ferré-D'Amaré

Journal:

Chemistry & Biology

Year:

2006

Language:

english

File:

PDF, 1.28 MB

english, 2006

9

Structural Basis for Specific, High-Affinity Tetracycline Binding by an In Vitro Evolved Aptamer and Artificial Riboswitch

Hong Xiao, Thomas E. Edwards, Adrian R. Ferré-D'Amaré

Journal:

Chemistry & Biology

Year:

2008

Language:

english

File:

PDF, 1.04 MB

english, 2008

10

Probing the solution structure of the DNA-binding protein Max by a combination of proteolysis and mass spectrometry

Steven L. Cohen, Brian T. Chait, Adrian R. Ferré-D'Amaré, Stephen K. Burley

Journal:

Protein Science

Year:

1995

Language:

english

File:

PDF, 4.46 MB

english, 1995

11

Mitfmi-enu122is a missense mutation in the HLH dimerization domain

Eiríkur Steingrímsson, Jack Favor, Adrian F. Ferré-D’Amaré, Neal G. Copeland, Nancy A. Jenkins

Journal:

Mammalian Genome

Year:

1998

Language:

english

File:

PDF, 1.89 MB

english, 1998

12

10.1038/26912

Doudna, Jennifer A., Ferré-D'Amaré, Adrian R., Zhou, Kaihong

Journal:

Year:

1998

Language:

english

File:

PDF, 680 KB

english, 1998

13

A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor

Basu, Soumitra, P. Rambo, Robert, Strauss-Soukup, Juliane, H.Cate, Jamie, R. Ferré-D´Amaré, Adrian, Strobel, Scott A., Doudna, Jennifer A.

Journal:

Natural Structural Biology

Year:

1998

Language:

english

File:

PDF, 1011 KB

english, 1998

14

10.1038/35071009

Rupert, Peter B., Ferré-D'Amaré, Adrian R.

Journal:

Year:

2001

Language:

english

File:

PDF, 442 KB

english, 2001

15

Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain

Ferré-D'Amaré, Adrian R., Prendergast, George C., Ziff, Edward B., Burley, Stephen K.

Journal:

Year:

1993

File:

PDF, 1.28 MB

1993

16

Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme

Xiao, Hong, Murakami, Hiroshi, Suga, Hiroaki, Ferré-D’Amaré, Adrian R.

Journal:

Year:

2008

Language:

english

File:

PDF, 831 KB

english, 2008

17

Synthetic biology: An RNP switch raises a roadblock

Ferré-D'Amaré, Adrian R

Journal:

Nature Chemical Biology

Year:

2010

Language:

english

File:

PDF, 211 KB

english, 2010

18

Molecular basis of mouse microphthalmia (mi) mutations helps explain their developmental and phenotypic consequences

Steingrímsson, Eiríkur, Moore, Karen J., Lamoreux, M. Lynn, Ferré-D'Amaré, Adrian R., Burley, Stephen K., Sanders Zimring, Debra C., Skow, Loren C., Hodgkinson, Colin A., Arnheiter, Heinz, Copeland, N

Journal:

Nature Genetics

Year:

1994

File:

PDF, 990 KB

1994

19

Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase

Klein, Daniel J, Edwards, Thomas E, Ferré-D'Amaré, Adrian R

Journal:

Nature Structural and Molecular Biology

Year:

2009

Language:

english

File:

PDF, 406 KB

english, 2009

20

How RNA closes a Diel

Pitt, Jason N, Ferré-D'Amaré, Adrian R

Journal:

Nature Structural and Molecular Biology

Year:

2005

Language:

english

File:

PDF, 314 KB

english, 2005

21

The Cbf5–Nop10 complex is a molecular bracket that organizes box H/ACA RNPs

Hamma, Tomoko, Reichow, Steve L, Varani, Gabriele, Ferré-D'Amaré, Adrian R

Journal:

Nature Structural and Molecular Biology

Year:

2005

Language:

english

File:

PDF, 750 KB

english, 2005

22

Precursor complex structure of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA-sequestering peripheral protein domain

Charmaine Hoang, Christopher S. Hamilton, Eugene G.Mueller, Adrian R. Ferré-D'Amaré

Journal:

Protein Science

Year:

2005

Language:

english

File:

PDF, 322 KB

english, 2005

23

Riboswitches: Discovery of Drugs That Target Bacterial Gene-Regulatory RNAs

Deigan, Katherine E., FerrÉ-D’AmarÉ, Adrian R.

Journal:

Accounts of Chemical Research

Year:

2011

Language:

english

File:

PDF, 1.01 MB

english, 2011

24

Riboswitches: small-molecule recognition by gene regulatory RNAs

Thomas E Edwards, Daniel J Klein, Adrian R Ferré-D’Amaré

Journal:

Current Opinion in Structural Biology

Year:

2007

Language:

english

File:

PDF, 1009 KB

english, 2007

25

Structure of Protein L7Ae Bound to a K-Turn Derived from an Archaeal Box H/ACA sRNA at 1.8 Å Resolution

Tomoko Hamma, Adrian R Ferré-D'Amaré

Journal:

Year:

2004

Language:

english

File:

PDF, 656 KB

english, 2004

26

Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive RNA-Small Molecule Recognition

Thomas E. Edwards, Adrian R. Ferré-D'Amaré

Journal:

Year:

2006

Language:

english

File:

PDF, 627 KB

english, 2006

27

Use of dynamic light scattering to assess crystallizability of macromolecules and macromolecular assemblies

Adrian R Ferré-D'Amaré, Stephen K Burley

Journal:

Year:

1994

Language:

english

File:

PDF, 339 KB

english, 1994

28

SRPrises in RNA–protein recognition

Peter B Rupert, Adrian R Ferré-D’Amaré

Journal:

Year:

2000

Language:

english

File:

PDF, 343 KB

english, 2000

29

Co-crystal structure of sterol regulatory element binding protein 1a at 2.3 å resolution

A Parraga, L Bellsolell, AR Ferré-D'Amaré, Stephen K Burley

Journal:

Year:

1998

Language:

english

File:

PDF, 413 KB

english, 1998

30

A general module for RNA crystallization

Adrian R Ferré-D’Amaré, Kaihong Zhou, Jennifer A Doudna

Journal:

Journal of Molecular Biology

Year:

1998

Language:

english

File:

PDF, 417 KB

english, 1998

31

Crystallization and structure determination of a hepatitis delta virus ribozyme: use of the RNA-binding protein U1A as a crystallization module

Adrian R. Ferré-D’Amaré, Jennifer A. Doudna

Journal:

Journal of Molecular Biology

Year:

2000

Language:

english

File:

PDF, 896 KB

english, 2000

32

Requirement of Helix P2.2 and Nucleotide G1 for Positioning the Cleavage Site and Cofactor of the glmS Ribozyme

Daniel J. Klein, Sara R. Wilkinson, Michael D. Been, Adrian R. Ferré-D'Amaré

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 1.63 MB

english, 2007

33

Crystal Structure of Pseudouridine Synthase RluA: Indirect Sequence Readout through Protein-Induced RNA Structure

Charmaine Hoang, Junjun Chen, Caroline A. Vizthum, Jason M. Kandel, Christopher S. Hamilton, Eugene G. Mueller, Adrian R. Ferré-D'Amaré

Journal:

Year:

2006

Language:

english

File:

PDF, 1.76 MB

english, 2006

34

Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs

Adrian R. Ferré-D’Amaré

Journal:

Year:

2010

Language:

english

File:

PDF, 831 KB

english, 2010

35

RNA methods: From sequence to structure and dynamics

Adrian R. Ferré-D’Amaré

Journal:

Year:

2010

Language:

english

File:

PDF, 131 KB

english, 2010

36

Cocrystal Structure of a tRNA Ψ55 Pseudouridine Synthase: Nucleotide Flipping by an RNA-Modifying Enzyme

Charmaine Hoang, Adrian R. Ferré-D'Amaré

Journal:

Year:

2001

Language:

english

File:

PDF, 637 KB

english, 2001

37

Single Molecule Studies of the c-di-GMP Riboswitch

Wood, Sharla, Kulshina, Nadia, Ferre-D'Amare, Adrian, Rueda, David

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 35 KB

english, 2011

38

Glucosamine and Glucosamine-6-phosphate Derivatives: Catalytic Cofactor Analogues for the glmS Ribozyme

Posakony, Jeffrey J., Ferré-D’Amaré, Adrian R.

Journal:

Journal of Organic Chemistry

Year:

2013

Language:

english

File:

PDF, 510 KB

english, 2013

39

Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA

Zhang, Jinwei, Ferré-D’Amaré, Adrian R.

Journal:

Year:

2013

Language:

english

File:

PDF, 4.23 MB

english, 2013

40

Essential Role of an Active-Site Guanine in glmS Ribozyme Catalysis

Klein, Daniel J., Been, Michael D., Ferré-D'Amaré, Adrian R.

Journal:

Journal of the American Chemical Society

Year:

2007

Language:

english

File:

PDF, 123 KB

english, 2007

41

Global analysis of riboswitches by small-angle X-ray scattering and calorimetry

Zhang, Jinwei, Jones, Christopher P., Ferré-D'Amaré, Adrian R.

Journal:

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms

Year:

2014

Language:

english

File:

PDF, 1.05 MB

english, 2014

42

Validating Fragment-Based Drug Discovery for Biological RNAs: Lead Fragments Bind and Remodel the TPP Riboswitch Specifically

Warner, Katherine Deigan, Homan, Philip, Weeks, Kevin M., Smith, Alison G., Abell, Chris, Ferré-D’Amaré, Adrian R.

Journal:

Chemistry & Biology

Year:

2014

Language:

english

File:

PDF, 741 KB

english, 2014

43

New molecular engineering approaches for crystallographic studies of large RNAs

Zhang, Jinwei, Ferré-D’Amaré, Adrian R

Journal:

Current Opinion in Structural Biology

Year:

2014

Language:

english

File:

PDF, 1.41 MB

english, 2014

44

Rapid Construction of Empirical RNA Fitness Landscapes

Pitt, J. N., Ferre-D'Amare, A. R.

Journal:

Year:

2010

Language:

english

File:

PDF, 2.48 MB

english, 2010

45

Direct Evaluation of tRNA Aminoacylation Status by the T-Box Riboswitch Using tRNA-mRNA Stacking and Steric Readout

Zhang, Jinwei, Ferré-D’Amaré, Adrian R.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.76 MB

english, 2014

46

An in vitro evolved glmS ribozyme has the wild-type fold but loses coenzyme dependence

Lau, Matthew W L, Ferré-D'Amaré, Adrian R

Journal:

Nature Chemical Biology

Year:

2013

Language:

english

File:

PDF, 1.24 MB

english, 2013

47

Structural basis for activity of highly efficient RNA mimics of green fluorescent protein

Warner, Katherine Deigan, Chen, Michael C, Song, Wenjiao, Strack, Rita L, Thorn, Andrea, Jaffrey, Samie R, Ferré-D'Amaré, Adrian R

Journal:

Nature Structural and Molecular Biology

Year:

2014

Language:

english

File:

PDF, 2.95 MB

english, 2014

48

RNA FOLDS: Insights from Recent Crystal Structures

Ferré-D'Amaré, Adrian R., Doudna, Jennifer A.

Journal:

Annual Review of Biophysics and Biomolecular Structure

Year:

1999

Language:

english

File:

PDF, 430 KB

english, 1999

49

Protein synthesis: Stop the nonsense

Ferré-D'Amaré, Adrian R.

Journal:

Year:

2011

Language:

english

File:

PDF, 325 KB

english, 2011

50

Direct p K a Measurement of the Active-Site Cytosine in a Genomic Hepatitis Delta Virus Ribozyme

Lupták, Andrej, Ferré-D'Amaré, Adrian R., Zhou, Kaihong, Zilm, Kurt W., Doudna, Jennifer A.

Journal:

Journal of the American Chemical Society

Year:

2001

Language:

english

File:

PDF, 88 KB

english, 2001