(Q35775781)

English

Folding of the hammerhead ribozyme: pyrrolo-cytosine fluorescence separates core folding from global folding and reveals a pH-dependent conformational change

scientific article published on 24 January 2012

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scholarly article

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

Folding of the hammerhead ribozyme: pyrrolo-cytosine fluorescence separates core folding from global folding and reveals a pH-dependent conformational change (English)

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

0 references

author name string

Iwona A Buskiewicz

1

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

John M Burke

2

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

language of work or name

0 references

publication date

24 January 2012

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

18

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

3

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

434-448

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

Identification of hammerhead ribozymes in all domains of life reveals novel structural variations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

DNA hairpins containing the cytidine analog pyrrolo-dC: structural, thermodynamic, and spectroscopic studies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Capturing Hammerhead Ribozyme Structures in Action by Modulating General Base Catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Solvent Structure and Hammerhead Ribozyme Catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Autolytic processing of dimeric plant virus satellite RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

The tolerance to exchanges of the Watson Crick base pair in the hammerhead ribozyme core is determined by surrounding elements

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Effects of the trinucleotide preceding the self-cleavage site on eggplant latent viroid hammerheads: differences in co- and post-transcriptional self-cleavage may explain the lack of trinucleotide AUC in most natural hammerheads

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

When to believe what you see.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Extraordinary rates of transition metal ion-mediated ribozyme catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Tertiary contacts distant from the active site prime a ribozyme for catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

The effect of substituents on the hydrogen bonding of adenine and uracil derivatives

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Separate metal requirements for loop interactions and catalysis in the extended hammerhead ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Linkage between proton binding and folding in RNA: implications for RNA catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Artificial tertiary motifs stabilize trans-cleaving hammerhead ribozymes under conditions of submillimolar divalent ions and high temperatures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Using pyrrolo-deoxycytosine to probe RNA/DNA hybrids containing the human immunodeficiency virus type-1 3' polypurine tract.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Folding and activity of the hammerhead ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

On the wobble GoU and related pairs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Electron transfer between bases in double helical DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Schistosome satellite DNA encodes active hammerhead ribozymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Real-time monitoring of hairpin ribozyme kinetics through base-specific quenching of fluorescein-labeled substrates.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Kinetic characterization of two I/II format hammerhead ribozymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Importance of exocyclic base functional groups of central core guanosines for hammerhead ribozyme activity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Dissection of the role of the conserved G.U pair in group I RNA self-splicing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

The 2,6-Diaminopurine Riboside.cntdot.5-Methylisocytidine Wobble Base Pair: An Isoenergetic Substitution for the Study of G.cntdot.U Pairs in RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

An oligodeoxyribonucleotide that supports catalytic activity in the hammerhead ribozyme domain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Circular dichroism measurements show that C.C+ base pairs can coexist with A.T base pairs between antiparallel strands of an oligodeoxynucleotide double-helix

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

RNA structure, not sequence, determines the 5' splice-site specificity of a group I intron

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Sequence requirements of the hammerhead RNA self-cleavage reaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Numbering system for the hammerhead

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Importance of specific purine amino and hydroxyl groups for efficient cleavage by a hammerhead ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Protonated polynucleotide structures. 16. Thermodynamics of the melting of the acid form of polycytidylic acid

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

27 July 2018

Evidence for a nonbase stacking effect for the environment-sensitive fluorescent base pyrrolocytosine--comparison with 2-aminopurine

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

25 September 2018

Minimal and extended hammerheads utilize a similar dynamic reaction mechanism for catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

25 September 2018

Idiosyncratic cleavage and ligation activity of individual hammerhead ribozymes and core sequence variants thereof.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

25 September 2018

Three conserved guanosines approach the reaction site in native and minimal hammerhead ribozymes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

25 September 2018

Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

25 September 2018

Hammerheads derived from sTRSV show enhanced cleavage and ligation rate constants.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

25 September 2018

Model for general acid-base catalysis by the hammerhead ribozyme: pH-activity relationships of G8 and G12 variants at the putative active site

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

25 September 2018

Photocrosslinking detects a compact, active structure of the hammerhead ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

25 September 2018

Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

25 September 2018

Diffusely bound Mg2+ ions slightly reorient stems I and II of the hammerhead ribozyme to increase the probability of formation of the catalytic core

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

25 September 2018

Solvent Protection of the Hammerhead Ribozyme in the Ground State: Evidence for a Cation-Assisted Conformational Change Leading to Catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

25 September 2018

A pH-dependent conformational change, rather than the chemical step, appears to be rate-limiting in the hammerhead ribozyme cleavage reaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

25 September 2018

Hammerhead ribozyme structure and function in plant RNA replication.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

25 September 2018

Ion-induced folding of the hammerhead ribozyme: a fluorescence resonance energy transfer study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

25 September 2018

2NH2A X T helices in the ribo- and deoxypolynucleotide series. Structural and energetic consequences of 2NH2A substitution.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

25 September 2018

Self-cleavage of virusoid RNA is performed by the proposed 55-nucleotide active site

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

25 September 2018

U2–U6 RNA folding reveals a group II intron-like domain and a four-helix junction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

15 November 2018

Fast Cleavage Kinetics of a Natural Hammerhead Ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285932

15 November 2018

Helix formation between polyribonucleotides and purines, purine nucleosides and nucleotides. II

1 reference

https://pubmed.ncbi.nlm.nih.gov/22274955

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Interaction of nucleic acids. 8. Binding of magnesium ions by nucleic acids

1 reference

https://pubmed.ncbi.nlm.nih.gov/22274955

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Hammerhead ribozymes with a faster cleavage rate

1 reference

https://pubmed.ncbi.nlm.nih.gov/22274955

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Properties of a new fluorescent cytosine analogue, pyrrolocytosine

1 reference

https://pubmed.ncbi.nlm.nih.gov/22274955

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Conformational stability of dinucleotides in solution

1 reference

https://pubmed.ncbi.nlm.nih.gov/22274955

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The binding of Mg++ ions to polyadenylate, polyuridylate, and their complexes

1 reference

https://pubmed.ncbi.nlm.nih.gov/22274955

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structure-mapping of the hairpin ribozyme. Magnesium-dependent folding and evidence for tertiary interactions within the ribozyme-substrate complex

1 reference

https://pubmed.ncbi.nlm.nih.gov/22274955

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A.T and C.C+ base pairs can form simultaneously in a novel multistranded DNA complex

1 reference

https://pubmed.ncbi.nlm.nih.gov/22274955

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Copolymers of adenylic and 2-aminoadenylic acids. Effect of progressive changes in hydrogen bonding and stacking on interaction with poly(uridylic acid)

1 reference

https://pubmed.ncbi.nlm.nih.gov/22274955

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Stabilities of consecutive A.C, C.C, G.G, U.C, and U.U mismatches in RNA internal loops: Evidence for stable hydrogen-bonded U.U and C.C.+ pairs

1 reference

https://pubmed.ncbi.nlm.nih.gov/22274955

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1261/RNA.030999.111

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

ResearchGate publication ID

0 references

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