Deoxyribozymes: selection design and serendipity in the development of DNA catalysts (Q37394252)

20 August 2017

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title

Deoxyribozymes: selection design and serendipity in the development of DNA catalysts (English)

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20 August 2017

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Scott K Silverman

1

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PMCID

2764829

20 August 2017

language of work or name

English

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publication date

1 October 2009

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Accounts of Chemical Research

20 August 2017

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20 August 2017

42

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20 August 2017

10

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20 August 2017

1521-1531

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DNA-catalyzed sequence-specific hydrolysis of DNA

20 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

Biologically inspired synthetic enzymes made from DNA.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

Controlling the direction of site-selectivity and regioselectivity in RNA ligation by Zn2+-dependent deoxyribozymes that use 2',3'-cyclic phosphate RNA substrates

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

Convergent and general one-step DNA-catalyzed synthesis of multiply branched DNA.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

Catalytic DNA (deoxyribozymes) for synthetic applications-current abilities and future prospects

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

Improvement of DNA adenylation using T4 DNA ligase with a template strand and a strategically mismatched acceptor strand

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

Ty1 reverse transcriptase does not read through the proposed 2',5'-branched retrotransposition intermediate in vitro

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

Site-selective depurination by a periodate-dependent deoxyribozyme

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

Adenosine is inherently favored as the branch-site RNA nucleotide in a structural context that resembles natural RNA splicing

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

A general two-step strategy to synthesize lariat RNAs

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

In vitro selection, characterization, and application of deoxyribozymes that cleave RNA

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

Efficient one-step synthesis of biologically related lariat RNAs by a deoxyribozyme

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

DNA catalysis: potential, limitations, open questions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

A deoxyribozyme that synthesizes 2',5'-branched RNA with any branch-site nucleotide

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

Zn2+-dependent deoxyribozymes that form natural and unnatural RNA linkages

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

DNAzymes: from creation in vitro to application in vivo.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

Structure-function correlations derived from faster variants of a RNA ligase deoxyribozyme

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

A deoxyribozyme that harnesses light to repair thymine dimers in DNA.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

6 September 2017

Ribozyme speed limits

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

A DNA enzyme with N-glycosylase activity

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

Joining of RNAs by splinted ligation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

Relationship between internucleotide linkage geometry and the stability of RNA.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

Crystal structure of an 82-nucleotide RNA-DNA complex formed by the 10-23 DNA enzyme

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

A DNA enzyme that cleaves RNA

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

A general purpose RNA-cleaving DNA enzyme

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

The chemistry of self-splicing RNA and RNA enzymes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

A common speed limit for RNA-cleaving ribozymes and deoxyribozymes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

A small catalytic RNA motif with Diels-Alderase activity.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

Site-specific modification of pre-mRNA: the 2'-hydroxyl groups at the splice sites

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

A deoxyribozyme, Sero1C, uses light and serotonin to repair diverse pyrimidine dimers in DNA.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

DNA and RNA can be equally efficient catalysts for carbon-carbon bond formation

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

Engineering a selective small-molecule substrate binding site into a deoxyribozyme.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

Parallel selections in vitro reveal a preference for 2'-5' RNA ligation upon deoxyribozyme-mediated opening of a 2',3'-cyclic phosphate

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

A deoxyribozyme that forms a three-helix-junction complex with its RNA substrates and has general RNA branch-forming activity

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

A DNA enzyme that mimics the first step of RNA splicing

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

Characterization of deoxyribozymes that synthesize branched RNA.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

Optimization and generality of a small deoxyribozyme that ligates RNA.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

Characterization of a DNA-cleaving deoxyribozyme

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764829

General deoxyribozyme-catalyzed synthesis of native 3'-5' RNA linkages

2 September 2018

1 reference

12 December 2020

Mimicking the first step of RNA splicing: an artificial DNA enzyme can synthesize branched RNA using an oligonucleotide leaving group as a 5'-exon analogue

1 reference

12 December 2020

Experimental tests of two proofreading mechanisms for 5'-splice site selection

1 reference

12 December 2020

Deoxyribozyme-catalyzed labeling of RNA

1 reference

12 December 2020

Deoxyribozymes with 2'-5' RNA ligase activity

1 reference

12 December 2020

In Vitro Evolution of an RNA-Cleaving DNA Enzyme into an RNA Ligase Switches the Selectivity from 3‘−5‘ to 2‘−5‘

1 reference

12 December 2020

Deoxyribozymes that synthesize branched and lariat RNA

1 reference

12 December 2020

A DNA metalloenzyme with DNA ligase activity

1 reference

12 December 2020

A catalytic DNA for porphyrin metallation

1 reference

12 December 2020

Rational modification of a selection strategy leads to deoxyribozymes that create native 3'-5' RNA linkages

1 reference

12 December 2020

Directing the outcome of deoxyribozyme selections to favor native 3'-5' RNA ligation

1 reference

12 December 2020

Allosteric control of ribozyme catalysis by using DNA constraints

1 reference

12 December 2020

DNA-catalyzed formation of nucleopeptide linkages

1 reference

12 December 2020

Identifiers

DOI

10.1021/AR900052Y

1 reference

20 August 2017

1 reference

20 August 2017

1 reference

PMCID

2764829