Survey and summary: The applications of universal DNA base analogues (Q34285001)

1 August 2017

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title

Survey and summary: The applications of universal DNA base analogues (English)

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1 August 2017

D Loakes

1

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1 August 2017

language of work or name

English

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publication date

1 June 2001

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1 August 2017

published in

Nucleic Acids Research

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1 August 2017

volume

29

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1 August 2017

issue

12

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1 August 2017

page(s)

2437-2447

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Experimental Measurement of Aromatic Stacking Affinities in the Context of Duplex DNA

1 August 2017

cites work

1 reference

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Aromatic Nonpolar Nucleosides as Hydrophobic Isosteres of Pyrimidines and Purine Nucleosides

6 July 2018

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Formation of Stable DNA Loops by Incorporation of Nonpolar, Non‐Hydrogen‐Bonding Nucleoside Isosteres

6 July 2018

1 reference

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Hydrophobic, Non-Hydrogen-Bonding Bases and Base Pairs in DNA

6 July 2018

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Factors Contributing to Aromatic Stacking in Water: Evaluation in the Context of DNA.

6 July 2018

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Selective and Stable DNA Base Pairing without Hydrogen Bonds

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Sequencing-by-hybridization at the information-theory bound: an optimal algorithm

6 July 2018

1 reference

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NMR structure of a DNA duplex containing nucleoside analog 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole and the structure of the unmodified control

6 July 2018

1 reference

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The N(8)-(2'-deoxyribofuranoside) of 8-aza-7-deazaadenine: a universal nucleoside forming specific hydrogen bonds with the four canonical DNA constituents

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Universal bases for hybridization, replication and chain termination

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Quantification of syntrophic fatty acid-beta-oxidizing bacteria in a mesophilic biogas reactor by oligonucleotide probe hybridization.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Melting studies of short DNA hairpins containing the universal base 5-nitroindole

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Recognition of nonhybridizing base pairs during nucleotide excision repair of DNA

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Nucleotide analogs facilitate base conversion with 3' mismatch primers

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Triple helix formation: binding avidity of acridine-conjugated AG motif third strands containing natural, modified and surrogate bases opposed to pyrimidine interruptions in a polypurine target

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

The use of tailed octamer primers for cycle sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

MODIFIED OLIGONUCLEOTIDES: Synthesis and Strategy for Users

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Exploratory studies on azole carboxamides as nucleobase analogs: thermal denaturation studies on oligodeoxyribonucleotide duplexes containing pyrrole-3-carboxamide

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Triple helices formed at oligopyrimidine*oligopurine sequences with base pair inversions: effect of a triplex-specific ligand on stability and selectivity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Test of the potential of a dATP surrogate for sequencing via MALDI-MS.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Template directed incorporation of nucleotide mixtures using azole-nucleobase analogs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Extension of the range of DNA sequences available for triple helix formation: stabilization of mismatched triplexes by acridine-containing oligonucleotides

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Modification of DNA duplexes to smooth their thermal stability independently of their base content for DNA sequencing by hybridization

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Comparison of the base pairing properties of a series of nitroazole nucleobase analogs in the oligodeoxyribonucleotide sequence 5'-d(CGCXAATTYGCG)-3'.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Effect of the 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole residue on the stability of DNA duplexes and triplexes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Group-specific small-subunit rRNA hybridization probes to characterize filamentous foaming in activated sludge systems

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Improving the fidelity of Thermus thermophilus DNA ligase

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

DNA sequencing by hybridization to microchip octa-and decanucleotides extended by stacked pentanucleotides

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Non-hydrogen bonding 'terminator' nucleosides increase the 3'-end homogeneity of enzymatic RNA and DNA synthesis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Mutagenically separated PCR (MS-PCR): a highly specific one step procedure for easy mutation detection

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

5-Nitroindole as an universal base analogue

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Azole substituted oligonucleotides promote antiparallel triplex formation at non-homopurine duplex targets

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Oligonucleotides containing fluorescent 2′-deoxyisoinosine: solid-phase synthesis and duplex stability

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

3-Nitropyrrole and 5-nitroindole as universal bases in primers for DNA sequencing and PCR

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

RNA template-directed RNA synthesis by T7 RNA polymerase

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

An acyclic 5-nitroindazole nucleoside analogue as ambiguous nucleoside

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Synthesis and biophysical studies of short oligodeoxynucleotides with novel modifications: a possible approach to the problem of mixed base oligodeoxynucleotide synthesis.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Base pairing involving deoxyinosine: implications for probe design

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Molecular cloning of the human cholecystokinin gene by use of a synthetic probe containing deoxyinosine

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

An alternative approach to deoxyoligonucleotides as hybridization probes by insertion of deoxyinosine at ambiguous codon positions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Studies on nucleic acid interactions. I. Stabilities of mini-duplexes (dG2A4XA4G2-dC2T4YT4C2) and self-complementary d(GGGAAXYTTCCC) containing deoxyinosine and other mismatched bases

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

The three-dimensional structure of a DNA duplex containing looped-out bases

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Novel non-templated nucleotide addition reactions catalyzed by procaryotic and eucaryotic DNA polymerases

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Optimal reconstruction of a sequence from its probes.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Use of 5-nitroindole-2'-deoxyribose-5'-triphosphate for labelling and detection of oligonucleotides

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Cloning and developmental expression of a membrane-type matrix metalloproteinase from chicken.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

A universal nucleoside for use at ambiguous sites in DNA primers.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

PCR amplification using deoxyinosine to replace an entire codon and at ambiguous positions.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=55727

Melting studies of short DNA hairpins: influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability

28 October 2018

1 reference

12 December 2020

Mimicking the Structure and Function of DNA: Insights into DNA Stability and Replication

1 reference

12 December 2020

Nitroazole universal bases in peptide nucleic acids

1 reference

12 December 2020

Sequence determinants for the recognition of the fork junction DNA containing the -10 region of promoter DNA by E. coli RNA polymerase

1 reference

12 December 2020

Stable and Selective Hybridization of Oligonucleotides with Unnatural Hydrophobic Bases This work was supported by the National Institutes of Health (GM 60005 to F.E.R.) and the Skaggs Institute for Chemical Biology (F.E.R. and P.G.S.). A.K.O. thank

1 reference

12 December 2020

Synthesis and Structure of 1-Deoxy-1-phenyl-beta-D-ribofuranose and Its Incorporation into Oligonucleotides

1 reference

12 December 2020

Quantification of Methanosaeta Species in Anaerobic Bioreactors Using Genus- and Species-Specific Hybridization Probes

1 reference

12 December 2020

In vitro replication study of modified bases in ras sequences

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12 December 2020

Adenylate oligomers in single- and double-strand conformation

1 reference

12 December 2020

Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp

1 reference

12 December 2020

Extra adenosine stacks into the self-complementary d(CGCAGAATTCGCG) duplex in solution

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12 December 2020

Inosine-containing primers for mRNA differential display

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Making the perfect mismatch

1 reference

12 December 2020

Enhanced discrimination of single nucleotide polymorphisms by artificial mismatch hybridization

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12 December 2020

Stability and structure of DNA oligonucleotides containing non-specific base analogues

1 reference

12 December 2020

Stabilizating effect of 5-nitroindole (universal base) on DNA duplexes immobilized on gel matrix

1 reference

12 December 2020

Replication of non-hydrogen bonded bases by DNA polymerases: a mechanism for steric matching

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/29.12.2437

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1 August 2017

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1 August 2017

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