List of works - Douglas H. Turner

A CA(+) pair adjacent to a sheared GA or AA pair stabilizes size-symmetric RNA internal loops

scientific article published on June 2009

A chemical synthesis of LNA-2,6-diaminopurine riboside, and the influence of 2'-O-methyl-2,6-diaminopurine and LNA-2,6-diaminopurine ribosides on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes

scientific article published on 12 June 2007

A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation

scientific article

Accurate geometrical restraints for Watson–Crick base pairs

scientific article published on 27 March 2019

Activity of Hoechst 33258 against Pneumocystis carinii f. sp. muris, Candida albicans, and Candida dubliniensis

scientific article published in April 2005

Antisense Oligonucleotides Targeting Influenza A Segment 8 Genomic RNA Inhibit Viral Replication

scientific article published on 27 July 2016

Benchmarking AMBER Force Fields for RNA: Comparisons to NMR Spectra for Single-Stranded r(GACC) Are Improved by Revised χ Torsions ⬇️

scientific article published on July 28, 2011

Biophysical Analysis of Influenza A Virus RNA Promoter at Physiological Temperatures ⬇️

scientific article published on May 9, 2011

Chemical synthesis of LNA-2-thiouridine and its influence on stability and selectivity of oligonucleotide binding to RNA.

scientific article

Comparisons between chemical mapping and binding to isoenergetic oligonucleotide microarrays reveal unexpected patterns of binding to the Bacillus subtilis RNase P RNA specificity domain

scientific article published on September 2010

Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations.

scientific article

Contributions of stacking, preorganization, and hydrogen bonding to the thermodynamic stability of duplexes between RNA and 2'-O-methyl RNA with locked nucleic acids

scientific article

Correction to NMR of CCCC RNA Reveals a Right-HandedHelix and Revised Parameters for AMBER Force Field Torsions Improve Structural Predictions from Molecular Dynamics.

scientific article published on 29 April 2013

Correction: The 3′ Splice Site of Influenza A Segment 7 mRNA Can Exist in Two Conformations: A Pseudoknot and a Hairpin.

scientific article published on 18 September 2012

Crystal structure of a poly(rA) staggered zipper at acidic pH: evidence that adenine N1 protonation mediates parallel double helix formation

scientific article published on 10 June 2016

Dynalign: an algorithm for finding the secondary structure common to two RNA sequences

scientific article (publication date: 22 March 2002)

Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs

scientific article

Experimentally Derived Nearest-Neighbor Parameters for the Stability of RNA Three- and Four-Way Multibranch Loops ⬇️

scientific article published on January 22, 2002

Facilitating RNA structure prediction with microarrays

scientific article

Fluorescence Competition and Optical Melting Measurements of RNA Three-Way Multibranch Loops Provide a Revised Model for Thermodynamic Parameters ⬇️

scientific article published on January 14, 2011

Folding and Finding RNA Secondary Structure ⬇️

scientific article published on August 4, 2010

Fundamental interactions in RNA: Questions answered and remaining ⬇️

scientific article published on December 1, 2013

Hoechst 33258 selectively inhibits group I intron self-splicing by affecting RNA folding

scientific article published in December 2004

Identification of conserved RNA secondary structures at influenza B and C splice sites reveals similarities and differences between influenza A, B, and C.

scientific article published on 09 January 2014

Identification of potential conserved RNA secondary structure throughout influenza A coding regions

scientific article

In vivo analysis of influenza A mRNA secondary structures identifies critical regulatory motifs

scientific article published on 26 July 2019

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

scientific article

Influenza A virus coding regions exhibit host-specific global ordered RNA structure ⬇️

scientific article published on April 25, 2012

Influenza B virus has global ordered RNA structure in (+) and (−) strands but relatively less stable predicted RNA folding free energy than allowed by the encoded protein sequence ⬇️

scientific article published on August 19, 2013

Inhibition of Escherichia coli RNase P by oligonucleotide directed misfolding of RNA ⬇️

scientific article published on December 1, 2003

Interpreting oligonucleotide microarray data to determine RNA secondary structure: application to the 3' end of Bombyx mori R2 RNA.

scientific article

Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function

scientific article

Laser Raman temperature-jump study of the kinetics of the triiodide equilibrium. Relaxation times in the 10-8 -10-7 second range

article by Douglas H. Turner et al published March 1972 in Journal of the American Chemical Society

Microarrays for identifying binding sites and probing structure of RNAs

scientific article

Molecular Dynamics Correctly Models the Unusual Major Conformation of the GAGU RNA Internal Loop and with NMR Reveals an Unusual Minor Conformation

scientific article published on 6 February 2018

Molecular Mechanics Investigation of an Adenine–Adenine Non-Canonical Pair Conformational Change ⬇️

scientific article published on November 8, 2011

Molecular recognition by the Candida albicans group I intron: tertiary interactions with an imino G.A pair facilitate binding of the 5' exon and lower the KM for guanosine

scientific article

Molecular recognition in purine-rich internal loops: thermodynamic, structural, and dynamic consequences of purine for adenine substitutions in 5'(rGGCAAGCCU)2

scientific article

Mutations Designed by Ensemble Defect to Misfold Conserved RNA Structures of Influenza A Segments 7 and 8 Affect Splicing and Attenuate Viral Replication in Cell Culture

scientific article

NMR Structures of (rGC U GA G GCU) 2 and (rGC G GA U GCU) 2 : Probing the Structural Features That Shape the Thermodynamic Stability of GA Pairs † , ‡

scientific article

NMR reveals the absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA

scientific article

NMR studies of DNA single strands and DNA:RNA hybrids with and without 1-propynylation at C5 of oligopyrimidines

scientific article (publication date: 21 May 2003)

NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon

scientific article published on 10 July 2008

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

scientific article

Nearest neighbor parameters for Watson-Crick complementary heteroduplexes formed between 2'-O-methyl RNA and RNA oligonucleotides

scientific article published on 26 July 2006

New approaches to targeting RNA with oligonucleotides: inhibition of group I intron self-splicing

scientific article published on January 2004

Novel Conformation of an RNA Structural Switch

scientific article

Nuclear Magnetic Resonance Reveals That GU Base Pairs Flanking Internal Loops Can Adopt Diverse Structures.

scientific article

Nuclear Magnetic Resonance Spectra and AMBER OL3 and ROC-RNA Simulations of UCUCGU Reveal Force Field Strengths and Weaknesses for Single-Stranded RNA

scientific article published on 06 January 2022

Nuclear Magnetic Resonance Structure of an 8 × 8 Nucleotide RNA Internal Loop Flanked on Each Side by Three Watson-Crick Pairs and Comparison to Three-Dimensional Predictions

scientific article

Nuclear Magnetic Resonance of Single-Stranded RNAs and DNAs of CAAU and UCAAUC as Benchmarks for Molecular Dynamics Simulations

scientific article published on 17 February 2020

Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints

scientific article

Oligonucleotide directed misfolding of RNA inhibits Candida albicans group I intron splicing

scientific article

Optical Melting Measurements of Nucleic Acid Thermodynamics ⬇️

scientific article published on November 17, 2009

Optimization of an AMBER force field for the artificial nucleic acid, LNA, and benchmarking with NMR of L(CAAU).

scientific article published on 24 January 2014

Physics-based all-atom modeling of RNA energetics and structure

scientific article published in September 2017

Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models ⬇️

scientific article

Prediction of RNA secondary structure by free energy minimization

scientific article

RNA Internal Loops with Tandem AG Pairs: The Structure of the 5′G AG U/3′U GA G Loop Can Be Dramatically Different from Others, Including 5′A AG U/3′U GA A

scientific article

RNA Secondary Structure Prediction

scientific article

RNA challenges for computational chemists

scientific article

RNA pseudoknots: folding and finding

scientific article

RNA secondary structure prediction

scientific article published on March 2007

Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.

scientific article published on 16 April 2010

Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs

scientific article published on December 2011

Secondary structure models of the 3' untranslated regions of diverse R2 RNAs

scientific article

Secondary structure of a conserved domain in an intron of influenza A M1 mRNA

scientific article

Secondary structure of a conserved domain in the intron of influenza A NS1 mRNA

scientific article (publication date: 2013)

Secondary structures for 5' regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints

scientific article

Selective quenching of fluorescence from unbound oligonucleotides by gold nanoparticles as a probe of RNA structure

scientific article

Self-Folding of Naked Segment 8 Genomic RNA of Influenza A Virus

scientific article

Sheared Aanti.Aanti base pairs in a destabilizing 2 x 2 internal loop: the NMR structure of 5'(rGGCAAGCCU)2

scientific article

Solution structure of an RNA internal loop with three consecutive sheared GA pairs

scientific article

Stacking Effects on Local Structure in RNA: Changes in the Structure of Tandem GA Pairs when Flanking GC Pairs Are Replaced by isoG−isoC Pairs †

scientific article

Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics

scientific article (publication date: 9 June 2015)

Structural features of a 3' splice site in influenza a

scientific article published on 21 May 2015

Structure determination of noncanonical RNA motifs guided by ¹H NMR chemical shifts

scientific article published on 02 March 2014

Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops.

scientific article published on 23 March 2018

Testing the Nearest Neighbor Model for Canonical RNA Base Pairs: Revision of GU Parameters ⬇️

scientific article published on April 10, 2012

The 3′ Splice Site of Influenza A Segment 7 mRNA Can Exist in Two Conformations: A Pseudoknot and a Hairpin ⬇️

scientific article published on June 7, 2012

The Influenza A PB1-F2 and N40 Start Codons Are Contained within an RNA Pseudoknot

scientific article published on 27 May 2015

The Nuclear Magnetic Resonance of CCCC RNA Reveals a Right-Handed Helix, and Revised Parameters for AMBER Force Field Torsions Improve Structural Predictions from Molecular Dynamics ⬇️

scientific article published on January 29, 2013

The R2 retrotransposon RNA families

scientific article

The contribution of pseudouridine to stabilities and structure of RNAs

scientific article published on 24 December 2013

The crystal structure at 1.5 angstroms resolution of an RNA octamer duplex containing tandem G.U basepairs

scientific article

The determination of RNA folding nearest neighbor parameters

scientific article published on January 2014

The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes

scientific article

The influenza A segment 7 mRNA 3′ splice site pseudoknot/hairpin family ⬇️

scientific article published on October 12, 2012

The thermodynamics of 3'-terminal pyrene and guanosine for the design of isoenergetic 2'-O-methyl-RNA-LNA chimeric oligonucleotide probes of RNA structure

scientific article published on 5 January 2008

Thermodynamic stability and structural features of the J4/5 loop in a Pneumocystis carinii group I intron

scientific article published on December 2003

Uptake and antifungal activity of oligonucleotides in Candida albicans

scholarly article

Use of fluorescence spectroscopy to elucidate RNA folding pathways

scientific article

List of works by Douglas H. Turner

A CA(+) pair adjacent to a sheared GA or AA pair stabilizes size-symmetric RNA internal loops

A chemical synthesis of LNA-2,6-diaminopurine riboside, and the influence of 2'-O-methyl-2,6-diaminopurine and LNA-2,6-diaminopurine ribosides on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes

A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation

Accurate geometrical restraints for Watson–Crick base pairs

Activity of Hoechst 33258 against Pneumocystis carinii f. sp. muris, Candida albicans, and Candida dubliniensis

Antisense Oligonucleotides Targeting Influenza A Segment 8 Genomic RNA Inhibit Viral Replication

Benchmarking AMBER Force Fields for RNA: Comparisons to NMR Spectra for Single-Stranded r(GACC) Are Improved by Revised χ Torsions ⬇️

Biophysical Analysis of Influenza A Virus RNA Promoter at Physiological Temperatures ⬇️

Chemical synthesis of LNA-2-thiouridine and its influence on stability and selectivity of oligonucleotide binding to RNA.

Comparisons between chemical mapping and binding to isoenergetic oligonucleotide microarrays reveal unexpected patterns of binding to the Bacillus subtilis RNase P RNA specificity domain

Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations.

Contributions of stacking, preorganization, and hydrogen bonding to the thermodynamic stability of duplexes between RNA and 2'-O-methyl RNA with locked nucleic acids

Correction to NMR of CCCC RNA Reveals a Right-HandedHelix and Revised Parameters for AMBER Force Field Torsions Improve Structural Predictions from Molecular Dynamics.

Correction: The 3′ Splice Site of Influenza A Segment 7 mRNA Can Exist in Two Conformations: A Pseudoknot and a Hairpin.

Crystal structure of a poly(rA) staggered zipper at acidic pH: evidence that adenine N1 protonation mediates parallel double helix formation

Dynalign: an algorithm for finding the secondary structure common to two RNA sequences

Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs

Experimentally Derived Nearest-Neighbor Parameters for the Stability of RNA Three- and Four-Way Multibranch Loops ⬇️

Facilitating RNA structure prediction with microarrays

Fluorescence Competition and Optical Melting Measurements of RNA Three-Way Multibranch Loops Provide a Revised Model for Thermodynamic Parameters ⬇️

Folding and Finding RNA Secondary Structure ⬇️

Fundamental interactions in RNA: Questions answered and remaining ⬇️

Hoechst 33258 selectively inhibits group I intron self-splicing by affecting RNA folding

Identification of conserved RNA secondary structures at influenza B and C splice sites reveals similarities and differences between influenza A, B, and C.

Identification of potential conserved RNA secondary structure throughout influenza A coding regions

In vivo analysis of influenza A mRNA secondary structures identifies critical regulatory motifs

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

Influenza A virus coding regions exhibit host-specific global ordered RNA structure ⬇️

Influenza B virus has global ordered RNA structure in (+) and (−) strands but relatively less stable predicted RNA folding free energy than allowed by the encoded protein sequence ⬇️

Inhibition of Escherichia coli RNase P by oligonucleotide directed misfolding of RNA ⬇️

Interpreting oligonucleotide microarray data to determine RNA secondary structure: application to the 3' end of Bombyx mori R2 RNA.

Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function

Laser Raman temperature-jump study of the kinetics of the triiodide equilibrium. Relaxation times in the 10-8 -10-7 second range

Microarrays for identifying binding sites and probing structure of RNAs

Molecular Dynamics Correctly Models the Unusual Major Conformation of the GAGU RNA Internal Loop and with NMR Reveals an Unusual Minor Conformation

Molecular Mechanics Investigation of an Adenine–Adenine Non-Canonical Pair Conformational Change ⬇️

Molecular recognition by the Candida albicans group I intron: tertiary interactions with an imino G.A pair facilitate binding of the 5' exon and lower the KM for guanosine

Molecular recognition in purine-rich internal loops: thermodynamic, structural, and dynamic consequences of purine for adenine substitutions in 5'(rGGCAAGCCU)2

Mutations Designed by Ensemble Defect to Misfold Conserved RNA Structures of Influenza A Segments 7 and 8 Affect Splicing and Attenuate Viral Replication in Cell Culture

NMR Structures of (rGC U GA G GCU) 2 and (rGC G GA U GCU) 2 : Probing the Structural Features That Shape the Thermodynamic Stability of GA Pairs † , ‡

NMR reveals the absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA

NMR studies of DNA single strands and DNA:RNA hybrids with and without 1-propynylation at C5 of oligopyrimidines

NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

Nearest neighbor parameters for Watson-Crick complementary heteroduplexes formed between 2'-O-methyl RNA and RNA oligonucleotides

New approaches to targeting RNA with oligonucleotides: inhibition of group I intron self-splicing

Novel Conformation of an RNA Structural Switch

Nuclear Magnetic Resonance Reveals That GU Base Pairs Flanking Internal Loops Can Adopt Diverse Structures.

Nuclear Magnetic Resonance Spectra and AMBER OL3 and ROC-RNA Simulations of UCUCGU Reveal Force Field Strengths and Weaknesses for Single-Stranded RNA

Nuclear Magnetic Resonance Structure of an 8 × 8 Nucleotide RNA Internal Loop Flanked on Each Side by Three Watson-Crick Pairs and Comparison to Three-Dimensional Predictions

Nuclear Magnetic Resonance of Single-Stranded RNAs and DNAs of CAAU and UCAAUC as Benchmarks for Molecular Dynamics Simulations

Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints

Oligonucleotide directed misfolding of RNA inhibits Candida albicans group I intron splicing

Optical Melting Measurements of Nucleic Acid Thermodynamics ⬇️

Optimization of an AMBER force field for the artificial nucleic acid, LNA, and benchmarking with NMR of L(CAAU).

Physics-based all-atom modeling of RNA energetics and structure

Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models ⬇️

Prediction of RNA secondary structure by free energy minimization

RNA Internal Loops with Tandem AG Pairs: The Structure of the 5′G AG U/3′U GA G Loop Can Be Dramatically Different from Others, Including 5′A AG U/3′U GA A

RNA Secondary Structure Prediction

RNA challenges for computational chemists

RNA pseudoknots: folding and finding

RNA secondary structure prediction

Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.

Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs

Secondary structure models of the 3' untranslated regions of diverse R2 RNAs

Secondary structure of a conserved domain in an intron of influenza A M1 mRNA

Secondary structure of a conserved domain in the intron of influenza A NS1 mRNA

Secondary structures for 5' regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints

Selective quenching of fluorescence from unbound oligonucleotides by gold nanoparticles as a probe of RNA structure

Self-Folding of Naked Segment 8 Genomic RNA of Influenza A Virus

Sheared Aanti.Aanti base pairs in a destabilizing 2 x 2 internal loop: the NMR structure of 5'(rGGCAAGCCU)2

Solution structure of an RNA internal loop with three consecutive sheared GA pairs

Stacking Effects on Local Structure in RNA: Changes in the Structure of Tandem GA Pairs when Flanking GC Pairs Are Replaced by isoG−isoC Pairs †

Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics

Structural features of a 3' splice site in influenza a

Structure determination of noncanonical RNA motifs guided by ¹H NMR chemical shifts

Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops.

Testing the Nearest Neighbor Model for Canonical RNA Base Pairs: Revision of GU Parameters ⬇️