Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications

Specific Inhibition of Viral MicroRNAs by Carbon Dots-Mediated Delivery of Locked Nucleic Acids for Therapy of Virus-Induced Cancer

(2020) Enguo Ju et al.   ACS Nano

4′-Fluorinated RNA: Synthesis, Structure, and Applications as a Sensitive 19F NMR Probe of RNA Structure and Function

(2020) Qiang Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

RNA Phosphorothioate Modification in Prokaryotes and Eukaryotes

(2020) Ying Wu et al.   ACS Chemical Biology

Antisense Oligonucleotide in LNA-Gapmer Design Targeting TGFBR2—A Key Single Gene Target for Safe and Effective Inhibition of TGFβ Signaling

(2020) Sabrina Kuespert et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Alpha-l-Locked Nucleic Acid-Modified Antisense Oligonucleotides Induce Efficient Splice Modulation In Vitro

(2020) Prithi Raguraman et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Origins of the Increased Affinity of Phosphorothioate-Modified Therapeutic Nucleic Acids for Proteins

(2020) Malwina Hyjek-Składanowska et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Enhanced affinity of racemic phosphorothioate DNA with transcription factor SATB1 arising from diastereomer-specific hydrogen bonds and hydrophobic contacts

(2020) Kazuhiko Yamasaki et al.   NUCLEIC ACIDS RESEARCH

Chimeric siRNAs with chemically modified pentofuranose and hexopyranose nucleotides: altritol-nucleotide (ANA) containing GalNAc–siRNA conjugates: in vitro and in vivo RNAi activity and resistance to 5′-exonuclease

(2020) Pawan Kumar et al.   NUCLEIC ACIDS RESEARCH

Amide-Modified RNA: Using Protein Backbone to Modulate Function of Short Interfering RNAs

(2020) Venubabu Kotikam et al.   ACCOUNTS OF CHEMICAL RESEARCH

Advances in oligonucleotide drug delivery

(2020) Thomas C. Roberts et al.   NATURE REVIEWS DRUG DISCOVERY

Incorporating a Thiophosphate Modification into a Common RNA Tetraloop Motif Causes an Unanticipated Stability Boost

(2020) Pradeep S. Pallan et al.   BIOCHEMISTRY

De Novo Nucleic Acids: A Review of Synthetic Alternatives to DNA and RNA That Could Act as Bio-Information Storage Molecules

(2020) Kevin G Devine et al.   Life-Basel

Synthesis of 3′-fluoro-4′-amino-hexitol nucleosides with a pyrimidine nucleobase as building blocks for oligonucleotides

(2019) Amit M. Jabgunde et al.   TETRAHEDRON

RNA 2’-O-Methylation (Nm) Modification in Human Diseases

(2019) Dilyana G. Dimitrova et al.   Genes

Enhanced Dispersion and Polarization Interactions Achieved through Dithiophosphate Group Incorporation Yield a Dramatic Binding Affinity Increase for an RNA Aptamer–Thrombin Complex

(2019) Martin Egli et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Re-Engineering RNA Molecules into Therapeutic Agents

(2019) Martin Egli et al.   ACCOUNTS OF CHEMICAL RESEARCH

DNAmod: the DNA modification database

(2019) Ankur Jai Sood et al.   Journal of Cheminformatics

Synthesis of the Methyl Analog of 2′-O,4′-C-Ethylene-Bridged 5-Methyluridine via Intramolecular Radical Cyclization and Properties of Modified Oligonucleotides

(2019) Yuta Ito et al.   JOURNAL OF ORGANIC CHEMISTRY

Modification of messenger RNA by 2′-O-methylation regulates gene expression in vivo

(2019) Brittany A. Elliott et al.   Nature Communications

Synthesis of selenomethylene-locked nucleic acids (SeLNA) nucleoside unit bearing an adenine base

(2019) Yoshihiro Moai et al.   NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS

A Single Amide Linkage in the Passenger Strand Suppresses Its Activity and Enhances Guide Strand Targeting of siRNAs

(2018) Travis Hardcastle et al.   ACS Chemical Biology

The evolution of nucleoside analogue antivirals: A review for chemists and non-chemists. Part 1: Early structural modifications to the nucleoside scaffold

(2018) Katherine L. Seley-Radtke et al.   ANTIVIRAL RESEARCH

Synthesis of 4′- C -aminoalkyl-2′- O -methyl modified RNA and their biological properties

(2018) Kana Koizumi et al.   BIOORGANIC & MEDICINAL CHEMISTRY

RNA-Targeted Therapeutics

(2018) Stanley T. Crooke et al.   Cell Metabolism

Adjusting the Structure of 2′-Modified Nucleosides and Oligonucleotides via C4′-α-F or C4′-α-OMe Substitution: Synthesis and Conformational Analysis

(2018) Elise Malek-Adamian et al.   JOURNAL OF ORGANIC CHEMISTRY

Novel conformationally constrained 2′-C-methylribonucleosides: synthesis and incorporation into oligonucleotides

(2018) Kim Vejlegaard et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Synthesis and properties of 4′-C-aminoalkyl-2′-fluoro-modified RNA oligomers

(2018) Toshifumi Kano et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Structural basis for the synergy of 4′- and 2′-modifications on siRNA nuclease resistance, thermal stability and RNAi activity

(2018) Joel M Harp et al.   NUCLEIC ACIDS RESEARCH

Evaluation of the effect of 2′-O-methyl, fluoro hexitol, bicyclo and Morpholino nucleic acid modifications on potency of GalNAc conjugated antisense oligonucleotides in mice

(2018) Thazha P. Prakash et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Synthesis of Protected Amino Hexitol Nucleosides as Building Blocks for Oligonucleotide Synthesis

(2018) Swarup De et al.   JOURNAL OF ORGANIC CHEMISTRY

Detection and Analysis of RNA Ribose 2′-O-Methylations: Challenges and Solutions

(2018) Yuri Motorin et al.   Genes

Chemical Modifications of Nucleic Acid Aptamers for Therapeutic Purposes

(2017) Shuaijian Ni et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Chirality Dependent Potency Enhancement and Structural Impact of Glycol Nucleic Acid Modification on siRNA

(2017) Mark K. Schlegel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

4′-C-Methoxy-2′-deoxy-2′-fluoro Modified Ribonucleotides Improve Metabolic Stability and Elicit Efficient RNAi-Mediated Gene Silencing

(2017) Elise Malek-Adamian et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Control of phosphorothioate stereochemistry substantially increases the efficacy of antisense oligonucleotides

(2017) Naoki Iwamoto et al.   NATURE BIOTECHNOLOGY

Oxidation of phosphorothioate DNA modifications leads to lethal genomic instability

(2017) Stefanie Kellner et al.   Nature Chemical Biology

Mechanistic insights into precursor messenger RNA splicing by the spliceosome

(2017) Yigong Shi   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine

(2017) Sebastian M Fica et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs

(2017) Daniel Mutisya et al.   NUCLEIC ACIDS RESEARCH

MODOMICS: a database of RNA modification pathways. 2017 update

(2017) Pietro Boccaletto et al.   NUCLEIC ACIDS RESEARCH

Chemistry, mechanism and clinical status of antisense oligonucleotides and duplex RNAs

(2017) Xiulong Shen et al.   NUCLEIC ACIDS RESEARCH

Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine

(2017) Sebastian M Fica et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural Basis of Duplex Thermodynamic Stability and Enhanced Nuclease Resistance of 5′-C-Methyl Pyrimidine-Modified Oligonucleotides

(2016) Alexander V. Kel′in et al.   JOURNAL OF ORGANIC CHEMISTRY

Small Details Matter: The 2′-Hydroxyl as a Conformational Switch in RNA

(2016) Leonardo Darré et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Integrated Safety Assessment of 2′-O-Methoxyethyl Chimeric Antisense Oligonucleotides in NonHuman Primates and Healthy Human Volunteers

(2016) Stanley T Crooke et al.   MOLECULAR THERAPY

Evoking picomolar binding in RNA by a single phosphorodithioate linkage

(2016) N. Dinuka Abeydeera et al.   NUCLEIC ACIDS RESEARCH

Effect of an N-substituent in sulfonamide-bridged nucleic acid (SuNA) on hybridization ability and duplex structure

(2016) Yasunori Mitsuoka et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

LNA modification of single-stranded DNA oligonucleotides allows subtle gene modification in mismatch-repair-proficient cells

(2016) Thomas W. van Ravesteyn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Locked 2′-Deoxy-2′,4′-Difluororibo Modified Nucleic Acids: Thermal Stability, Structural Studies, and siRNA Activity

(2015) Saúl Martínez-Montero et al.   ACS Chemical Biology

DNA and RNA derivatives to optimize distribution and delivery

(2015) Eric Wickstrom   ADVANCED DRUG DELIVERY REVIEWS

Age-Dependent Levels of 5-Methyl-, 5-Hydroxymethyl-, and 5-Formylcytosine in Human and Mouse Brain Tissues

(2015) Mirko Wagner et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Modular Synthesis of Constrained Ethyl (cEt) Purine and Pyrimidine Nucleosides

(2015) Helen Blade et al.   JOURNAL OF ORGANIC CHEMISTRY

Synthesis and Properties of 2′-Deoxy-2′,4′-difluoroarabinose-Modified Nucleic Acids

(2015) Saúl Martínez-Montero et al.   JOURNAL OF ORGANIC CHEMISTRY

Xylonucleic acid: synthesis, structure, and orthogonal pairing properties

(2015) Mohitosh Maiti et al.   NUCLEIC ACIDS RESEARCH

The structural diversity of artificial genetic polymers

(2015) Irina Anosova et al.   NUCLEIC ACIDS RESEARCH

Straightforward Synthesis of Purine 4′-Alkoxy-2′-deoxynucleosides: First Report of Mixed Purine–Pyrimidine 4′-Alkoxyoligodeoxynucleotides as New RNA Mimics

(2015) Magdalena Petrová et al.   ORGANIC LETTERS

AZD9150, a next-generation antisense oligonucleotide inhibitor of STAT3 with early evidence of clinical activity in lymphoma and lung cancer

(2015) David Hong et al.   Science Translational Medicine

2′-N-Guanidino,4′-C-ethylene bridged thymidine (GENA-T) modified oligonucleotide exhibits triplex formation with excellent enzymatic stability

(2015) Jharna Barman et al.   RSC Advances

Scaffolding along Nucleic Acid Duplexes Using 2′-Amino-Locked Nucleic Acids

(2014) I. Kira Astakhova et al.   ACCOUNTS OF CHEMICAL RESEARCH

Improvement of a streptavidin-binding aptamer by LNA- and α-l-LNA-substitutions

(2014) Anna S. Jørgensen et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Rigid 2′,4′-Difluororibonucleosides: Synthesis, Conformational Analysis, and Incorporation into Nascent RNA by HCV Polymerase

(2014) Saúl Martínez-Montero et al.   JOURNAL OF ORGANIC CHEMISTRY

Synthesis, biophysical properties and biological activity of second generation antisense oligonucleotides containing chiral phosphorothioate linkages

(2014) W. Brad Wan et al.   NUCLEIC ACIDS RESEARCH

Amides are excellent mimics of phosphate internucleoside linkages and are well tolerated in short interfering RNAs

(2014) Daniel Mutisya et al.   NUCLEIC ACIDS RESEARCH

2′-OMe-phosphorodithioate-modified siRNAs show increased loading into the RISC complex and enhanced anti-tumour activity

(2014) Sherry Y. Wu et al.   Nature Communications

Crystal structure, stability and Ago2 affinity of phosphorodithioate-modified RNAs

(2014) Pradeep S. Pallan et al.   RSC Advances

Selenomethylene Locked Nucleic Acid Enables Reversible Hybridization in Response to Redox Changes

(2013) Kunihiko Morihiro et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Backbone FCH⋅⋅⋅O Hydrogen Bonds in 2′F-Substituted Nucleic Acids

(2013) Nerea Martin-Pintado et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Why nature really chose phosphate

(2013) Shina C. L. Kamerlin et al.   QUARTERLY REVIEWS OF BIOPHYSICS

The Steric Hypothesis for DNA Replication and Fluorine Hydrogen Bonding Revisited in Light of Structural Data

(2012) Martin Egli   ACCOUNTS OF CHEMICAL RESEARCH

Gene Silencing Activity of siRNA Molecules Containing Phosphorodithioate Substitutions

(2012) Xianbin Yang et al.   ACS Chemical Biology

2′-Fluoro RNA Shows Increased Watson-Crick H-Bonding Strength and Stacking Relative to RNA: Evidence from NMR and Thermodynamic Data

(2012) Amritraj Patra et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The Structure of Human Argonaute-2 in Complex with miR-20a

(2012) Elad Elkayam et al.   CELL

Designing Chemically Modified Oligonucleotides for Targeted Gene Silencing

(2012) Glen F. Deleavey et al.   CHEMISTRY & BIOLOGY

Synthesis, Gene Silencing, and Molecular Modeling Studies of 4′-C-Aminomethyl-2′-O-methyl Modified Small Interfering RNAs

(2012) Kiran R. Gore et al.   JOURNAL OF ORGANIC CHEMISTRY

Dissecting Chemical Interactions Governing RNA Polymerase II Transcriptional Fidelity

(2012) Matthew W. Kellinger et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Intrinsic Contribution of the 2′-Hydroxyl to RNA Conformational Heterogeneity

(2012) Elizabeth J. Denning et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Measurement and Theory of Hydrogen Bonding Contribution to Isosteric DNA Base Pairs

(2012) Omid Khakshoor et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The solution structure of double helical arabino nucleic acids (ANA and 2′F-ANA): effect of arabinoses in duplex-hairpin interconversion

(2012) Nerea Martín-Pintado et al.   NUCLEIC ACIDS RESEARCH

The Molecular Interactions That Stabilize RNA Tertiary Structure: RNA Motifs, Patterns, and Networks

(2011) Samuel E. Butcher et al.   ACCOUNTS OF CHEMICAL RESEARCH

Unique Gene-Silencing and Structural Properties of 2′-Fluoro-Modified siRNAs

(2011) Muthiah Manoharan et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Amides as Excellent Mimics of Phosphate Linkages in RNA

(2011) Chelliah Selvam et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Insights from Crystal Structures into the Opposite Effects on RNA Affinity Caused by the S- and R-6′-Methyl Backbone Modifications of 3′-Fluoro Hexitol Nucleic Acid

(2011) Pradeep S. Pallan et al.   BIOCHEMISTRY

Importance of Steric Effects on the Efficiency and Fidelity of Transcription by T7 RNA Polymerase

(2011) Sébastien Ulrich et al.   BIOCHEMISTRY

Structural requirements for hybridization at the 5′-position are different in α-l-LNA as compared to β-d-LNA

(2011) Punit P. Seth et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Locked vs. unlocked nucleic acids (LNA vs. UNA): contrasting structures work towards common therapeutic goals

(2011) Meghan A. Campbell et al.   CHEMICAL SOCIETY REVIEWS

An Overview of Sugar-Modified Oligonucleotides for Antisense Therapeutics

(2011) Thazha P. Prakash   CHEMISTRY & BIODIVERSITY

The Crystal Structure of the CeNA:RNA Hybrid ce(GCGTAGCG):r(CGCUACGC)

(2011) Margriet Ovaere et al.   CHEMISTRY-A EUROPEAN JOURNAL

On the Structure and Dynamics of Duplex GNA

(2011) Andrew T. Johnson et al.   JOURNAL OF ORGANIC CHEMISTRY

Synthesis, Improved Antisense Activity and Structural Rationale for the Divergent RNA Affinities of 3′-Fluoro Hexitol Nucleic Acid (FHNA and Ara-FHNA) Modified Oligonucleotides

(2011) Martin Egli et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Ribose 2′-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5

(2011) Roland Züst et al.   NATURE IMMUNOLOGY

4′-Alkoxy oligodeoxynucleotides: a novel class of RNA mimics

(2011) Radek Liboska et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Synthesis and Properties of the Simplified Nucleic Acid Glycol Nucleic Acid

(2010) Eric Meggers et al.   ACCOUNTS OF CHEMICAL RESEARCH

Nucleic Acids with a Six-Membered ‘Carbohydrate’ Mimic in the Backbone

(2010) Piet Herdewijn   CHEMISTRY & BIODIVERSITY

Synthesis and Biophysical Evaluation of 2′,4′-Constrained 2′O-Methoxyethyl and 2′,4′-Constrained 2′O-Ethyl Nucleic Acid Analogues

(2010) Punit P. Seth et al.   JOURNAL OF ORGANIC CHEMISTRY

An Exocyclic Methylene Group Acts As a Bioisostere of the 2′-Oxygen Atom in LNA

(2010) Punit P. Seth et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Unexpected origins of the enhanced pairing affinity of 2′-fluoro-modified RNA

(2010) Pradeep S. Pallan et al.   NUCLEIC ACIDS RESEARCH

Differential stability of 2′F-ANA•RNA and ANA•RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility

(2010) Jonathan K. Watts et al.   NUCLEIC ACIDS RESEARCH

Atomic resolution duplex structure of the simplified nucleic acidGNA

(2009) Mark K. Schlegel et al.   CHEMICAL COMMUNICATIONS

Synthesis of Conformationally Locked Carba-LNAs through Intramolecular Free-Radical Addition to C═N. Electrostatic and Steric Implication of the Carba-LNA Substituents in the Modified Oligos for Nuclease and Thermodynamic Stabilities

(2009) Jianfeng Xu et al.   JOURNAL OF ORGANIC CHEMISTRY

N2′→P3′ Phosphoramidate Glycerol Nucleic Acid as a Potential Alternative Genetic System

(2009) Jesse J. Chen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Pairing Geometry of the Hydrophobic Thymine Analogue 2,4-Difluorotoluene in Duplex DNA as Analyzed by X-ray Crystallography

(2009) Pradeep S. Pallan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Amide bond formation: beyond the myth of coupling reagents

(2008) Eric Valeur et al.   CHEMICAL SOCIETY REVIEWS

Duplex Structure of a Minimal Nucleic Acid

(2008) Mark K. Schlegel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Potent inhibition of microRNA in vivo without degradation

(2008) Scott Davis et al.   NUCLEIC ACIDS RESEARCH