Journal ArticleDOI
Locked Nucleic Acid (LNA) Recognition of RNA: NMR Solution Structures of LNA:RNA Hybrids
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TLDR
It is suggested that the change in electronic density at the brim of the minor groove, introduced by the LNA modification, is causing an alteration of the pseudorotational profile of the 3'-flanking nucleotide, thus shifting this sugar equilibrium toward N-type conformation.Abstract:
Locked nucleic acids (LNAs) containing one or more 2‘-O,4‘-C-methylene-linked bicyclic ribonucleoside monomers possess a number of the prerequisites of an effective antisense oligonucleotide, e.g. ...read more
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Book ChapterDOI
Diastereomer-Specific Repertoire of 7′R- or 7′S-Me-Carba-Locked Nucleic Acids (cLNAs) in Antisense Oligo/RNA Duplexes and Engineering of Physico-chemical and Enzymological Properties
Qing Li,Oleksandr Plashkevych,Ram Shankar Upadhayaya,Sachin Gangadhar Deshpande,András Földesi,Jyoti Chattopadhyaya +5 more
TL;DR: MD simulations of the AON/RNA duplexes with 7′S- or 7′R-Me-cLNA have demonstrated that the modifications have only small local effect on the duplex structures, stacking and Watson–Crick base pairing.
Journal ArticleDOI
Two carbocyclic locked nucleic acid analogues give structural information about the role of hydration in A-type duplexes.
TL;DR: In this paper, two locked nucleic acid (LNA) analogues with three-carbon 2'-4' linkages, saturated or unsaturated, are synthesized using a ring-closing metathesis based strategy.
Journal ArticleDOI
SN- and NS-puckered sugar conformers are precursors of the (6-4) photoproduct in thymine dinucleotide.
Jouda Jakhlal,Clément Denhez,Stéphanie Coantic-Castex,Agathe Martinez,Dominique Harakat,Thierry Douki,Dominique Vuillaume,Pascale Clivio +7 more
TL;DR: It is experimentally demonstrated that the presence of one sugar presenting some amount of South puckering, at any of the extremities, is sufficient to trigger the (6-4) adduct formation in the thymine dinucleotide TpT.
Dissertation
Molecular modeling and thermodynamics simulation of nucleic acids
TL;DR: Computational studies of both RNA and DNA structures are covered, showing with modifications the structural stability, nucleotide conformation and base pair maintenance are almost better than those without modifications.
Journal ArticleDOI
機能解析を目的としたmicroRNAの検出／発現／阻害システムの確立 ～It’s a small miRNA World～
TL;DR: A system to detect, knockdown, and / or overexpress miRNAs, and establish the system to introduce synthetic oligos or RNAs expressed from lentiviral vectors to cells to improve affinity and single nucleotide discrimination is investigated.
References
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Journal ArticleDOI
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model
TL;DR: In this paper, the authors present an approach to generate electrostatic potential (ESP) derived charges for molecules, which optimally reproduce the intermolecular interaction properties of molecules with a simple two-body additive potential, provided that a suitably accurate level of quantum mechanical calculation is used to derive the ESP around the molecule.
Journal ArticleDOI
Antisense oligonucleotides: a new therapeutic principle
Eugen Uhlmann,Anusch Peyman +1 more
Journal ArticleDOI
LNA (Locked Nucleic Acids): Synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition
Alexei A. Koshkin,Sanjay K. Singh,Poul Nielsen,Vivek K. Rajwanshi,Ravindra Kumar,Michael Meldgaard,Carl Erik Olsen,Jesper Wengel +7 more
TL;DR: Studies of mis-matched sequences show that LNA obey the Watson-Crick base pairing rules with generally improved selectivities compared to the corresponding unmodified reference strands.
Journal ArticleDOI
The ups and downs of nucleic acid duplex stability: Structure-stability studies on chemically-modified DNA:RNA duplexes
TL;DR: From results, structure-activity relationships that correlate hybridization affinity with changes in oligonucleotide structure are determined and C-5-substituted pyrimidines stood out as substantially increasing duplex stability.
Journal ArticleDOI
The Definition of Generalized Helicoidal Parameters and of Axis Curvature for Irregular Nucleic Acids
Richard Lavery,Heinz Sklenar +1 more
TL;DR: An algorithm is presented which solves the problem of obtaining a rigorous helicoidal description of an irregular nucleic acid segment by definition of a function describing simultaneously the curvature of the nucleic acids segment and the corresponding stepwise variation of helicoidal parameters along the segment.