Sequence-Dependent Thermodynamic Parameters for Locked Nucleic Acid (LNA)−DNA Duplex Formation†

Biochemistry ◽  
2004 ◽  
Vol 43 (18) ◽  
pp. 5388-5405 ◽  
Author(s):  
Patricia M. McTigue ◽  
Raymond J. Peterson ◽  
Jason D. Kahn
Keyword(s):  
Nucleic Acid ◽  
Thermodynamic Parameters ◽  
Locked Nucleic Acid ◽  
Dna Duplex ◽  
Sequence Dependent ◽  
Duplex Formation

Thermodynamic and Kinetic Characterization of Duplex Formation between 2′-O, 4′-C-Methylene-modified Oligoribonucleotides, DNA and RNA

2007 ◽  
Vol 27 (6) ◽  
pp. 327-333 ◽  
Author(s):  
Ulla Christensen
Keyword(s):  
Nucleic Acid ◽  
Full Length ◽  
Locked Nucleic Acid ◽  
Complementary Dna ◽  
High Affinity ◽  
Thermodynamics And Kinetics ◽  
Dna And Rna ◽  
Reaction Thermodynamics ◽  
Duplex Formation

2′-O,4′-C-methylene-linked ribonucleotide derivatives, named LNA (locked nucleic acid) and BNA (bridged nucleic acid) are nucleic acid analogoues that have shown high-affinity recognition of DNA and RNA, and the employment of LNA oligomers for antisense activity, gene regulation and nucleic acid diagnostics seems promising. Here we show kinetic and thermodynamic results on the interaction of a series of 10 bases long LNA–DNA mixmers, gabmers as well as full length LNA's with the complementary DNA, RNA and LNA oligonucleotides in the presence and absence of 10 mM Mg2+- ions. Our results show no significant differences in the reaction thermodynamics and kinetics between the LNA species, only a tendency to stronger duplex formation with the gabmer and mixmer. Introduction of a few LNA's thus may be a better strategy, than using full length LNA's to obtain an oligonucleotide that markedly increases the strength of duplexes formed with the complementary DNA and RNA.

scholarly journals Effect of Locked Nucleic Acid (LNA) modification on Hybridization Kinetics of DNA duplex

2008 ◽  
Vol 52 (1) ◽  
pp. 417-418 ◽  
Author(s):  
A. Arora ◽  
H. Kaur ◽  
J. Wengel ◽  
S. Maiti
Keyword(s):  
Nucleic Acid ◽  
Locked Nucleic Acid ◽  
Dna Duplex ◽  
Kinetics Of

Novel nucleic acid architectures involving locked nucleic acid (LNA) and pyrene residues: Results from an Indo-Danish collaboration

2005 ◽  
Vol 77 (1) ◽  
pp. 319-326 ◽  
Author(s):  
B. Ravindra Babu ◽  
Mads D. Sørensen ◽  
Patrick J. Hrdlicka ◽  
Smriti Trikha ◽  
Ashok K. Prasad ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Dna Synthesis ◽  
Surface Area ◽  
Locked Nucleic Acid ◽  
Planar Surface ◽  
Dna Duplex ◽  
Fluorescent Tag ◽  
Conformationally Locked ◽  
Covalently Bound

We report herein our results for locked nucleic acid (LNA)-type oligonucleotides containing pyrene residues. Pyrene has a large hydrophobic and planar surface area and is therefore a potential intercalating unit; furthermore, it is interesting as a fluorescent tag when covalently bound to DNA. Synthesis and hybridization of conformationally locked universal base surrogates are described together with efficient interstrand communication as shown by the formation of pyrene excimer bands for duplexes containing 2'-N-(pyren-1-yl)methyl-2'-amino-LNA monomers positioned in a zipper-like manner within a DNA duplex.

scholarly journals Improved Thermodynamic Parameters and Helix Initiation Factor to Predict Stability of DNA Duplexes

1996 ◽  
Vol 24 (22) ◽  
pp. 4501-4505 ◽  
Author(s):  
Naoki Sugimoto ◽  
Shu-ich Nakano ◽  
Mari Yoneyama ◽  
Kei-ich Honda
Keyword(s):  
Thermodynamic Parameters ◽  
Nearest Neighbor ◽  
Enthalpy Change ◽  
Initiation Factor ◽  
Dna Duplexes ◽  
Dna Duplex ◽  
Dna And Rna ◽  
Sequence Dependent ◽  
Experimental Values

Abstract To improve the previous DNA/DNA nearest-neighbor parameters, thermodynamic parameters (Δ H °, Δ S ° and Δ G °) of 50 DNA/DNA duplexes were measured. Enthalpy change of a helix initiation factor is also considered though the parameters reported recently did not contain the factor. A helix initiation factor for DNA/DNA duplex determined here was the same as that of RNA/RNA duplex (ΔG° 37 = 3.4 kcal/mol). The improved nearest-neighbor parameters reproduced not only these 50 experimental values used here but also 15 other experimental values obtained in different studies. Comparing Δ G ° 37 values of DNA/DNA nearest-neighbor parameters obtained here with those of RNA/RNA and RNA/DNA, RNA/RNA duplex was generally the most stable of the three kinds of duplexes with the same nearest-neighbor sequences. Which is more stable between DNA/DNA and RNA/DNA duplexes is sequence dependent.

Stopped-flow kinetics of locked nucleic acid (LNA)–oligonucleotide duplex formation: studies of LNA–DNA and DNA–DNA interactions

2001 ◽  
Vol 354 (3) ◽  
pp. 481-484 ◽  
Author(s):  
Ulla CHRISTENSEN ◽  
Nana JACOBSEN ◽  
Vivek K. RAJWANSHI ◽  
Jesper WENGEL ◽  
Troels KOCH
Keyword(s):  
Nucleic Acid ◽  
Dissociation Constants ◽  
Locked Nucleic Acid ◽  
Stopped Flow ◽  
Complementary Dna ◽  
Conformationally Restricted ◽  
Dna And Rna ◽  
Melting Curves ◽  
Oligonucleotide Duplex ◽  
Duplex Formation

The locked nucleic acid (LNA) monomer is a conformationally restricted nucleotide analogue with an extra 2′-O,4′-C-methylene bridge added to the ribose ring. Oligonucleotides that contain LNA monomers have shown greatly enhanced thermal stability when hybridized to complementary DNA and RNA and are considered most promising candidates for efficient recognition of a given mixed sequence in a nucleic acid duplex and as an antisense molecule. Here the kinetics and thermodynamics of a series of oligonucleotide duplex formations of DNA–DNA and DNA–LNA octamers were studied using stopped-flow absorption measurements at 25°C and melting curves. The reactions of the DNA octamer 5′-CAGGAGCA-3′ with its complementary DNA octamer 5′-TGCTCCTG-3′, and with the LNA octamers 5′-TLGCTCCTG-3′ (LNA-1), 5′-TLGCTLCCTG-3′ (LNA-2) and 5′-TLGCTLCCTLG-3′(LNA-3), containing respectively one, two or three thymidine 2′-O,4′-C-methylene-(D-ribofuranosyl) nucleotide monomers, designated TL, were studied. In all cases were seen fast second-order association reactions with kobs = 2×107M-1˙s-1. At 25°C the dissociation constants of the duplexes obtained from melting curves were: DNA–DNA, 10nM; DNA–LNA-1, 20nM; DNA–LNA-2, 2nM; and DNA–LNA-3, 0.3nM; thus the greatly enhanced duplex stability induced by LNA is confirmed. Since the association rates were all equal this increase in stability is due to slower rates of dissociation of the complexes.

Kinetic Effect of Cationic Comb-Type Copolymers on DNA Hybridization

2008 ◽  
Vol 47-50 ◽  
pp. 1355-1358
Author(s):  
Atsushi Maruyama ◽  
Long Liang Wu ◽  
Naohiko Shimada ◽  
Arihiro Kano
Keyword(s):  
Nucleic Acid ◽  
Dna Hybridization ◽  
Binding Proteins ◽  
Nucleic Acid Binding ◽  
Kinetic Effect ◽  
Dna Duplex ◽  
Interpolyelectrolyte Complexes ◽  
Nucleic Acid Binding Proteins ◽  
Duplex Formation

We have been interested in the soluble interpolyelectrolyte complexes (IPEC) between DNA and the cationic comb-type copolymers, poly(L-lysine)-graft-dextran (PLL-g-Dex), consisting of a polylysine backbone and abundant hydrophilic graft chains of dextran as a model of nucleic acid-binding proteins. In this paper, we described the kinetic effect of the copolymers on the DNA hybridization. We found that the cationic copolymer at nano molar concentrations in cationic groups accelerated DNA duplex formation by two orders under physiologically relevant conditions.

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