Modeling Stopped-Flow Data for Nucleic Acid Duplex Formation Reactions: The Importance of Off-Path Intermediates

2013 ◽  
Vol 117 (30) ◽  
pp. 8966-8976 ◽  
Author(s):  
Jacqueline R. Sikora ◽  
Brittany Rauzan ◽  
Rachel Stegemann ◽  
Alice Deckert
Keyword(s):  
Nucleic Acid ◽  
Stopped Flow ◽  
Flow Data ◽  
Duplex Formation

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.

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.

On-line computer processing of stopped-flow data

1970 ◽  
Vol 42 (12) ◽  
pp. 1340-1349 ◽  
Author(s):  
Barry G. Willis ◽  
John A. Bittikofer ◽  
Harry L. Pardue ◽  
Dale W. Margerum
Keyword(s):  
Computer Processing ◽  
Stopped Flow ◽  
Flow Data ◽  
On Line

On the Sensitivity of Peptide Nucleic Acid Duplex Formation and Crystal Dissolution to a Variation of Force-Field Parameters

2013 ◽  
Vol 10 (1) ◽  
pp. 391-400 ◽  
Author(s):  
Stephan J. Bachmann ◽  
Zhixiong Lin ◽  
Thorsten Stafforst ◽  
Wilfred F. van Gunsteren ◽  
Jožica Dolenc
Keyword(s):  
Nucleic Acid ◽  
Force Field ◽  
Peptide Nucleic Acid ◽  
Crystal Dissolution ◽  
Force Field Parameters ◽  
Duplex Formation

scholarly journals Evaluating the Effect of Ionic Strength on PNA:DNA Duplex Formation Kinetics

2021 ◽  
Author(s):  
Colin Swenson ◽  
Hershel H Lackey ◽  
Eric James Reece ◽  
Joel M. Harris ◽  
Jennifer Heemstra ◽  
...  
Keyword(s):  
Ionic Strength ◽  
Nucleic Acid ◽  
Peptide Nucleic Acid ◽  
Biological Applications ◽  
Base Pairing ◽  
Formation Kinetics ◽  
Acid Analog ◽  
Duplex Formation

Peptide nucleic acid (PNA) is a unique synthetic nucleic acid analog that has been adopted for use in many biological applications. These applications rely upon the robust Franklin-Watson-Crick base pairing...

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