Kinetic Property of Bulged Helix Formation:  Analysis of Kinetic Behavior Using Nearest-Neighbor Parameters

Ohmichi, Tatsuo; Nakamuta, Hiroyuki; Yasuda, and Kyohko; Sugimoto, Naoki

doi:10.1021/ja001779f

Cited by 30 publications

(25 citation statements)

References 49 publications

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“…For example, codon-anticodon duplex within ribosome is 2-3 base pair stretch of A-form helix 31 . In duplex formation of oligonucleotide, double helix zips up after formation of a nucleus composed of 2-3 hydrogen-bonded base pairs 32,33 . The present study confirmed that hybridization of short nucleotides could be controlled inside the TMAP-modified silica mesopore.…”

Section: Discussionmentioning

confidence: 99%

Trinucleotide duplex formation inside a confined nanospace under supercooled conditions

et al. 2014

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Self-assembly of nucleotides of fewer than three base pairs is often found in proteinnucleotide conjugations, despite their energetic instability, and is regarded as the potential starting point for the creation of artificial hydrogen-bonded supramolecular complexes. Here we report duplex formation of 3-mer DNA fragments confined within silica mesopores modified with a positively charged trimethyl aminopropyl monolayer, and their further stabilization under supercooled conditions (To273 K). We load 3-mer DNA fragments with donor-or acceptor-dye into modified silica mesopores and examine their hybridization behaviours using FRET measurements. The FRET results clearly reveal that efficient duplex formation through at least two A-T base pairs can be achieved at 233 K. Enthalpy changes for duplex formation are found to be nearly equal between complementary and single-mismatched 3-mer DNA duplexes. These results confirm confined mesoscale cavities to be a novel low-temperature reaction space for hydrogen-bonded supramolecular complexes.

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Section: Discussionmentioning

confidence: 99%

Trinucleotide duplex formation inside a confined nanospace under supercooled conditions

et al. 2014

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“…5, 14 -19 Clearly, the NN concept can be extended to similar molecules, for example DNA-RNA hybrid duplexes, 20 mismatches, [21][22][23][24][25] kinetic parameters for helix formation, 26 and RNA multi-branch loops. 27 A number of application packages exist that use literature values of parameters to simulate the melting behavior of any given DNA sequence.…”

Section: Discussionmentioning

confidence: 99%

“…35 Ohmichi et al examined the kinetics of the formation of bulged helices using a NN model. 26 Their UV melting experiments were conducted using 10-bp oligonucleotides in 1 M NaCl. The kinetics of their control oligonucleotide (no bulges) revealed a forward activation energy (helix formation) of Ϫ14 kJ/ mol and a reverse activation energy equal to 259 kJ/mol.…”

Section: Discussionmentioning

confidence: 99%

Volumetric properties of the formation of double stranded DNA: A nearest‐neighbor analysis

Dubins

Macgregor

2003

Biopolymers

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The kinetics of the helix-coil transition have been studied by performing UV-monitored melting and reannealing curves of DNA and analyzing the resultant hysteresis between these curves. The analysis assumes a single-step bimolecular transition with duplex formation defined as the forward reaction. Volume parameters of the helix-coil transition were obtained by measuring the pressure dependence of the rate constants from 5-200 MPa. The data were interpreted in terms of several possible nearest-neighbor models, ranging from one to eleven parameters. Twenty-four oligonucleotide duplexes 22 base pairs in length were used to solve for individual nearest-neighbor activation volumes and transition volumes. Statistically, the most valid fit of the volumetric data was obtained with a six-parameter model in which the directionality of the dinucleotide steps is not considered, for example, 5'AG/CT is the same as 5'GA/TC. The resultant transition volumes at 48 degrees C ranged from -7.1 +/- 0.8 mL/mol (GC/CG) to +2.9 +/- 0.3 mL/mol (AA/TT). The success of the six-parameter model suggests that the relative size of the nearest-neighbor dinucleotides is the most important factor determining the magnitude of the volumetric parameters. The finding that the magnitude of the volumetric parameters correlates with the change in the solvent accessible surface area of the bases during the helix-coil transition corroborates this hypothesis.

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“…The nearest neighbor model has been used to predict thermodynamic parameters of duplex (33,37,38) and energy profiles of helix formation (39), approximately. By assuming a DNA hybridization pathway involving formation of n base pairs between two single strands, the intermediate values for , and were predicted with nearest neighbor parameters (33) (at a condition of 10 mM Na + ).…”

Section: Methodsmentioning

confidence: 99%

Influence of secondary structure on kinetics and reaction mechanism of DNA hybridization

Chen

Wang

et al. 2007

Nucleic Acids Research

105

127

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Hybridization of nucleic acids with secondary structure is involved in many biological processes and technological applications. To gain more insight into its mechanism, we have investigated the kinetics of DNA hybridization/denaturation via fluorescence resonance energy transfer (FRET) on perfectly matched and single-base-mismatched DNA strands. DNA hybridization shows non-Arrhenius behavior. At high temperature, the apparent activation energies of DNA hybridization are negative and independent of secondary structure. In contrast, when temperature decreases, the apparent activation energies of DNA hybridization change to positive and become structure dependent. The large unfavorable enthalpy of secondary structure melting is compensated for by concomitant duplex formation. Based on our results, we propose a reaction mechanism about how the melting of secondary structure influences the hybridization process. A significant point in the mechanism is that the rate-limiting step switches along with temperature variation in the hybridization process of structured DNA, because the free energy profile of hybridization in structured DNA varies with the variation in temperature.

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Kinetic Property of Bulged Helix Formation: Analysis of Kinetic Behavior Using Nearest-Neighbor Parameters

Cited by 30 publications

References 49 publications

Trinucleotide duplex formation inside a confined nanospace under supercooled conditions

Trinucleotide duplex formation inside a confined nanospace under supercooled conditions

Volumetric properties of the formation of double stranded DNA: A nearest‐neighbor analysis

Influence of secondary structure on kinetics and reaction mechanism of DNA hybridization

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