Steric Crowding and the Kinetics of DNA Hybridization within a DNA Nanostructure System

ACS Nano ◽  
2012 ◽  
Vol 6 (6) ◽  
pp. 5521-5530 ◽  
Author(s):  
Andre V. Pinheiro ◽  
Jeanette Nangreave ◽  
Shuoxing Jiang ◽  
Hao Yan ◽  
Yan Liu
Keyword(s):  
Dna Hybridization ◽  
Dna Nanostructure ◽  
Steric Crowding ◽  
Kinetics Of

scholarly journals Real-time reliable determination of binding kinetics of DNA hybridization using a multi-channel graphene biosensor

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Shicai Xu ◽  
Jian Zhan ◽  
Baoyuan Man ◽  
Shouzhen Jiang ◽  
Weiwei Yue ◽  
...  
Keyword(s):  
Real Time ◽  
Dna Hybridization ◽  
Binding Kinetics ◽  
Reliable Determination ◽  
Kinetics Of

Kinetics of base stacking-aided DNA hybridization

2008 ◽  
pp. 6600 ◽  
Author(s):  
Bi-feng Yuan ◽  
Xing-ying Zhuang ◽  
Yu-hua Hao ◽  
Zheng Tan
Keyword(s):  
Dna Hybridization ◽  
Base Stacking ◽  
Kinetics Of

Kinetics of Diffusion-Mediated DNA Hybridization in Lipid Monolayer Films Determined by Single-Molecule Fluorescence Spectroscopy

ACS Nano ◽  
2012 ◽  
Vol 7 (1) ◽  
pp. 308-315 ◽  
Author(s):  
Jonas K. Hannestad ◽  
Ralf Brune ◽  
Ilja Czolkos ◽  
Aldo Jesorka ◽  
Afaf H. El-Sagheer ◽  
...  
Keyword(s):  
Fluorescence Spectroscopy ◽  
Single Molecule ◽  
Dna Hybridization ◽  
Lipid Monolayer ◽  
Single Molecule Fluorescence ◽  
Monolayer Films ◽  
Single Molecule Fluorescence Spectroscopy ◽  
Kinetics Of

Labilization by steric crowding. Hydrolysis and racemization kinetics of Co(tmen)33+, tmen = 2,3-diamino-2,3-dimethylbutane

1990 ◽  
Vol 175 (1) ◽  
pp. 83-89 ◽  
Author(s):  
Hussam Diab ◽  
Philip Hendry ◽  
Andreas Ludi ◽  
Kedika Bal Reddy ◽  
Rudi van Eldik
Keyword(s):  
Steric Crowding ◽  
Kinetics Of

scholarly journals Predicting DNA Hybridization Kinetics from Sequence

2017 ◽  
Author(s):  
Jinny X. Zhang ◽  
John Z. Fang ◽  
Wei Duan ◽  
Lucia R. Wu ◽  
Angela W. Zhang ◽  
...  
Keyword(s):  
Rate Constants ◽  
Dna Hybridization ◽  
Sequence Information ◽  
Efficient Design ◽  
Nucleic Acid Probes ◽  
Hybridization Rate ◽  
Predictive Understanding ◽  
Leave One Out ◽  
Kinetics Of ◽  
Unknown Sequence

Hybridization is a key molecular process in biology and biotechnology, but to date there is no predictive model for accurately determining hybridization rate constants based on sequence information. To approach this problem systematically, we first performed 210 fluorescence kinetics experiments to observe the hybridization kinetics of 100 different DNA target and probe pairs (subsequences of the CYCS and VEGF genes) at temperatures ranging from 28 °C to 55 °C. Next, we rationally designed 38 features computable based on sequence, each feature individually correlated with hybridization kinetics. These features are used in our implementation of a weighted neighbor voting (WNV) algorithm, in which the hybridization rate constant of an unknown sequence is predicted based on similarity reactions with known rate constants (a.k.a. labeled instances). Automated feature selection and weighting optimization resulted in a final 6-feature WNV model, which can predict hybridization rate constants of new sequences to within a factor of 2 with ≈74% accuracy and within a factor of 3 with ≈92% accuracy, based on leave-one-out cross-validation. Predictive understanding of hybridization kinetics allows more efficient design of nucleic acid probes, for example in allowing sparse hybrid-capture panels to more quickly and economically enrich desired regions from genomic DNA.

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