The thermodynamics of DNA structural motifs.

By J. SantaLucia, D. Hicks. Annual Review of Biophysics and Biomolecular Structure, 2004

1,268 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/9e484b59ffc51f70df56579aabeb2079dd822d77

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Citations in the corpus

ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis (2011, methodology): “N is the total number of phosphates in the duplex, R is the universal gas constant, C is the total DNA concentration from (30) and Nais the concentration of salt cations.”
Stability and kinetics of G-quadruplex structures (2008, methodology): “For oligomers of 19–20 bp long, the nearest neighbor parameters of SantaLucia (127,248,249) can be used to estimate the G of the duplex at equimolar strand concentrations of 0.25 mM.”
Enhancements and modifications of primer design program Primer3 (2007, background): “Improved sets of thermodynamic parameters and improved formulae are now available (Owczarzy et al., 1998; Panjkovich et al., 2005; SantaLucia, 1998; SantaLucia et al., 2004).”
ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases (2010, methodology): “Tm was calculated in ecoPCR based on a thermodynamic nearest neighbor model [26].”
NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure (2009, methodology): “Parameters for DNA have also been assembled for predicting Watson– Crick pair free energy and enthalpy change and free energy changes of loops (6,7).”
Primer3—new capabilities and interfaces (2012, background): “The relevant parameters are taken from the following: (13–20).”
ViennaRNA Package 2.0 (2011, methodology): “Here we provide a parameter set compiled by Douglas Turner and David Math-ews [67] from published data, incorporating in particular earlier work by the group of John SantaLucia [68].”
Dynamic DNA nanotechnology using strand-displacement reactions. (2011, background): “957--> The thermodynamics of DNA hybridization have been carefully characterized within the past few decade”
Programming an in vitro DNA oscillator using a molecular networking strategy (2011, positive): “DNA strands, with their predictable base pairing, together with computable thermodynamic (Santalucia and Hicks, 2004) and kinetic (Zhang and Winfree, 2009) features enable unambiguous encoding at the molecular level.”