Thermodynamic dependence of DNA/DNA and DNA/RNA hybridization reactions on temperature and ionic strength

Lang, Brian E.; Schwarz, Frederick P.

doi:10.1016/j.bpc.2007.09.007

Cited by 36 publications

(39 citation statements)

References 20 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…50 As the salt concentration is further increased, the Debye-Hückel model is no longer valid, a transition to a different behavior occurs owing to steric effects and the rate increase becomes more moderate. These results are consistent with measurements by Owczarzy et al, 51 and Lang et al 52 Figure 4c presents fluorescence images of end-point results at different ionic strengths. At high ionic strength of 1 M NaCl, we observe a relatively high level of off-target signal in the nucleus.…”

Section: Ionic Strengthsupporting

confidence: 92%

Real-Time Monitoring of Fluorescence in Situ Hybridization Kinetics

et al. 2018

View full text Add to dashboard Cite

We present a novel method for real-time monitoring and kinetic analysis of fluorescence in situ hybridization (FISH). We implement the method using a vertical microfluidic probe containing a microstructure designed for rapid switching between probe solution and nonfluorescent imaging buffer. The FISH signal is monitored in real time during the imaging buffer wash, during which signal associated with unbound probes is removed. We provide a theoretical description of the method as well as a demonstration of its applicability using a model system of centromeric probes (Cen17). We demonstrate the applicability of the method for characterization of FISH kinetics under conditions of varying probe concentration, destabilizing agent (formamide) content, volume exclusion agent (dextran sulfate) content, and ionic strength. We show that our method can be used to investigate the effect of each of these variables and provide insight into processes affecting in situ hybridization, facilitating the design of new assays.

show abstract

Section: Ionic Strengthsupporting

confidence: 92%

Real-Time Monitoring of Fluorescence in Situ Hybridization Kinetics

et al. 2018

View full text Add to dashboard Cite

show abstract

“…Ionic strength is known to affect DNA hybridization [34]. As cations can reduce charge repulsion between the negatively charged phosphodiester backbones of double stranded DNA, we sought to investigate the assembly efficiency in relation to the concentrations of MgCl 2 or NaCl.…”

Section: Resultsmentioning

confidence: 99%

Combinatorial Engineering of 1-Deoxy-D-Xylulose 5-Phosphate Pathway Using Cross-Lapping In Vitro Assembly (CLIVA) Method

et al. 2013

View full text Add to dashboard Cite

The ability to assemble multiple fragments of DNA into a plasmid in a single step is invaluable to studies in metabolic engineering and synthetic biology. Using phosphorothioate chemistry for high efficiency and site specific cleavage of sequences, a novel ligase independent cloning method (cross-lapping in vitro assembly, CLIVA) was systematically and rationally optimized in E. coli. A series of 16 constructs combinatorially expressing genes encoding enzymes in the 1-deoxy-D-xylulose 5-phosphate (DXP) pathway were assembled using multiple DNA modules. A plasmid (21.6 kb) containing 16 pathway genes, was successfully assembled from 7 modules with high efficiency (2.0 x 103 cfu/ µg input DNA) within 2 days. Overexpressions of these constructs revealed the unanticipated inhibitory effects of certain combinations of genes on the production of amorphadiene. Interestingly, the inhibitory effects were correlated to the increase in the accumulation of intracellular methylerythritol cyclodiphosphate (MEC), an intermediate metabolite in the DXP pathway. The overexpression of the iron sulfur cluster operon was found to modestly increase the production of amorphadiene. This study demonstrated the utility of CLIVA in the assembly of multiple fragments of DNA into a plasmid which enabled the rapid exploration of biological pathways.

show abstract

“…The melting temperatures (T m ) of unmodified, short DNA duplexes have been well-characterized and a thermodynamic model exists for their prediction over a range of environmental conditions (18)(19)(20)(21)(22)(23)(24)(25)(26)(27). It has also been found that the modification of DNA strands with ''dangling ends'' of small molecules, such as fluorophores and quenchers, can increase T m by up to 4.3 C (20).…”

Section: Introductionmentioning

confidence: 99%

DNA as Membrane-Bound Ligand-Receptor Pairs: Duplex Stability Is Tuned by Intermembrane Forces

Beales

Vanderlick

2009

Biophysical Journal

View full text Add to dashboard Cite

We use membrane-anchored DNA as model adhesion receptors between lipid vesicles. By studying the thermal stability of DNA duplex formation, which tethers the vesicles into superstructures, we show that the melting temperature of a 10-base DNA sequence is dependent on the lipid composition of the tethered vesicles. We propose a simple model that describes how the intermembrane interactions tilt the free energy landscape for DNA binding. From our model, we estimate the area per DNA in the binding sites between vesicles and also the total area of the adhesion plaques. We find that vesicles containing a small proportion of cationic lipid that are modified with membrane-anchored DNA can be reversibly tethered by specific DNA interactions and that the DNA also induces a small attraction between these membranes, which stabilizes the DNA duplex. By increasing the equilibrium intermembrane distance on binding, we show that intermembrane interactions become negligible for the binding thermodynamics of the DNA and hence the thermal stability of vesicle aggregates becomes independent of lipid composition at large enough intervesicle separations. We discuss the implications of our findings with regards to cell adhesion and fusion receptors, and the programmable self-assembly of nano-structured materials by DNA hybridization.

show abstract

Thermodynamic dependence of DNA/DNA and DNA/RNA hybridization reactions on temperature and ionic strength

Cited by 36 publications

References 20 publications

Real-Time Monitoring of Fluorescence in Situ Hybridization Kinetics

Real-Time Monitoring of Fluorescence in Situ Hybridization Kinetics

Combinatorial Engineering of 1-Deoxy-D-Xylulose 5-Phosphate Pathway Using Cross-Lapping In Vitro Assembly (CLIVA) Method

DNA as Membrane-Bound Ligand-Receptor Pairs: Duplex Stability Is Tuned by Intermembrane Forces

Contact Info

Product

Resources

About