Harnessing DNA intercalation

Numerous small molecules are known to bind to DNA through base pair intercalation. Fluorescent dyes commonly used for nucleic acid staining, such as ethidium, are familiar examples. Biological and physical studies of DNA intercalation have historically been motivated by mutation and drug discovery research. However, this same mode of binding is now being harnessed for the creation of novel molecular assemblies. Recent studies have used DNA scaffolds and intercalators to construct supramolecular assemblies that function as fluorescent 'nanotags' for cell labeling. Other studies have demonstrated how intercalators can be used to promote the formation of otherwise unstable nucleic acid assemblies. These applications illustrate how intercalators can be used to facilitate and expand DNA-based nanotechnology.


Modeling and simulation of metabolic networks for estimation of biomass accumulation parameters
Kaplan, U.; TÜRKAY, METİN; Biegler, L.; Karasözen, Bülent (2009-05-28)
Metabolic networks are defined as the collection of biochemical reactions within a cell that define the functions of that cell. Due to the growing need to understand the functions of biological organisms for industrial and medical purposes, modeling and simulation of metabolic networks has attracted a lot of attention recently. Traditionally, metabolic networks are modeled such as flux-balance analysis that considers the steady state nature of the cell. However, it is important to consider the dynamic behav...
Comparison of conventional and collapsed region operation of capacitive micromachined ultrasonic transducers
Huang, Yongli; Haeggstrom, Edward; Bayram, Barış; Zhuang, Xuefeng; Ergun, Arif Sanh; Cheng, Ching-Hsiang; Khuri-Yakub, Butrus T. (2006-10-01)
We report experimental results from a comparative study on collapsed region and conventional region operation of capacitive micromachined ultrasonic transducers (CMUTs) fabricated with a wafer bonding technique. Using ultrasonic pulse-echo and pitch-catch measurements, we characterized single elements of 1-D CMUT arrays operating in oil. The experimental results from this study agreed with the simulation results: a CMUT operating in the collapsed region produced a higher maximum output pressure than a CMUT ...
Development and characterization of layered Li(NixMnyCo1-x-y)O-2 cathode materials for lithium ion batteries
Piskin, Berke; Aydınol, Mehmet Kadri (Elsevier BV, 2016-06-22)
The structure of the layered Li(NixMnyCo1-x-y)O-2 in different amounts of x and y ranging between 0.2 and 0.6, have been synthesized and investigated by powder X-ray diffraction and electron microscopy techniques. In the current work spray pyrolysis was used to obtain spherical fine-sized morphology followed by heat treatment to obtain better electrochemical activity. The precursor powders were prepared using aqueous solution via spray pyrolysis. Synthesized samples were then heat treated at 850 degrees C. ...
Applications of terahertz spectroscopy in biosystems
Plusquellic, David F.; SİEGRİST, Karen; Heilweil, Edwin J.; Esentürk, Okan (Wiley, 2007-12-03)
Terahertz (THz) spectroscopic investigations of condensed-phase biological samples are reviewed ranging from the simple crystalline forms of amino acids, carbohydrates and polypeptides to the more complex aqueous forms of small proteins, DNA and RNA. Vibrationally resolved studies of crystalline samples have revealed the exquisite sensitivity of THz modes to crystalline order, temperature, conformational form, peptide sequence and local solvate environment and have given unprecedented measures of the bindin...
ODYSSEY: a tool for microRNA-mRNA expression and interaction visualization
Taciroğlu, Alperen; Acar, Aybar Can; Konu Karakayalı, Özlen; Department of Bioinformatics (2018)
MicroRNAs (miRNAs) are non-coding short RNA molecules that are found in all metazoa studied so far. When distinct metazoa genomes considered up to 200 genes encode for unique miRNAs that show variability between species. Regulatory functions of miRNAs have been studied for 20 years starting after their discovery. The research suggests that they are involved in a wide spectrum of biological activities including apoptosis, tumorigenesis, development, homeostasis and viral infections. miRNAs regulate these cel...
Citation Formats
Ö. Persil Çetinkol, “Harnessing DNA intercalation,” TRENDS IN BIOTECHNOLOGY, pp. 433–436, 2007, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/46321.