Chinh T. Bui

Permanganate Oxidation Reactions of DNA: Perspective in Biological Studies

Abstract KMnO4 has been well known as a powerful chemical probe for numerous applications in biological fields, particularly for those used in conformational studies of DNA. The KMnO4 assay provides essential information for understanding biochemical processes and detecting aberrant DNA, which is associated with many genetic diseases. Elegant examples are sequencing techniques, foot-printing assays for transcriptional studies, an interference method for hormone receptor binding assays as well as DNA conformational studies of Z-DNA, Z-Z junctions, hairpins, curvatures, short nucleotide base repeats, binding of intercalators and groove binders, etc. Recently, KMnO4 has been successfully applied to detect single base changes and mutations in DNA (chemical cleavage of mismatch method, CCM) as well as other types of base damage (8-oxoguanine and thymine dimers). This paper aims to review the usefulness and limitations of the permanganate oxidation reaction used in various biological studies of DNA.

Site-selective reactions of imperfectly matched DNA with small chemical molecules: applications in mutation detection

The last decade has witnessed many exciting scientific publications associated with site-selective reactions of small chemical molecules with imperfectly matched DNA. Typical examples are carbodiimide, hydroxylamine, potassium permanganate, osmium tetroxide, chemical tagging probes, biotinylated, chemiluminescent and fluorescent probes, and all of them selectively react with imperfectly matched DNA. More recently, some therapeutic agents including DNA intercalating drugs and groove binders have been found to promote the in vivo repair system to recognize and repair the mismatch more effectively. The results have established a novel method for detection of mismatches. Development of new chemical reactions for detection of imperfectly matched DNA and mutations is a rapidly growing field and has attracted significant interest of scientists from both chemical and biological fields and it is the main focus of this review.

Solid phase synthesis of C-terminal peptide amides: development of a new aminoethyl-polystyrene linker on the Multipin solid support.

A new aminoethyl‐polystyrene linker, stable at low concentrations of TFA, has been developed for the solid phase synthesis of peptide amides. The described linker is stable under conditions which remove But protecting groups (30–50% TFA in DCM) and the desired product can be finally cleaved off the solid support in 95% TFA (5% H2O). Model peptide amides and other N‐alkylated peptide amides have been successfully synthesized in good yield and purity. Copyright

Novel α-hydroxyethyl-polystyrene, α-chloroethyl-polystyrene and α-amino-oxyethyl-polystyrene linkers on the multipin™ solid support for solid-phase organic synthesis

A simple method for the generation of three novel linkers, α-hydroxyethyl-polystyrene, α-chloroethyl-polystyrene and α-amino-oxyethyl-polystyrene on Multipin supports (SynPhase™ Crowns) has been developed. Applications of these linkers have been successfully demonstrated for solid-phase synthesis of dipeptide, oxime, and hydroxamic acid compounds in good yields and purities.

Chapter 3 – Enzymatic and Chemical Cleavage Methods to Identify Genetic Variation

Publisher Summary This chapter discusses two high sensitivity mutation detection methods to identify genetic variation: chemical and enzymatic cleavage of mismatch. Although there are several methods for high sensitivity detection of known mutations, unknown mutations are more difficult to uncover. However, methods for the latter have improved significantly and are utilized in practical applications. These include the establishment of a single nucleotide polymorphism (SNP) map for a specific part of the genome in a specific animal population or the screening for unknown mutations in important genes, such as cancer susceptibility genes. These genes are large, with many exons, and thus hundreds of possible mutations that affect the functions of those proteins are found. The mutation detection methods serve as tools for reverse genetics to screen for chemically induced point mutations in specific regions of specific genes and for specific mutations in the genome of emerging pathogenic microorganisms. In mutation screening methods, the mutated DNA helix is first converted to mismatch heteroduplexes when the polymerase chain reaction products of two alleles of the gene of interest are amplified, mixed, denatured, and rehybridized. Next, the chemical or enzymatic properties of a mismatched base are exploited to lead to a break in the DNA strand near the mismatch. Finally, a suitable fragment analysis method is used to visualize the shortened DNA fragments that are produced by the DNA break in either single-stranded or double-stranded form.

Enzymatic and Chemical Cleavage Methods to Identify Genetic Variation

Publisher Summary This chapter discusses two high sensitivity mutation detection methods to identify genetic variation: chemical and enzymatic cleavage of mismatch. Although there are several methods for high sensitivity detection of known mutations, unknown mutations are more difficult to uncover. However, methods for the latter have improved significantly and are utilized in practical applications. These include the establishment of a single nucleotide polymorphism (SNP) map for a specific part of the genome in a specific animal population or the screening for unknown mutations in important genes, such as cancer susceptibility genes. These genes are large, with many exons, and thus hundreds of possible mutations that affect the functions of those proteins are found. The mutation detection methods serve as tools for reverse genetics to screen for chemically induced point mutations in specific regions of specific genes and for specific mutations in the genome of emerging pathogenic microorganisms. In mutation screening methods, the mutated DNA helix is first converted to mismatch heteroduplexes when the polymerase chain reaction products of two alleles of the gene of interest are amplified, mixed, denatured, and rehybridized. Next, the chemical or enzymatic properties of a mismatched base are exploited to lead to a break in the DNA strand near the mismatch. Finally, a suitable fragment analysis method is used to visualize the shortened DNA fragments that are produced by the DNA break in either single-stranded or double-stranded form.