Rapid DNA mutation identification and fingerprinting using base excision sequence scanning

Abstract

Base excision sequence scanning (BESS) is a new polymerase chain reaction (PCR)-based mutation scanning method that locates and identifies all DNA mutations. The BESS method consists of two procedures that generate "T" (BESS T-Scan) and "G" ladders (BESS G-Tracker) analogous to T and G ladders of dideoxy sequencing. The BESS procedures are simple to perform and require no special equipment or gels, no reaction optimization beyond PCR, and no heteroduplex formation. The samples are analyzed on standard sequencing gels or on automated DNA sequencers, and the data produced are easy to interpret, requiring a simple comparison of the sequence of normal and mutant DNA. The BESS method is versatile, having applications not only for mutation detection, but also single nucleotide polymorphism (SNP) discovery and analysis, DNA fingerprinting (including viral and bacterial typing), and clone identification. In this study, we utilize BESS in two of these applications: detection of a point mutation in BRCA1, and DNA typing of human papilloma virus (HPV).

A study of association between genetic markers in candidate genes and reproductive traits in one generation of a commercial broiler breeder hen population

“…Detection of polymorphisms The majority of polymorphism detection was carried out by Base Excision Sequence Scanning (T-Scan, Epicentre Technologies; Cambio Ltd, Cambridge, UK) (Hawkins and Hoffman, 1999) and the remainder by bulk amplified restriction fragment length polymorphism detection. Detection was carried out on 30 sires from the pedigree dam line.…”

A Novel and Rapid PCR-Based Method for Genotyping Human Papillomaviruses in Clinical Samples

“…As discussed above, verification of the genotype can be provided by BESS-T Base Reader Kit analysis of other regions of the papillomavirus genomes for which there exist degenerate oligonucleotide pairs that permit detection of multiple genotypes. Alternatively, one can perform BESS-T Base Reader Kit analysis of the same region but analyze the opposite strand (i.e., by end labeling the other oligonucleotide, e.g., GP6 ϩ in this study) or use the BESS-G Base Reader Kit, a similar methodology that allows one to establish the G-residue pattern in a given sequence (10). These extensions of the basic methodology described in this study could increase the precision of this genotyping approach where necessary.…”

“…The banding patterns were visualized with a PhosphorImager (Molecular Dynamics) and by radiography. Fluorescently labeled samples were run on an ABI 310 automated sequencer and analyzed with GeneScan software (10).…”

DNA Differential Diagnosis of Human Taeniid Cestodes by Base Excision Sequence Scanning Thymine-Base Reader Analysis with Mitochondrial Genes

“…This system originally was developed for the identification of genetic variations (10,11) and then was applied to virus isolates (3) and tumor suppressor genes (2). It detects mutations by incorporating limiting amounts of dUTP into a PCR product, resulting in the removal of the uracil base and cleavage of the phosphodiester bond at these abasic sites to produce a DNA ladder virtually identical to a thymine (T) sequencing ladder.…”