title: DMSO resolves certain compressions and signal dropouts in fluorescent dye labeled primer-based DNA sequencing reactions.
abstract: Automated base calling algorithms are more sensitive to the quality of the DNA sequencing data than are the labor intensive visual methods of base calling. To improve this quality, data from DNA sequencing reactions have been compared in order to determine the effects of the inclusion of dimethyl sulfoxide (DMSO). Inclusion of 10% DMSO into the reaction cocktail resolves at least one type of sequence compression. This compression may be due to the lack of ability in T7 DNA polymerase to read through certain sequences correctly. The poor quality of these data is seen as radioactive bands or fluorescent signal peaks that have an abnormal alignment, either in the wrong order or as single bands/peaks. The inclusion of DMSO also resolves sequences where the peak signal is absent or severely diminished, leading to a "gap" in the chromatogram profile. DMSO is better than deaza-dITP for resolving certain compressions. Addition of DMSO is a cheaper and more efficient method for high-throughput DNA sequencing than repeating reactions with base analogs.
authors.affiliation: Division of Biology (147-75), California Institute of Technology, Pasadena 91125, USA.
authors.forename: D
authors.initials: D
authors.lastname: Seto
authors.forename: J
authors.initials: J
authors.lastname: Seto
authors.forename: P
authors.initials: P
authors.lastname: Deshpande
authors.forename: L
authors.initials: L
authors.lastname: Hood
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D017931:DNA Primers / Q000737:chemistry*; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry; D004121:Dimethyl Sulfoxide / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry*; D006801:Humans; D007293:Inosine Triphosphate / Q000031:analogs & derivatives / Q000378:metabolism; D008969:Molecular Sequence Data; D011755:Pyrophosphatases / Q000737:chemistry; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D017931:DNA Primers; D005456:Fluorescent Dyes; D016693:Receptors, Antigen, T-Cell, alpha-beta; D007293:Inosine Triphosphate; C072875:7-deaza-2'-deoxyinosine triphosphate; C034970:bacteriophage T7 induced DNA polymerase; D004259:DNA-Directed DNA Polymerase; D011755:Pyrophosphatases; D004121:Dimethyl Sulfoxide