title: Identification of stable RNA hairpins causing band compression in transcriptional sequencing and their elimination by use of inosine triphosphate.
abstract: To identify stable RNA secondary structure causing band compression, 30 lambda DNA clones and four cDNA clones (about 10 kb in total length) were sequenced using Transcriptional Sequencing, which is based on the phage RNA polymerase chain termination reaction with fluorescent 3' deoxynucleoside triphosphate, using the canonical set of rNTPs for the substrate. Electrophoresis was performed on acrylamide gel containing 7 M urea at 50 degrees C using ABI 377 DNA sequencer. A total of 159 band compressions were identified, and most compression sites seem to be due to hairpin structures. We also found that the presence of rITP in place of rGTP in the sequencing reaction can entirely eliminate all band compressions. The use of rITP gave a better peak uniformity and resolution in the sequencing gel in the case of lambda DNA than with c7rGTP, leading to improved accuracy in the sequence determination. Substitution of the base analog rITP for rGTP should be useful for accurate sequencing determination.
authors.affiliation: Laboratory for Genome Exploration Research Project, Genomic Sciences Center (GSC) and Genome Science Laboratory, Tsukuba Life Science Center, The Institute of Physical and Chemical Research (RIKEN), 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japa.
authors.forename: N
authors.initials: N
authors.lastname: Sasaki
authors.forename: M
authors.initials: M
authors.lastname: Izawa
authors.forename: Y
authors.initials: Y
authors.lastname: Sugahara
authors.forename: T
authors.initials: T
authors.lastname: Tanaka
authors.forename: M
authors.initials: M
authors.lastname: Watahiki
authors.forename: K
authors.initials: K
authors.lastname: Ozawa
authors.forename: E
authors.initials: E
authors.lastname: Ohara
authors.forename: H
authors.initials: H
authors.lastname: Funaki
authors.forename: Y
authors.initials: Y
authors.lastname: Yoneda
authors.forename: S
authors.initials: S
authors.lastname: Matsuura
authors.forename: M
authors.initials: M
authors.lastname: Muramatsu
authors.forename: Y
authors.initials: Y
authors.lastname: Okazaki
authors.forename: Y
authors.initials: Y
authors.lastname: Hayashizaki
mesh_terms: D010582:Bacteriophage lambda / Q000235:genetics; D001483:Base Sequence; D018076:DNA, Complementary / Q000096:biosynthesis; D004279:DNA, Viral / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D006160:Guanosine Triphosphate / Q000378:metabolism; D007293:Inosine Triphosphate / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D017422:Sequence Analysis, DNA / Q000295:instrumentation / Q000379:methods*; D014158:Transcription, Genetic
chemical_list: D018076:DNA, Complementary; D004279:DNA, Viral; D007293:Inosine Triphosphate; D012313:RNA; D006160:Guanosine Triphosphate; D012321:DNA-Directed RNA Polymerases