Comparison of RNA, single-stranded DNA and double-stranded DNA behavior during capillary electrophoresis in semidilute polymer solutions.
We present a study of the separation of RNA, single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) in semidilute linear hydroxyethylcellulose (HEC) solution. Our results strive to provide a better understanding of the mechanisms of nucleic acid migration during electrophoresis in polymer solutions under native and denaturing conditions. From a study of the dependence of mobility on chain length and applied electric field, we found that RNA and ssDNA show better separation and higher resolution over a larger range of sizes compared to dsDNA. In addition, RNA reptation without orientation extends to longer chain lengths in comparison to ssDNA, possibly as a result of different type of short-lived secondary structure formations. Such a comparative study between nucleic acid capillary electrophoresis helps to optimize RNA separation and provides better understanding of RNA migration mechanisms in semidilute polymer solutions under denaturing conditions.
Todorov
Todor I
TI
Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
Morris
Michael D
MD
D004247:DNA / Q000737:chemistry* / Q000302:isolation & purification; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000302:isolation & purification; D019075:Electrophoresis, Capillary / Q000379:methods*; D011108:Polymers; D012996:Solutions; D014508:Urea / Q000737:chemistry
D004277:DNA, Single-Stranded; D011108:Polymers; D012996:Solutions; D014508:Urea; D004247:DNA