Electromigration behavior of nucleic acids in capillary electrophoresis under pulsed-field conditions.
We have presented a study focused on the migration pattern of double-stranded DNA (dsDNA) and RNA under pulsed field conditions. By calculating the dependence of nucleic acid mobility on its molecular size in a double logarithm plot, we found that (I) dsDNA molecules proceeded by a sigmoidal migration regime which was probably related to Ogston sieving, transition regime, and reptation model. Furthermore, the transition regime disappeared if DNA was resolved in a higher molecular mass HEC. (II) The migration pattern of RNA was relevant to the denaturant used for separation. When RNA was denatured by acetic acid, its mobility parabolically declined with its molecular size. The mobility was linearly decreased with the molecular size if urea was employed as denaturant. (III) RNA may migrate by Ogston, reptation without orientation mechanism when denatured by urea, whereas these two models were not suitable for RNA if denatured by acetic acid. Even though the electrophoretic conditions of PFCE were varied, the sigmoidal, linear, parabolic migration patterns could still be observed. (IV) Under certain modulation depth, the migration time (Tm) of acetic acid decreased with the increase of average separation voltage (Va), and when RNA denatured in 4.0M urea, Tm showed a linear correlation with Va. (V) The mobility of nucleic acids increased with the growth of artificial temperature in the capillary volume due to the decrease in the viscosity of the polymer. This is the first systematic and comparative research of high molecular mass nucleic acids in PFCE, which provides us deep insight into RNA and DNA migration behavior under pulsed electric field conditions.
Engineering Research Center of Optical Instrument and System, Ministry of Education, Shanghai Key Lab of Modern Optical System, Univesity of Shanghai for Science and Technology, No. 516 Jungong Road, Shanghai 200093, China; Institute for Biomedical Engineering, Consolidated Research Institute for Advanced Science and Medical Care (ASMeW), Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan. Electronic address: zhenqingli@163.com.
Zhenqing
Z
Li
Engineering Research Center of Optical Instrument and System, Ministry of Education, Shanghai Key Lab of Modern Optical System, Univesity of Shanghai for Science and Technology, No. 516 Jungong Road, Shanghai 200093, China.
Chenchen
C
Liu
Engineering Research Center of Optical Instrument and System, Ministry of Education, Shanghai Key Lab of Modern Optical System, Univesity of Shanghai for Science and Technology, No. 516 Jungong Road, Shanghai 200093, China; Institute for Biomedical Engineering, Consolidated Research Institute for Advanced Science and Medical Care (ASMeW), Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan. Electronic address: xiaomingdou@yeah.net.
Xiaoming
X
Dou
Engineering Research Center of Optical Instrument and System, Ministry of Education, Shanghai Key Lab of Modern Optical System, Univesity of Shanghai for Science and Technology, No. 516 Jungong Road, Shanghai 200093, China.
Yi
Y
Ni
Engineering Research Center of Optical Instrument and System, Ministry of Education, Shanghai Key Lab of Modern Optical System, Univesity of Shanghai for Science and Technology, No. 516 Jungong Road, Shanghai 200093, China.
Jiaxuan
J
Wang
Photonics Advanced Research Center, Graduate School of Engineering, Osaka University, Yamadaoka Suita-city, Osaka 565-0871, Japan; Institute for Biomedical Engineering, Consolidated Research Institute for Advanced Science and Medical Care (ASMeW), Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan; Engineering Research Center of Optical Instrument and System, Ministry of Education, Shanghai Key Lab of Modern Optical System, Univesity of Shanghai for Science and Technology, No. 516 Jungong Road, Shanghai 200093, China.
Yoshinori
Y
Yamaguchi
D019342:Acetic Acid; D002482:Cellulose / Q000031:analogs & derivatives; D004247:DNA / Q000737:chemistry*; D019075:Electrophoresis, Capillary / Q000379:methods; D008970:Molecular Weight; D009691:Nucleic Acid Denaturation; D012313:RNA / Q000737:chemistry*; D014508:Urea; D014783:Viscosity
D012313:RNA; D014508:Urea; D002482:Cellulose; C002283:hydroxyethylcellulose; D004247:DNA; D019342:Acetic Acid
DNA/RNA/Pulsed field capillary electrophoresis/urea/acetic acid