Activation energy of single-stranded DNA moving through cross-linked polyacrylamide gels at 300 V/cm. Effect of temperature on sequencing rate in high-electric-field capillary gel electrophoresis.
In DNA sequencing, single-stranded DNA fragments are separated by gel electrophoresis. This separation is based on a sieving mechanism where DNA fragments are retarded as they pass through pores in the gel. In this paper, we present the mobility of DNA sequencing fragments as a function of temperature; mobility is determined in 4% T LongRanger gels at an electric field of 300 V/cm. The temperature dependence is compared with the predictions of the biased reptation model. The model predicts that the fragment length for the onset of biased reptation with stretching increases with the square of temperature; the data show that the onset of biased reptation with stretching decreases with temperature. Biased reptation fails to model accurately the temperature dependence of mobility. We analyzed the data and extracted the activation energy for passage of sequencing fragments through the gel. For fragments containing less than ca. 200 bases, the activation energy increases linearly with the number of bases at a rate of 25 J/mol per base; for longer fragments, the activation energy increases at a rate of 6.5 J/mol per base. This transition in the activation energy presumably reflects a change in conformation of the DNA fragments; small fragments exist in a random coil configuration and larger fragments migrate in an elongated configuration.
Lu
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Department of Chemistry, University of Alberta, Edmonton, Canada.
Arriaga
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E
Chen
D Y
DY
Figeys
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D
Dovichi
N J
NJ
D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003432:Cross-Linking Reagents; D004247:DNA / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry; D003838:Deoxyadenine Nucleotides / Q000737:chemistry; D054306:Dideoxynucleotides; D004563:Electrochemistry; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods*; D009690:Nucleic Acid Conformation; D017422:Sequence Analysis, DNA / Q000379:methods*; D013696:Temperature; D013816:Thermodynamics; D013942:Thymine Nucleotides / Q000737:chemistry
D003432:Cross-Linking Reagents; D004277:DNA, Single-Stranded; D003838:Deoxyadenine Nucleotides; D054306:Dideoxynucleotides; D013942:Thymine Nucleotides; C037773:2',3'-dideoxyadenosine triphosphate; D004247:DNA; C017216:2',3'-dideoxythymidine triphosphate