Document Detail


Free-solution oligonucleotide separation in nanoscale channels.
MedLine Citation:
PMID:  17883279     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
In this paper, we report an experimental study of electrokinetic transport and separation of double-stranded deoxyribonucleic acid (dsDNA) oligonucleotides in custom-fabricated fused-silica nanochannels filled with a gel-free sodium borate aqueous buffer. Mixtures of fluorescently labeled dsDNA molecules in the range of 10-100 base pair (bp), fluorescein, and fluorescein-12-UTP (UTP) were separated in less than 120 s in channels of depth ranging from 40 to 1560 nm. We varied the channel depth and background buffer concentration to achieve a 0.006-0.2 range of Debye length-to-channel-half-depth ratio (lambdaD/h), and a 0.004-1.7 range of the ratio of length of dsDNA molecule to channel half-depth (l/h). We find observed oligonucleotide migration times depend on both l/h and lambdaD/h. Electrophoretic mobility estimates agree well with published (micrometer-scale channel) values for background electrolyte (BGE) concentrations greater than approximately 10 mM. At BGE concentrations of 1 and 5 mM, mobility estimates in our nanochannels are higher than published values. Of the cases studied, the highest separation sensitivities were achieved in 100 nm channels with 1-10 mM ion density buffers. Potential applications of this technology include rapid small-scale sequencing and other fluorescence-based oligonucleotide separation and detection assays.
Authors:
Sumita Pennathur; Fabio Baldessari; Juan G Santiago; Michael G Kattah; Jonathan B Steinman; Paul J Utz
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.     Date:  2007-09-21
Journal Detail:
Title:  Analytical chemistry     Volume:  79     ISSN:  0003-2700     ISO Abbreviation:  Anal. Chem.     Publication Date:  2007 Nov 
Date Detail:
Created Date:  2007-10-31     Completed Date:  2007-12-21     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  0370536     Medline TA:  Anal Chem     Country:  United States    
Other Details:
Languages:  eng     Pagination:  8316-22     Citation Subset:  IM    
Affiliation:
Mechanical Engineering Department, Stanford University, Stanford, California 94305, USA.
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MeSH Terms
Descriptor/Qualifier:
Borates / chemistry
DNA / analysis*
Microfluidics* / instrumentation,  methods
Nanotechnology* / instrumentation,  methods
Oligonucleotides / analysis*
Reproducibility of Results
Sensitivity and Specificity
Silicon Dioxide / chemistry*
Time Factors
Water / chemistry
Grant Support
ID/Acronym/Agency:
N01-HV-28183/HV/NHLBI NIH HHS
Chemical
Reg. No./Substance:
0/Borates; 0/Oligonucleotides; 1330-43-4/sodium borate; 7631-86-9/Silicon Dioxide; 7732-18-5/Water; 9007-49-2/DNA

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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