title: Base sequence- and T m-dependent DNA oligomer separation by open tubular capillary columns carrying complementary DNA oligomers as probes.
abstract: DNA chips prepared on a flat glass surface have unavoidable drawbacks when used for quantitative analysis. In an attempt to overcome this problem, we constructed an HPLC-type system suitable for quantitative analysis that enables base sequence- and T (m)-dependent DNA oligomer separation in a flow system. A small open tubular capillary column (300-mm x 100-microm I.D.) was used. The DNA oligomers used as probes had an amino group at the 5'-end and were immobilized on the inner silica surface of the capillary column which had been sequentially treated with 3-aminopropyltriethoxysilane, butyltrimethoxysilane, and disuccinimidylglutarate. Using the combination of probe-immobilized column placed in a column oven equipped with temperature gradient function, a nano-flow-controllable pump, a small sample-loading injector, and a capillary-fitted UV detector, we succeeded in separating complementary and non-complementary DNA oligomers in specific and quantitative modes. We also designed a temperature gradient strategy for efficient separation of target DNA oligomers in DNA mixture samples. Using a column carrying two different probes with similar T (m) values, their complementary target DNA oligomers were also separated and detected. The developed DNA open tubular capillary column system investigated in the present study could be further improved as an alternative tool to DNA chips to be used for the quantitative analysis of DNA or mRNA samples.
authors: Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, Japan.
authors: Kamakshaiah Charyulu
authors: KC
authors: Devarayapalli
authors: Seung Pil
authors: SP
authors: Pack
authors: Nagendra Kumar
authors: NK
authors: Kamisetty
authors: Mitsuru
authors: M
authors: Nonogawa
authors: Seiya
authors: S
authors: Watanabe
authors: Tsutomu
authors: T
authors: Kodaki
authors: Keisuke
authors: K
authors: Makino
mesh_terms: D001483:Base Sequence; D015374:Biosensing Techniques; D002851:Chromatography, High Pressure Liquid / Q000295:instrumentation / Q000379:methods*; D004247:DNA / Q000737:chemistry / Q000302:isolation & purification*; D015342:DNA Probes / Q000032:analysis* / Q000737:chemistry; D011437:Propylamines; D012333:RNA, Messenger / Q000032:analysis / Q000737:chemistry; D012821:Silanes / Q000737:chemistry; D013388:Succinimides / Q000737:chemistry; D013499:Surface Properties; D013696:Temperature; D013997:Time Factors
chemical_list: D015342:DNA Probes; D011437:Propylamines; D012333:RNA, Messenger; D012821:Silanes; D013388:Succinimides; C096464:disuccinimidyl glutarate; D004247:DNA; C477625:amino-propyl-triethoxysilane; C071717:trimethoxysilane