title: DNA melting analysis: application of the "open tube" format for detection of mutant KRAS.
abstract: High-resolution melting (HRM) analysis is a very effective method for genotyping and mutation scanning that is usually performed just after PCR amplification (the "closed tube" format). Though simple and convenient, the closed tube format makes the HRM dependent on the PCR mix, not generally optimal for DNA melting analysis. Here, the "open tube" format, namely the post-PCR optimization procedure (amplicon shortening and solution chemistry modification), is proposed. As a result, mutation scanning of short amplicons becomes feasible on a standard real-time PCR instrument (not primarily designed for HRM) using SYBR Green I. This approach has allowed us to considerably enhance the sensitivity of detecting mutant KRAS using both low- and high-resolution systems (the Bio-Rad iQ5-SYBR Green I and Bio-Rad CFX96-EvaGreen, respectively). The open tube format, though more laborious than the closed tube one, can be used in situations when maximal sensitivity of the method is needed. It also permits standardization of DNA melting experiments and the introduction of instruments of a "lower level" into the range of those suitable for mutation scanning.
authors: Blokhin Russian Cancer Research Center, Russian Academy of Medical Sciences, Kashirskoe Shosse 24, 115478 Moscow, Russia.
authors: Irina V
authors: IV
authors: Botezatu
authors: Valentina N
authors: VN
authors: Kondratova
authors: Valery P
authors: VP
authors: Shelepov
authors: Anatoly V
authors: AV
authors: Lichtenstein
mesh_terms: D020137:Base Pair Mismatch / Q000187:drug effects / Q000235:genetics; D052160:Benzothiazoles; D003959:Diamines; D006863:Hydrogen-Ion Concentration / Q000187:drug effects; D009154:Mutation / Q000235:genetics*; D009691:Nucleic Acid Denaturation / Q000187:drug effects / Q000235:genetics*; D009930:Organic Chemicals / Q000378:metabolism; D009994:Osmolar Concentration; D016133:Polymerase Chain Reaction / Q000295:instrumentation* / Q000379:methods*; D011804:Quinolines; D012965:Sodium Chloride / Q000494:pharmacology; D018631:ras Proteins / Q000235:genetics*
chemical_list: D052160:Benzothiazoles; D003959:Diamines; D009930:Organic Chemicals; D011804:Quinolines; C098022:SYBR Green I; D012965:Sodium Chloride; D018631:ras Proteins