[4] Use of denaturing gradient gel electrophoresis to study conformational transitions in nucleic acids

Comparative analysis of denaturing gradient gel electrophoresis and temporal temperature gradient gel electrophoresis in separating Escherichia coli uidA amplicons differing in single base substitutions

“…Although simultaneous analysis of single base substitutions by heteroduplex and homoduplex mixtures allowed the clear detection of sequence variations, considering homoduplexes alone (as used in this study) resulted in low migration length differences of the respective bands (Bjùrheim et al 1998). Using heteroduplex (hybridized from wild type and mutant homoduplexes) analysis for the detection of single base substitutions leads to a signi®cant increase in detection ef®-ciency (Abrams and Stanton 1992). To date, heteroduplexes have been used for human genetic screening applications using TTGE (Bùrresen-Dale et al 1997;Bjùrheim et al 1998;Marsh et al 1998).…”

“…1). Sequence changes may increase or decrease the melting temperature and multiple base changes may have additive or compensatory effects (Abrams and Stanton 1992). For example, amplicons of ST1, ST8 and ST10 showed a gradual increase in melting temperature (Fig.…”

“…To calculate the ESEGR for TTGE, the temporal temperature increase (ramping rate) was converted into a hypothetical chemical denaturant increase by using a conversion factor of 0Á3 C temperature increase per 1% chemical denaturant (Abrams and Stanton 1992) and related to the uidA amplicon migration rate in the gel; the amplicon migration rate was determined in a TTGE gel below denaturation conditions for the uidA fragment. The TTGE analysis, performed according to Bùrresen-Dale et al (1997), showed an ESEGR of 2Á3% cm À1 chemical denaturant increase.…”

Concurrent disruption of p16INK4a and the ARF-p53 pathway predicts poor prognosis in aggressive non-Hodgkin's lymphoma

“…The 'GCclamped' PCR products were analyzed in a 6% polyacrylamide/10-60% denaturing gradient gel (100% denaturant = 7 mol/l urea and 40% formamide). 61 The gel was run at 160 V for 4 h in 1 × TAE buffer kept at a constant temperature of 54°C, stained with ethidium bromide, and photographed under UV transillumination.…”

Evolution of Ciona intestinalis Tumor necrosis factor alpha ( Ci TNFα): Polymorphism, tissues expression, and 3D modeling

“…It is one of the most efficient and widely applied methods for detection of nucleotide differences through an increasing denaturant gradient of urea formamide (Abrams and Stanton, 1992;Lerman and Beldjord, 1998). DGGE has been applied to different biological purposes from genetic mutations (Sheffield et al, 1989) to bacterial diversity (Muyzer et al, 1993;Van der Gucht and Vandekerckhove, 2005) and genetic polymorphism (Ge et al, 1999;Cantet et al, 2012).…”