2003
DOI: 10.1101/gr.997703
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Allele-Specific Holliday Junction Formation: A New Mechanism of Allelic Discrimination for SNP Scoring

Abstract: We report here a new mechanism for allelic discrimination-allele-specific Holliday Junction formation. The Holliday Junction (HJ) is a unique DNA structure that can be formed in a sequence-nonspecific manner by routine PCR. To cause the PCR-based HJ formation to occur in an allele-specific manner, the PCR primers are manipulated such that an extra mismatch next to a SNP of interest is introduced between a target and a reference amplicon and a GC-clamp is added. Based on this new mechanism, novel SNP genotyping… Show more

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Cited by 135 publications
(20 citation statements)
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“…12). Our findings suggest that exposed vRNA is degraded in target cells with a half-life of Ď˝2 h. This correlates with a similarly high decay rate seen for mammalian mRNAs (53). It has been proposed that the AU-rich nucleotide content may destabilize HIV-1 RNAs following their synthesis (54)(55)(56), much like several other cellular mRNAs encoding cytokines and growth factors (57).…”
Section: Fates Of Eccentric Hiv-1 Particles In Target Cellssupporting
confidence: 52%
“…12). Our findings suggest that exposed vRNA is degraded in target cells with a half-life of Ď˝2 h. This correlates with a similarly high decay rate seen for mammalian mRNAs (53). It has been proposed that the AU-rich nucleotide content may destabilize HIV-1 RNAs following their synthesis (54)(55)(56), much like several other cellular mRNAs encoding cytokines and growth factors (57).…”
Section: Fates Of Eccentric Hiv-1 Particles In Target Cellssupporting
confidence: 52%
“…While the stability of transcripts and proteins vary according to their functional characteristics [8, 23], the rate of translation has been found to be the most important factor in predicting protein expression [24]. At the categorical level, translation rate weighs only slightly positively on the predictive value of transcript to protein abundance.…”
Section: Discussionmentioning
confidence: 99%
“…Rather than affecting all transcripts equally, postmortem degradation appears to target different classes of transcripts at varying rates [15]. Specifically, longer coding regions and 3’ UTRs correlate with more rapid degradation than the rest of the transcriptome [15, 23, 27, 28]. The most severe postmortem degradation occurs after 8 h and would not be a factor in our study [15].…”
Section: Discussionmentioning
confidence: 99%
“…It has been known that Holliday junction is similar with k-armed branched DNA molecule. The processing of the Holliday junction by some proteins was studied by Yamada K., et al [13] in 2004, and it was reported that this unique DNA structure could be formed in a sequence-nonspecific manner by routine PCR [14] . Based on these results, 3D DNA computing can be fulfilled.…”
Section: Discussionmentioning
confidence: 99%