a) In DNA microarrays, the typical probe is ~20 nucleotides. Describe the effect
ID: 272050 • Letter: A
Question
a) In DNA microarrays, the typical probe is ~20 nucleotides. Describe the effects of using a shorter probe on the sensitivity and selectivity of an analysis.(1 sentence each) Sensitivity: Selectivity: b) Describe the effects of using a longer probe on the sensitivity and selectivity of an analysis. (1 sentence each) Sensitivity: Selectivity: c) Would a shorter or longer probe be more effective at distinguishing between a target DNA and a single-nucleotide polymorphism of that DNA? Circle one: shorter probe longer probe Explain(1 or 2 sentences): d) Describe some of the similarities and differences between sequencing and microarrays, and when you ay want to use onetechnique versus the other Similarities (2 sentences): Differences (2 sentences):Explanation / Answer
a) sensitivity refers to the ability of the technique to detect the transcript which are having low abundance, or which are rarely expressing.
Using shorter probe typically of 20 nucloetides will be having less sensitivity compared to larger.
To improve the sensitivity multiple number of probes per gene are required to increase the sensitivity.
selectivity - smaller probes will be less selective, to improve selectivity multiple probes are required for any target.
b) Sensitivity- Sensitivity will be higher in case of longer probe , and less number of probes are required for any particular target. 150 mer is considered as optimal probe for measuring expression.
Selectivity - Long oligonucleotide probe displays high selectivity and can be used only one per target, if it is designed targeting regions which are showing less sequence similarity.
c)Longer probe will be more effective in distinguishing between target DNA and SNP because Shorter probes which are less tha 32mer will give higher false negatives. Thus probe length must be more to cover the sequence variants present beyond any conserved SNP, so that the hybridisation free energy equalises.
d) Microarray and sequencing
1)similarity - both are fast and effective means of analysing genomes or transcriptomes.
Entire genome or transcriptome can be analysed at a time.
2) differences - Microarray is based on comparative genomic hybridisation to identify the differences which are present due to mutation, deletion, duplication or structural variations.
The amplified DNA/cDNA's/oligos are used as probe, which are spotted onto a high density pattern onto the chips.
Sequencing is based on the synthesis rather than hybridisation explioting the natural ability of DNA polymerase to add nuclotides.
Microarray is made/fabricated on glass or silicon chips, creating high density array.
Microarray is easier to use and very less labor intensive method.
Related Questions
Navigate
Integrity-first tutoring: explanations and feedback only — we do not complete graded work. Learn more.