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#tandem repeats

3 public questions tagged with this topic.

Transcriptome analysis

Which of the following detects tandem repeats poorly?

Interphase FISH uses decondensed nuclear chromatin, where spatial resolution and signal coalescence are suboptimal. Tandem repeat clusters, being repetitive and often closely spaced, produce merged or diffuse fluorescent signals that are hard to quantitate and enumerate in interphase nuclei. Metaphase chromosomes provide condensed, linearly ordered targets where repeat arrays are linearly resolved. Microarray and SAGE interrogate sequence content differently. Hence, interphase FISH suffers reduced sensitivity and specificity for enumerating tandem repeats compared to metaphase FISH, which offers superior cytogenetic resolution of repeated sequences and breakpoints.

Ref: NCERT Biology Class XII Principles on Klenow fill-in labeling, Lehninger Chapter 9 DNA cloning techniques, and Molecular Cloning by Sambrook Chapter 10 documenting end-labeling of cohesive termini.

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Molecular Marker

Microsatellites vary in:

Microsatellites consist of tandemly repeated units of one to six base pairs dispersed throughout genomes. Variation among individuals originates from difference in copy number of repeat motifs at orthologous loci, caused by replication slippage leading to expansion or contraction of repeats. Base composition of repeat motif remains constant, for example CA dinucleotide, and genomic location is conserved. Length variation is secondary consequence of repeat number change. Therefore, allelic diversity at microsatellite loci directly reflects hypervariability in number of repeat iterations.

Ref: NCERT Biology Class XII Principles on Klenow fill-in labeling, Lehninger Chapter 9 DNA cloning techniques, and Molecular Cloning by Sambrook Chapter 10 documenting end-labeling of cohesive termini.

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Restriction Digestion & Mapping

How can tandem repeats be identified in a plasmid?

Tandem repeats create duplicated restriction recognition sites at regular intervals, altering expected fragment number and size predictably. Simple single enzyme digestion that should linearize plasmid may instead produce multiple bands or an unusually large fragment if repeats are head-to-tail and sites are duplicated. Restriction mapping using several enzymes, double digests, and comparison of observed versus predicted fragment patterns reveals duplications, insertions, or rearrangements. While PCR and sequencing can ultimately confirm repeat structure, initial screening by restriction mapping provides quick physical evidence of repeat expansion, orientation, and stability needed for plasmid quality assessment.

Ref: NCERT Biology Class XII Principles on Klenow fill-in labeling, Lehninger Chapter 9 DNA cloning techniques, and Molecular Cloning by Sambrook Chapter 10 documenting end-labeling of cohesive termini.

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