Publications by authors named "Nafisa N Nazipova"
Off-target oligoprobe's interaction with partially complementary nucleotide sequences represents a problem for many bio-techniques. The goal of the study was to identify oligoprobe sequence characteristics that control the ratio between on-target and off-target hybridization. To understand the complex interplay between specific and genome-wide off-target (cross-hybridization) signals, we analyzed a database derived from genomic comparison hybridization experiments performed with an Affymetrix tiling array.
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- The study investigates how the characteristics of oligo-probes affect their ability to hybridize specifically to targeted DNA sequences while minimizing unwanted hybridization across the entire genome.
- Researchers defined hybridization specificity as the ratio of target-specific hybridization to genome-wide cross-hybridization and analyzed two types of oligo-probes from a microarray database.
- Findings indicate that certain features, like low duplex stability and G-rich sequences, lead to decreased hybridization specificity, and filtering these 'negative' characteristics can significantly enhance probe design, resulting in probes with twice the specificity.
Small hairpin RNAs (shRNAs) became an important research tool in cell biology. Reliable design of these molecules is essential for the needs of large functional genomics projects. To optimize the design of efficient shRNAs, we performed comparative, thermodynamic, and correlation analyses of ~18,000 miR30-based shRNAs with known functional efficiencies, derived from the Sensor Assay project (Fellmann et al.
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