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Nucleic acid thermodynamics is the study of how temperature affects the nucleic acid structure of double-stranded DNA (dsDNA). The melting temperature (T m) is defined as the temperature at which half of the DNA strands are in the random coil or single-stranded (ssDNA) state. T m depends on the length of the DNA molecule and its specific ...
High Resolution Melt (HRM) analysis is a powerful technique in molecular biology for the detection of mutations, polymorphisms and epigenetic differences in double-stranded DNA samples. It was discovered and developed by Idaho Technology and the University of Utah. [1] It has advantages over other genotyping technologies, namely:
In this study they used thiazole orange as the indicator. The helicase unwinds the dsDNA to make ssDNA. The fluorescence intensity of thiazole orange has a greater affinity for dsDNA than ssDNA and its fluorescence intensity increases when it is bound to dsDNA than when it is unbound. [47] [48]
In gene therapy application utilizing rAAV, the virus transduces the cell with a single stranded DNA (ssDNA) flanked by two inverted terminal repeats (ITRs). These ITRs form hairpins at the end of the sequence to serve as primers to initiate synthesis of the second strand before subsequent steps of infection can begin.
DNA end resection, also called 5′–3′ degradation, is a biochemical process where the blunt end of a section of double-stranded DNA (dsDNA) is modified by cutting away some nucleotides from the 5' end to produce a 3' single-stranded sequence.
Given the difference in widths of the major groove and minor groove, many proteins which bind to DNA do so through the wider major groove. [6] Many double-helical forms are possible; for DNA the three biologically relevant forms are A-DNA , B-DNA , and Z-DNA , while RNA double helices have structures similar to the A form of DNA.
On the left is a drawing of the complex formed between alpha-hemolysin and dsDNA with linkage through an oligomer.On the right, movement of this complex in relation to a nanopore channel is shown sequentially in two steps (I) and (II).
A drawback of this method is that the product should be purified from double stranded DNA (dsDNA) and other left-over material from the PCR reaction. Enzymatic degradation of the unwanted strand can be performed by tagging this strand using a phosphate-probed primer, as it is recognized by enzymes such as Lambda exonuclease .