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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.
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]
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:
During the rolling circle replication, the ssDNA of geminivirus is converted to dsDNA and Rep is then attached to the dsDNA at the origin sequence TAATATTAC. After Rep, along with other replication proteins, binds to the dsDNA it forms a stem loop where the DNA is then cleaved at the nanomer sequence causing a displacement of the strand.
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.
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).
Restriction endonucleases may be found that cleave standard dsDNA (double-stranded DNA), or ssDNA (single-stranded DNA), or even RNA. [citation needed] This discussion is restricted to dsDNA; however, the discussion can be extended to the following: Standard dsDNA; Non-standard DNA; Holliday junctions