# DNA Melting - Glossary Basepairing probability: A probability pbp(i) that the basepair at sequence position i is closed (i.e. helix). Denaturation map: This term has been used in the DNA melting litterature to denote both probability profiles and temperature profiles. Derivative melting curve: A differentiated melting curve, i.e. -dθ/dT as a function of T. For intermediate length sequences (103-104 bp), this curve will show a series of peaks located at the temperatures where different regions (domains) of the sequence melt. The area under a peak corresponds roughly to the size of the domain. Helicity θ: Also called the mean degree of helicity. The average of all the basepairing probabilities, θ =(pbp(1) + pbp(2) + ... + pbp(N))/N. It is the average fraction of intact (not melted) basepairs (a value between 0 and 1). It is a measure of how much helix there is in the melting molecule. Melting curve: A plot of the helicity as a function of temperature. For intermediate length sequences (103-104 bp), the curve will drop from close to 1 to almost 0 in a stepwise manner depending on the sequence, showing the progress of the melting process, while for shorter and longer lengths the curve is more smooth. Calculated melting curves can be compared directly with the melting curves measured with UV spectroscopy and other techniques. Melting map: This term has been used in the DNA melting litterature to denote both probability profiles and temperature profiles. Melting profile: This term has been used in the DNA melting litterature to denote both melting curves, probability profiles and Tm profiles. Melting range: The temperature interval in which most of the melting process takes place and the helicity decreases from high to low. Melting temperature Tm: 1) The temperature Tm at which the helicity θ equals 0.5. It is the temperature where the molecule is halfway through the melting process.
2) Local melting temperatures can also be defined for a region of the sequence or for an individual basepair. For an individual basepair at position i, the basepair melting temperature Tm(i) is where the base-pairing probability pbp(i) equals 0.5.
Probability profile: A plot of the base-pairing probability pbp(i) as a function of sequence position i. (Alternatively, the plot can be turned upside-down and show 1 - pbp(i) which is the probability that the basepair is open, i.e. melted). A plot can contain several probability profiles at different temperatures in order to give an overview of the melting process. Stability map: This term has been used in the DNA melting litterature to denote Tm profiles. Stitch profile: A diagram that indicates the multitude of possible conformations that a DNA may adopt at a given temperature, by showing specifically what regions that can be basepaired (dsDNA) and what regions that can be melted (ssDNA). A stitch profile is a set of stitches, where each stitch indicates a possible state of a region. Each stitch corresponds to a peak in certain block probability functions, and in that sense a stitch profile represents some of the most likely conformations. A stitch profile is calculated on this web site by applying a peak finding method that uses two parameters to control the search: the probability cutoff pc and the maximum depth Dmax. Temperature profiles: A generalization of Tm profiles. Instead of using the value 0.5, one can plot a profile of temperatures where the basepairing probabilities pbp(i) equal some other value. Tm profile: A plot of the basepair melting temperature Tm(i) as a function of sequence position i. Usually, the curve has plateaus for regions of the sequence that melt together (cooperatively) at the same temperature.