Learn more about hiring developers or posting ads with us site design / logo © 2020 Stack Exchange Inc; user contributions licensed under Double helix linking number and DNA supercoiling. This study originated in response to questions that arise in the study of supercoiled double-stranded DNA rings. E) interconvert DNA and RNA. User account menu. When I give the two strands orientations and half the sums of signs of crossings, I do not get $23$. we would expect 500 360° turns of the DNA strands over the length of the circular genome.The result is that there are about 475 turns of the helix within the duplex DNA (i.e. 18. Is there a problem with this example? Press question mark to learn the rest of the keyboard shortcuts. the Linking number = 475).Thus for the 5300 bp SV40 genome, with a Linking number of 475, to maintain a value of 10.6 bp/twist, a total of 25 negative supercoils (Writhe=25) are needed:The enzymes that control DNA topology are critical to DNA replication and transcription.For example, during the early stages of SV40 replication, the duplex around the origin of replication may initially melt (open up) a region of 750 bases. And if not, is anyone able to explain (without using Calugareanu's Theorem, i.e. We want to hear from you.Unwinding of the helix during DNA replication (by the action of helicase) results in Cut two lengths of 1/8" rubber tubing, each about 20" long. (a) Calculate the writhe (W) of this DNA. Detailed answers to any questions you might have
By using our site, you acknowledge that you have read and understand our Biology Stack Exchange is a question and answer site for biology researchers, academics, and students. The linking number is the most descriptive property of supercoiled DNA. Adopted or used LibreTexts for your course? writhe)?In other words, in order to achieve the desired conformation of 10.6 bp/turn in the helix, exactly 500 turns are required over the length of 5300 base pairs.We can have integral values for the linkage number, and we can certainly introduce 500, which would require no Writhe at all:We can introduce either 490 or 491 as a linkage number, but not 490.6.
- Change the topological status of DNA by changing the linking number - Types: Type 1 - breaks only one strand of DNA (1A and 1B) Type 2 - Breaks both strands of DNA. It only takes a minute to sign up.The image below is taken from a molecular biology textbook. What happens if there is a linkage number of 490 in the DNA molecule?In this case, the DNA adopts a negative 0.6 supercoil (about 108° of a right-handed supercoil) which will increase the apparent linkage number from 490 to 490.6 (and achieve 10.6 basepairs per turn in the duplex).How many basepairs per turn would there be in the DNA if the DNA was not able to adopt any supercoil structure for this length of DNA with a linkage number of 490?The Simian Virus 40 (SV40) genome is a circular, closed, double stranded DNA genome. (b) Calculate the twist (T) and linking number (L) for this DNA. $\text{Lk}=\text{Tw}+\text{Wr}$) why the linking number is $23$? Learn more about Stack Overflow the company • Linking number--The number of times the two strands are intertwined.it is also the number of cleaves necessary for separating two DNA strands.It will be constant. By clicking “Post Your Answer”, you agree to our To subscribe to this RSS feed, copy and paste this URL into your RSS reader. When I give the two strands orientations and half the sums of signs of crossings, I do not get $23$. Biology Stack Exchange works best with JavaScript enabled Start here for a quick overview of the site 2. About the writhing number, mathematician W. F. Pohl says: It is well known that the writhing number is a standard measure of the global geometry of a closed space curve. share. (c) Calculate the circumference of the circular DNA when W = 0. Anybody can ask a question Ask Question Asked 2 years, ... is anyone able to explain (without using Calugareanu's Theorem, i.e. The unwinding of the DNA strands by helicases affects the overall topology of the DNA (Figure 5.23). Insert a smaller piece of tubing, or piece of pipette tip in the ends to allow the ends to be connected. We expect that under physiological conditions the DNA will exhibit 10.6 base pairs per turn (i.e. Discuss the workings and policies of this site The linking number has not changed, but the length of DNA which contains all the turns is effectively shorter. 9 comments. How does linking number for dna works? It is not clear to me that what is happening at the two writhe crossings matches up with the numbers provided. Starting with a closed circular DNA of 5250 base pairs with ˙ = -0.004 (assume 10.5 bp/turn for B-DNA). For the purposes of this discussion, it has 5300 bases. So we need a way to keep track of which end is which for each piece of tubing.This will allow you to maintain correct strand "orientation" when you "ligate" the strands of the duplex.Confirm that the correct linking number has been introduced by "melting" the duplex on one side and forcing all turns into a small region of the duplex (easy to count this way).Note that the "duplex" when held between thumb and forefinger and allowed to hang, prefers a "supercoiled" topology, as opposed to "relaxed" [Note: this is usually seen with very skinny tubing, larger diameter tubing may not readily adopt this topology].Thus, in response to the introduction of +2 Linking number, the "duplex" can adopt +2 (180°) "supercoils", such that the resulting A supercoil is considered positive, if it is "left handed").The twist value (apparent linkage number) for a given length of DNA is related to the number of base pairs per turn that the DNA wants to adopt:For example, if we have a circularly closed DNA molecule with a length of 5300 base pairs, and a preferred conformation of 10.6 basepairs per turn, can it achieve this conformation without having to introduce any supercoiling (i.e. Stack Exchange network consists of 177 Q&A communities including