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Home Q & A Board Biology-Related Homework Help Biochemistry
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spliceofslife spliceofslife
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14 years ago
The cloning vector pBR322 is a closed, circular double-stranded DNA containing 4.3 kbp of
DNA. During transcription, RNA polymerase causes local unwinding of 14 bp of DNA to expose
the template strand. If 10 RNA polymerases are transcribing each pBR322 molecule, what linking
number is required to prevent any supercoiling during transcription? (You can assume that there
are 10 bp per Watson-Crick helical repeat).
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14 years ago
So we have 10 polymerases transcribing the pBR322 molecule one after the other.

Since the linking number ''L'' of supercoiled DNA is the number of times the two strands are intertwined (and both strands remain covalently intact), ''L'' cannot change. The reference state (or parameter) ''L0'' of a circular DNA duplex is its relaxed state. In this state, its writhe ''W'' = 0. Since ''L = T + W'', in a relaxed state ''T = L''. Thus, if we have a 400 bp relaxed circular DNA duplex, ''L ~ 40'' (assuming ~10 bp per turn in B-DNA). Then ''T ~ 40''.

  • Positively supercoiling:

T = 0, W = 0, then L = 0
T = +3, W = 0, then L = +3
T = +2, W = +1, then L = +3

  • Negatively supercoiling:

T = 0, W = 0, then L = 0
T = -3, W = 0, then L = -3
T = -2, W = -1, then L = -3

Negative supercoils favor local unwinding of the DNA, allowing processes such as DNA transcription|transcription, DNA replication, and DNA recombination|recombination. Negative supercoiling is also thought to favour the transition between B-DNA and Z-DNA, and moderate the interactions of DNA binding proteins involved in gene regulation.
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