Journal
BIOCHEMISTRY
Volume 41, Issue 3, Pages 869-880Publisher
AMER CHEMICAL SOC
DOI: 10.1021/bi011441d
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Funding
- NIGMS NIH HHS [5T32 GM07356, GM 22939] Funding Source: Medline
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Algorithms for predicting RNA secondary structure require approximations for the free energies of multibranch loops, also called junctions. The stabilities of 62 RNA duplexes with three- and four-way multibranch loops were determined by optical melting. To account for the observed sequence dependence, a revised loop free-energy approximation is proposed that accounts for the strain in three-way junctions with fewer than two unpaired nucleotides, penalizes asymmetry in the distribution of unpaired nucleotides, and gives a bonus for four-way loops relative to three-way loops. Parameters for this equation were determined by linear regression.
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