TY - JOUR
T1 - The size of RNA as an ideal branched polymer
AU - Fang, Li Tai
AU - Gelbart, William M.
AU - Ben-Shaul, Avinoam
PY - 2011/10/21
Y1 - 2011/10/21
N2 - Because of the branching arising from partial self-complementarity, long single-stranded (ss) RNA molecules are significantly more compact than linear arrangements (e.g., denatured states) of the same sequence of monomers. To elucidate the dependence of compactness on the nature and extent of branching, we represent ssRNA secondary structures as tree graphs which we treat as ideal branched polymers, and use a theorem of Kramers for evaluating their root-mean-square radius of gyration, R̂g=√〈Rg2〈. We consider two sets of sequences-random and viral-with nucleotide sequence lengths (N) ranging from 100 to 10 000. The RNAs of icosahedral viruses are shown to be more compact (i.e., to have smaller R̂g) than the random RNAs. For the random sequences we find that R̂g varies as N1/3. These results are contrasted with the scaling of R̂g for ideal randomly branched polymers (N1/4), and with that from recent modeling of (relatively short, N ≤ 161) RNA tertiary structures (N2/5).
AB - Because of the branching arising from partial self-complementarity, long single-stranded (ss) RNA molecules are significantly more compact than linear arrangements (e.g., denatured states) of the same sequence of monomers. To elucidate the dependence of compactness on the nature and extent of branching, we represent ssRNA secondary structures as tree graphs which we treat as ideal branched polymers, and use a theorem of Kramers for evaluating their root-mean-square radius of gyration, R̂g=√〈Rg2〈. We consider two sets of sequences-random and viral-with nucleotide sequence lengths (N) ranging from 100 to 10 000. The RNAs of icosahedral viruses are shown to be more compact (i.e., to have smaller R̂g) than the random RNAs. For the random sequences we find that R̂g varies as N1/3. These results are contrasted with the scaling of R̂g for ideal randomly branched polymers (N1/4), and with that from recent modeling of (relatively short, N ≤ 161) RNA tertiary structures (N2/5).
UR - http://www.scopus.com/inward/record.url?scp=80155126880&partnerID=8YFLogxK
U2 - 10.1063/1.3652763
DO - 10.1063/1.3652763
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C2 - 22029339
AN - SCOPUS:80155126880
SN - 0021-9606
VL - 135
JO - Journal of Chemical Physics
JF - Journal of Chemical Physics
IS - 15
M1 - 155105
ER -