Maji Jaya, Bhattacharjee Somendra M, Seno Flavio, Trovato Antonio
Institute of Physics, Bhubaneswar 751005, India.
INFN, Dipartimento di Fisica e Astronomia 'Galileo Galilei', Università di Padova, Via Marzolo 8, 35131 Padova, Italy.
Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Jan;89(1):012121. doi: 10.1103/PhysRevE.89.012121. Epub 2014 Jan 15.
Thermal denaturation of DNA is often studied with coarse-grained models in which native sequential base pairing is mimicked by the existence of attractive interactions only between monomers at the same position along strands (Poland and Scheraga models). Within this framework, the existence of a three-stranded DNA bound state in conditions where a duplex DNA would be in the denaturated state was recently predicted from a study of three directed polymer models on simplified hierarchical lattices (d>2) and in 1+1 dimensions. Such a phenomenon which is similar to the Efimov effect in nuclear physics was named Efimov-DNA. In this paper we study the melting of the three-stranded DNA on a Sierpinski gasket of dimensions d<2 by assigning extra weight factors to fork openings and closings, to induce a two-strand DNA melting. In such a context we can find again the existence of the Efimov-DNA-like state but quite surprisingly we discover also the presence of a different phase, to be called a mixed state, where the strands are pair-wise bound but without three chain contacts. Whereas the Efimov DNA turns out to be a crossover near melting, the mixed phase is a thermodynamic phase.
DNA的热变性通常使用粗粒度模型进行研究,在这些模型中,天然的序列碱基配对仅通过链上相同位置的单体之间存在吸引力相互作用来模拟(波兰和谢拉加模型)。在此框架内,最近通过对简化层次晶格(d>2)和1 + 1维上的三个定向聚合物模型的研究预测,在双链DNA处于变性状态的条件下存在三链DNA结合状态。这种类似于核物理中埃菲莫夫效应的现象被命名为埃菲莫夫-DNA。在本文中,我们通过为叉口的打开和关闭赋予额外的权重因子来研究维度d<2的谢尔宾斯基垫片上三链DNA的解链,以诱导双链DNA解链。在这种情况下,我们再次发现了类似埃菲莫夫-DNA状态的存在,但令人惊讶的是,我们还发现了一种不同的相,称为混合相,其中链两两结合但没有三链接触。虽然埃菲莫夫-DNA在接近解链时是一个交叉点,但混合相是一个热力学相。