Effects Of YOYO-1 Intercalation On The Topological States Of Circular DNA And Micromechanics Properties Of DNA Molecules

YOYO-1 is a bisintercalating green fluorescent dye which is widely used to fluorescently label DNA molecule in experiments to study the mechanical and structural properties of DNA under varying conditions.YOYO-1 intercalation leads to the reduction of twist rigidity,unwinding,elongation of DNA contour length and the change of YOYO-1 concentration-dependent persistence length,but few theoretical or experimental work has comprehensively investigated the effect of topological state change of circular DNA ranging from minicircle to plasmid by YOYO-1 intercalation.Therefore,based on the Worm-like Chain Model and Worm-like Rod Model,the effects of YOYO-1 intercalation on the topological states of circular DNA is studied by using Monte Carlo simulation.(1)Based on the Worm-like Chain Model,Monte Carlo simulation is used to study the topological states change of circular DNA in the case of YOYO-1intercalation.Firstly,the twist number distribution of DNA is obtained analytically,and the writhe number distribution of circular DNA which is obtained by using simulation.Under the White-Fuller relation constraint,by means of the convolution of the writhe number distribution and the twist number distribution to obtain the linking number distribution of circular DNA,and the effects of YOYO-1 intercalation on the linking number distribution of circular DNA are predicted and identified.YOYO-1intercalation leads to larger fluctuation,but not obvious enlargement of the writhe number distribution,so that the variance of linking number distribution mainly depends on the variance of the twist distribution.the unwinding angle results in the deviation of the linking number distribution and the variance of the linking number distribution is not affected.In contrast,the reduction of twist rigidity affects thelinking number distribution.(2)Based on the Worm-like Rod Model,the writhe number distribution,the twist number distribution and the linking number distribution are obtained by using Monte Carlo simulation in the case of YOYO-1 intercalation,the effect of YOYO-1intercalation and spontaneous twist angle on the topological states of circular DNA are investigated.In the absence of YOYO-1 intercalation,with the change of the spontaneous twist angle,the mean twist number of the DNA minicircles changes sharply when the fractional part of the spontaneous twist numbe is very close to1/2;The transitions take place around half-integer values of the spontaneous twist numbe,and between two successive transitions,both(29)(35)(27)Tw and(29)(35)(27)Lk decrease linearly with the spontaneous twist angle.When the YOYO-1 is intercalating,with the spontaneous twist angle increases,the average twist number increases.The average deviation of the writhe number,the twist number,the linking number is not much.With the increase of concentration of YOYO-1,the twist number distribution is shifted back and forth.the reduction of twist rigidity affects the variance of the twist number distribution.The spontaneous twist angle and the unwinding angle results the twist number distribution to shift back and forth.The change of the linking number distribution of the minicircles DNA is almost identical with that of the twist number distribution.For the linking number distribution of plasmid DNA,the influence of writhe number on it is not significant,and the variance of the linking number distribution is strongly dependent on the variance of the torsion number distribution.