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For $G={\rm PGL}_n({\mathbb C})$ there is no complex algebraic Quillen line bundle on the complex character variety $Y$ as the cohomology class $[\omega]=\alpha_2\in H^2(Y;{\mathbb Q})$ is not pure by Proposition 4.1.8 in http://arxiv.org/abs/math.AG/0612668.

EDIT: It is instructive to think about the case $G={ GL}_1({\mathbb C})$. Then the character variety is $M_B=GL_1^{2g}$ the complex torus while $M_{DR}$ is an affine bundle over $Jac(C)$. Analytically $M_B\cong M_{DR}$ but the universal bundle $L$ on $M_{DR}\times C$ which is just the pull back of the Poincare bundle from $Jac(C)\times C$ is not algebraic on $M_B$, for example because the cohomology class $[\omega]$ of the symplectic form (which shows up in $c_1(L)^2$) has weight $2$ in $H^2(M_{DR};{\mathbb Q})$ but has weight $4$ (homogeneous weight $2$) in $H^2(M_B;{\mathbb Q})$. Thus in particular there is no complex algebraic Quillen bundle on $M_B$ with first Chern class $[\omega]$.

EDIT 2: To take David's example let $g=1$, then $M_B={\mathbb C}^* \times {\mathbb C}^*$ which does not have non-trivial pure cohomology in $H^2(M_B;{\mathbb Q})$ and even the Picard group is trivial (see an argument here); thus $M_B$ does not support any non-trivial algebraic line bundle.

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For $G={\rm PGL}_n({\mathbb C})$ there is no complex algebraic Quillen line bundle on the complex character variety $Y$ as the cohomology class $[\omega]=\alpha_2\in H^2(Y;{\mathbb Q})$ is not pure by Proposition 4.1.8 in http://arxiv.org/abs/math.AG/0612668.

EDIT: It is instructive to think about the case $G={ GL}_1({\mathbb C})$. Then the character variety is $M_B=GL_1^{2g}$ the complex torus while $M_{DR}$ is an affine bundle over $Jac(C)$. Analytically $M_B\cong M_{DR}$ but the universal bundle $L$ on $M_{DR}\times C$ which is just the pull back of the Poincare bundle from $Jac(C)\times C$ is not algebraic on $M_B$, for example because the cohomology class $[\omega]$ of the symplectic form (which shows up in $c_1(L)^2$) has weight $2$ in $H^2(M_{DR};{\mathbb Q})$ but has weight $4$ (homogeneous weight $2$) in $H^2(M_B;{\mathbb Q})$. Thus in particular there is no complex algebraic Quillen bundle on $M_B$ with first Chern class $[\omega]$.

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For $G={\rm PGL}_n({\mathbb C})$ there is no complex algebraic Quillen line bundle on the complex character variety $Y$ as the cohomology class $[\omega]=\alpha_2\in H^2(Y;{\mathbb Q})$ is not pure by Proposition 4.1.8 in http://arxiv.org/abs/math.AG/0612668.