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Complementary set sequences (CSSs) are useful for dealing with the high peak-to-average power ratio (PAPR) problem in orthogonal frequency division multiplexing (OFDM) systems. In practical OFDM transmission, however, certain sub-carriers maybe reserved and/or prohibited to transmit signals, leading to the so-called \emph{spectral null constraint} (SNC) design problem. For example, the DC sub-carrier is reserved to avoid the offsets in D/A and A/D converter in the LTE systems. While most of the current research focus on the design of low PAPR CSSs to improve the code-rate, few works address the aforementioned SNC in their designs. This motivates us to investigate CSSs with SNC as well as low PAPR property. In this paper, we present systematic constructions of CSSs under SNCs and low PAPR. First, we show that mutually orthogonal complementary sets (MOCSs) can be used as \emph{seed sequences} to generate new CSSs with SNC and low PAPR, and then provide an iterative technique for the construction of MOCSs which can be further used to generate complementary sets (CSs) with low PAPRs and spectral nulls at \emph{varying} positions in the designed sequences. Next, inspired by a recent idea of Chen, we propose a novel construction of these \emph{seed} MOCSs with non-power-of-two lengths from generalized Boolean functions.