Libraries of repetitive and block-copolymerized polypeptides and the fusion proteins have been prepared for the scaffold of nanoscale component assembly for nano/biotechnology applications. The DNA sequence libraries for expression vectors coding repetitive YEHK, HKYE, YE, HK, YE8HK8, HK8YE8, KYEY, and YKYE with adaptive amino acids of hexahistidine (H6) or dicysteine (C2) on the N- and C-terminals were constructed from 4 kinds of 8 amino acid-coding units GAGAGAGX where X=Tyr (Y), Glu (E), His (H), and Lys (K). The effects of sequence, the carbamylation of lysine residues, the terminal amino acids, and the acrylamide concentration on the relative mobility of the intact and carbamylated polypeptides on SDS PAGE are studied. The polypeptides that have clustered region of negative charge (YE, YE8HK8, HK8YE8, carbamylated YEHK, HKYE, KYEY, and YKYE) showed significantly lower mobility compared to the counterparts. The concentration of acrylamide of SDS PAGE also grately affects on shorter and negatively charged polypeptides in reducing the mobility.