New analogues of 2-deoxynucleotides and ribonucleotides incorporating a unique squaramide structure were synthesized. Because of the strong acidity of this moiety (pKa= 2.3), these nucleotide analogues exist in a monoanionic form, which can be regarded as an electronic isoster of 5-nucleotides under physiological conditions. The synthesis of the nucleotide analogues was achieved through the condensation of 5- or -aminonucleosides with link,whilst the selective removal of the methyl group was effectively accomplished by treatment with sodium bromide. In addition, we also synthesized 3,5-cyclic nucleotide analogues from the 3,5-diazidonucleoside derivatives. NMR analysis revealed that their ribose puckering was of an N-type form, identical to that in cAMP and cGMP. Because of the unique structural, electronic, and conformational properties of squaramide-type nucleotide analogues, these analogues should be quite interesting as potential biologically active compounds such as antiviral and anticancer agents.