A nucleotide derivative represented by the following general formula: wherein R 1 and R 2 independently represent hydrogen atom, an alkyl group which may have a substituent, an alkenyl group which may have a substituent, an alkynyl group which may have a substituent, an alkoxy group which may have a substituent, an aralkyl group which may have a substituent, or an aryl group which may have a substituent; R 3 represents an aryl group which may have a substituent, or an alkyl group which may have a substituent; R 4 and R 5 independently represent hydrogen atom, an alkyl group which may have a substituent, an alkenyl group which may have a substituent, an alkynyl group which may have a substituent, an alkoxy group which may have a substituent, an aralkyl group which may have a substituent, or an aryl group which may have a substituent; Y represents -Y 1 -Y 2 -, Y 1 represents -C(R 6)(R 7)- or an o-aryldiyl group which may have a substituent, wherein R 6 and R 7 independently represent hydrogen atom, an alkyl group which may have a substituent, an alkenyl group which may have a substituent, an alkynyl group which may have a substituent, an alkoxy group which may have a substituent, an aralkyl group which may have a substituent, or an aryl group which may have a substituent, and R 7 may bind with the aryl group represented by R 3 to form a ring; and the aryl ring of the aryldiyl group may bind with the aryl group represented by R 3 to form a ring; Y 2 represents a single bond or -C(R 8)(R 9)-, wherein R 8 and R 9 independently represent hydrogen atom, an alkyl group which may have a substituent, an alkenyl group which may have a substituent, an alkynyl group which may have a substituent, an alkoxy group which may have a substituent, an aralkyl group which may have a substituent, or an aryl group which may have a substituent; R 21 represents a protective group of hydroxyl group; R 22 represent hydrogen atom, an alkoxy group, fluorine atom, or a protected hydroxyl group; and Bs represents a nucleobase. wherein R 1 and R 2 independently represent hydrogen atom, an alkyl group which may have a substituent, an alkenyl group which may have a substituent, an alkynyl group which may have a substituent, an alkoxy group which may have a substituent, an aralkyl group which may have a substituent, or an aryl group which may have a substituent; R 3 represents an aryl group which may have a substituent, or an alkyl group which may have a substituent; R 4 and R 5 independently represent hydrogen atom, an alkyl group which may have a substituent, an alkenyl group which may have a substituent, an alkynyl group which may have a substituent, an alkoxy group which may have a substituent, an aralkyl group which may have a substituent, or an aryl group which may have a substituent; Y represents -Y 1 -Y 2 -, Y 1 represents -C(R 6)(R 7)- or an o-aryldiyl group which may have a substituent, wherein R 6 and R 7 independently represent hydrogen atom, an alkyl group which may have a substituent, an alkenyl group which may have a substituent, an alkynyl group which may have a substituent, an alkoxy group which may have a substituent, an aralkyl group which may have a substituent, or an aryl group which may have a substituent, and R 7 may bind with the aryl group represented by R 3 to form a ring; and the aryl ring of the aryldiyl group may bind with the aryl group represented by R 3 to form a ring; Y 2 represents a single bond or -C(R 8)(R 9)-, wherein R 8 and R 9 independently represent hydrogen atom, an alkyl group which may have a substituent, an alkenyl group which may have a substituent, an alkynyl group which may have a substituent, an alkoxy group which may have a substituent, an aralkyl group which may have a substituent, or an aryl group which may have a substituent; R 21 represents a protective group of hydroxyl group; R 22 represent hydrogen atom, an alkoxy group, fluorine atom, or a protected hydroxyl group; and Bs represents a nucleobase.