Patent ID: 6426407
Filing Date: 2002-07-30
Classification: C07H,C12Q

Abstract:
An oligonucleotide containing a backbone having a polarity associated therewith, and nucleotide bases and at least one synthetic residue bound to the backbone, the bases and residue(s) of said oligonucleotide being effective to bind in a sequence-specific manner to a target sequence of a duplex polynucleotide, said oligonucleotide capable of binding in a parallel orientation relative to a purine-rich or designated core or center strand of said duplex, said nucleotide bases consisting essentially of pyrimidine bases and/or base analogs thereof, and said residue(s) being substantially planar, such that when the oligonucleotide binds to the target sequence, base triplets are formed among each oligonucleotide base or residue and the corresponding bases of the duplex with at least one residue binding to an inverted base pair, and each residue conforms to the following parameters:a) the radius of the imaginary circle connecting the C1â€² ends of the two glycosyl bonds of the target base pair of the duplex polynucleotide and the atom of the oligonucleotide backbone which is linked to the corresponding residue of the oligonucleotide is from about 7.0 Ã¥ to about 8.6 Ã¥; b) the &THgr; value, measured from the C1â€² atom bound to the base in the core or center strand, to the atom of the oligonucleotide backbone which is bound to the residue, is from about 53Â° to about 82Â°; c) the &zgr; value indicating the angle between said imaginary circle radius passing through the atom of the residue which is bound to the oligonucleotide backbone, and the bond vector between the residue and the oligonucleotide backbone, is from about âˆ’90Â° to about +90Â°; and d) the residue forms a total of at least two hydrogen bonds with one or both bases of the corresponding target base pair of the duplex.