title: Scope and limitations of the nicking enzyme amplification reaction for the synthesis of base-modified oligonucleotides and primers for PCR.
abstract: Enzymatic synthesis of short (10-22 nt) base-modified oligonucleotides (ONs) was developed by nicking enzyme amplification reaction (NEAR) using Vent(exo-) polymerase, Nt.BstNBI nicking endonuclease, and a modified deoxyribonucleoside triphosphate (dNTP) derivative. The scope and limitations of the methodology in terms of different nucleobases, length, sequences, and modifications has been thoroughly studied. The methodology including isolation of the modified ONs was scaled up to nanomolar amounts and the modified ONs were successfully used as primers in primer extension and PCR. Two simple and efficient methods for fluorescent labeling of the PCR products were developed, based either on direct fluorescent labeling of primers or on NEAR synthesis of ethynylated primers, PCR, and final click labeling with fluorescent azides.
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic.
authors.forename: Petra
authors.initials: P
authors.lastname: Ménová
authors.forename: Veronika
authors.initials: V
authors.lastname: Raindlová
authors.forename: Michal
authors.initials: M
authors.lastname: Hocek
mesh_terms: D001386:Azides / Q000737:chemistry; D057930:Click Chemistry; D017931:DNA Primers / Q000096:biosynthesis* / Q000235:genetics; D003854:Deoxyribonucleotides / Q000138:chemical synthesis / Q000737:chemistry / Q000378:metabolism; D004720:Endonucleases / Q000378:metabolism*; D005456:Fluorescent Dyes / Q000737:chemistry; D015394:Molecular Structure; D021141:Nucleic Acid Amplification Techniques; D009841:Oligonucleotides / Q000096:biosynthesis*; D016133:Polymerase Chain Reaction
chemical_list: D001386:Azides; D017931:DNA Primers; D003854:Deoxyribonucleotides; D005456:Fluorescent Dyes; D009841:Oligonucleotides; D004720:Endonucleases