Chemistry of minor groove binder-oligonucleotide conjugates.
Various types of minor groove binders have been attached to synthetic oligodeoxynucleotides, and the interactions of these conjugates (MB-ODNs) with DNA are reviewed here. MB-ODNs have enhanced DNA affinity and have improved the hybridization properties of sequence-specific DNA probes. Short MB-ODNs hybridize with ssDNA to give more stable DNA duplexes than unmodified ODNs with similar lengths. Mismatch discrimination of short MB-ODNs is enhanced in comparison to longer unmodified ODNs. The stronger binding of MB-ODNs allows for more stringent hybridization conditions to be used in DNA probe-based assays. MB-ODNs are especially useful in quantitative "real-time" PCR assays since they bind efficiently during the high-temperature primer extension cycle. The synthesis and biophysical chemistry of MB-ODN conjugates are reviewed here. Four published structural classes of MB-ODNs and their various dsDNA binding modes are discussed, and the well-characterized DPI3-type MB-ODNs and their interactions with ssDNA target strands are described in detail.
Kutyavin
Igor
I
Epoch Biosciences, Bothell, Washington, USA.
Lokhov
Sergey
S
Lukhtanov
Eugene
E
Reed
Michael W
MW
D001482:Base Composition / Q000502:physiology; D020137:Base Pair Mismatch; D001665:Binding Sites; D006690:Bisbenzimidazole / Q000737:chemistry / Q000378:metabolism; D002395:Catecholamines / Q000737:chemistry / Q000378:metabolism; D003521:Cyclopropanes / Q000737:chemistry / Q000378:metabolism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D015342:DNA Probes / Q000138:chemical synthesis; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D004214:Distamycins / Q000737:chemistry / Q000378:metabolism; D005456:Fluorescent Dyes / Q000737:chemistry; D048288:Imidazolines / Q000737:chemistry / Q000378:metabolism; D007211:Indoles / Q000737:chemistry / Q000378:metabolism; D008954:Models, Biological; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry* / Q000378:metabolism; D016133:Polymerase Chain Reaction / Q000379:methods; D013816:Thermodynamics
D002395:Catecholamines; D003521:Cyclopropanes; D015342:DNA Probes; D004277:DNA, Single-Stranded; D004268:DNA-Binding Proteins; D004214:Distamycins; D005456:Fluorescent Dyes; D048288:Imidazolines; D007211:Indoles; D009841:Oligonucleotides; C110747:cyclopropapyrroloindole; C030000:stallimycin; D004247:DNA; C011775:(3,4-dihydroxyphenylamino)-2-imidazoline; D006690:Bisbenzimidazole