Detection of cyclin D1 mRNA by hybridization sensitive NIC-oligonucleotide probe

Marina Kovaliov, Meirav Segal, Pinhas Kafri, Eylon Yavin, Yaron Shav-Tal, Bilha Fischer

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


A large group of fluorescent hybridization probes, includes intercalating dyes for example thiazole orange (TO). Usually TO is coupled to nucleic acids post-synthetically which severely limits its use. Here, we have developed a phosphoramidite monomer, 10, and prepared a 2′-OMe-RNA probe, labeled with 5-(trans-N-hexen-1-yl-)-TO-2′-deoxy-uridine nucleoside, dUTO, (Nucleoside bearing an Inter-Calating moiety, NIC), for selective mRNA detection. We investigated a series of 15-mer 2′-OMe-RNA probes, targeting the cyclin D1 mRNA, containing one or several dUTO at various positions. dUTO-2′-OMe-RNA exhibited up to 7-fold enhancement of TO emission intensity upon hybridization with the complementary RNA versus that of the oligomer alone. This NIC-probe was applied for the specific detection of a very small amount of a breast cancer marker, cyclin D1 mRNA, in total RNA extract from cancerous cells (250 ng/μl). Furthermore, this NIC-probe was found to be superior to our related NIF (Nucleoside with Intrinsic Fluorescence)-probe which could detect cyclin D1 mRNA target only at high concentrations (1840 ng/μl). Additionally, dUT can be used as a monomer in solid-phase oligonucleotide synthesis, thus avoiding the need for post-synthetic modification of oligonucleotide probes. Hence, we propose dU TO oligonucleotides, as hybridization probes for the detection of specific RNA in homogeneous solutions and for the diagnosis of breast cancer.

Original languageEnglish
Pages (from-to)2613-2621
Number of pages9
JournalBioorganic and Medicinal Chemistry
Issue number9
StatePublished - 1 May 2014


  • Breast cancer
  • Cyclin D1
  • Fluorescent probe
  • RNA probe
  • mRNA diagnosis


Dive into the research topics of 'Detection of cyclin D1 mRNA by hybridization sensitive NIC-oligonucleotide probe'. Together they form a unique fingerprint.

Cite this