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Design and Characterization of DNA Aptamer for Breast Tumor Marker by an Advantageous Method

Nandita P. Agnihotri, Shikha Dubey, Mangla Bhide

Aptamers are agents able to bind tightly and selectively to disease markers, offering great potential for applications in disease diagnosis and therapy. Functionally they are ssDNA or RNA oligonucleotides which are highly specific and selective to their target along with highest affinity. We have selected DNA aptamer against breast tumor marker (CA 15-3) by using a modified SELEX methodology. For the selection round CA 15-3 were immobilized on magnetic beads and to check the affinity of selected aptamers for their target fluorescent labeled aptamers were used. Aptamers were selected from an initial library containing 25 base long variable regions for their ability to bind to the CA 15-3. After 12 rounds of the selection and amplification we found 90% pool of DNA sequences which are able to bind with CA 15-3. These aptamers were cloned, sequenced and labeled by fluorescent molecule. The binding affinity of these aptamers (KD value) was quantified by using FAM labeled aptamers. Our results aim to develop new diagnostic assays against breast tumor marker for the early diagnosis of breast cancer.