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DNA Aptamer Selected against Pancreatic Ductal Adenocarcinoma for in vivo Imaging and Clinical Tissue Recognition.

Wu X, Zhao Z, Bai H, Fu T, Yang C, Hu X, Liu Q, Champanhac C, Teng IT, Ye M, Tan W - Theranostics (2015)

Bottom Line: In this work, we have developed a truncated DNA aptamer, termed XQ-2d, with high affinity and specificity for pancreatic ductal adenocarcinoma (PDAC).Moreover, XQ-2d shows better recognition ratio for 40 tissue sections of clinical PDAC samples (82.5%) compared to the initial cell-SELEX selection library (5%).Therefore, XQ-2d can be considered a promising candidate as a tool for PDAC diagnosis and treatment.

View Article: PubMed Central - PubMed

Affiliation: 1. Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China.

ABSTRACT
In this work, we have developed a truncated DNA aptamer, termed XQ-2d, with high affinity and specificity for pancreatic ductal adenocarcinoma (PDAC). Aptamer XQ-2d selectively binds to PL45 cells with a dissociation constant in the nanomolar range, as determined by its recognition of PL45 tumor cells in mice. Moreover, XQ-2d shows better recognition ratio for 40 tissue sections of clinical PDAC samples (82.5%) compared to the initial cell-SELEX selection library (5%). Therefore, XQ-2d can be considered a promising candidate as a tool for PDAC diagnosis and treatment.

No MeSH data available.


Related in: MedlinePlus

Truncation of aptamer XQ-2 and characterization of XQ-2d. (a) Binding ability of different truncated versions by removing nucleotides at 5' and 3'-terminus (250 nM) on target PL45 cells. (b) Secondary structure of XQ-2d predicted by Nupack. (c) Binding assay of XQ-2d (250 nM) to PL45 cells in the presence of XQ-2 (2.5 µM) or unselected library (2.5 µM). (d) Dissociation constant of truncated XQ-2d for target PL45 cells.
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Figure 6: Truncation of aptamer XQ-2 and characterization of XQ-2d. (a) Binding ability of different truncated versions by removing nucleotides at 5' and 3'-terminus (250 nM) on target PL45 cells. (b) Secondary structure of XQ-2d predicted by Nupack. (c) Binding assay of XQ-2d (250 nM) to PL45 cells in the presence of XQ-2 (2.5 µM) or unselected library (2.5 µM). (d) Dissociation constant of truncated XQ-2d for target PL45 cells.

Mentions: To reduce the cost of DNA synthesis, the full-length aptamer XQ-2 (80nt, 1-80) is required truncation, but with minimal loss in binding ability. Six kinds of truncated versions of the XQ-2 aptamer were synthesized by gradually removing the nucleotides at the 5' and 3' termini (Supplementary Table S1) and then testing the binding ability to PL45 cells by flow cytometry. It could be seen that XQ-2a (65nt, 10-74) and XQ-2d (56nt, 15-70) kept strong binding affinity (Figure 6A). However, further truncation resulted in reduction of the binding ability shown by full-length XQ-2. The structure of XQ-2d was predicted by Nupack as a stem-loop structure with two hairpins on the loop (Figure 6B). When the stem of XQ-2d was replaced by other base pairs or random bases, or the loop of XQ-2d was replaced by random bases, respectively (Supplementary Table S2), these substitutions caused the loss of binding ability of XQ-2d (Supplementary Figure S2), indicating that the bases from stem and loop are responsible for the binding function of XQ-2d. When PL45 cells were incubated with XQ-2d in the presence of 15-fold XQ-2 or initial library, it was found that XQ-2, but not library, could inhibit the binding of XQ-2d to PL45 cells (Figure 6C). Since the binding inhibition might be derived from by the fact that the binding site of XQ-2d on the targeted PL45 cell surface were occupied by 10-fold molar excess of XQ-2, this competition assay proved that XQ-2 and XQ-2d bound to the same protein target on the surface of PL45 cells. Thus, XQ-2d was suggested as the most suitable truncated form of XQ-2 still able to maintain strong binding affinity based on their respective Kds (55.02 nM, Figure 6D vs. 82.5 nM, Supplementary Figure S1), while still retaining the selectivity of full-length XQ-2, which had little, to no, binding to hTERT-HPNE cells (Supplementary Figure S3).


DNA Aptamer Selected against Pancreatic Ductal Adenocarcinoma for in vivo Imaging and Clinical Tissue Recognition.

Wu X, Zhao Z, Bai H, Fu T, Yang C, Hu X, Liu Q, Champanhac C, Teng IT, Ye M, Tan W - Theranostics (2015)

Truncation of aptamer XQ-2 and characterization of XQ-2d. (a) Binding ability of different truncated versions by removing nucleotides at 5' and 3'-terminus (250 nM) on target PL45 cells. (b) Secondary structure of XQ-2d predicted by Nupack. (c) Binding assay of XQ-2d (250 nM) to PL45 cells in the presence of XQ-2 (2.5 µM) or unselected library (2.5 µM). (d) Dissociation constant of truncated XQ-2d for target PL45 cells.
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Related In: Results  -  Collection

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Figure 6: Truncation of aptamer XQ-2 and characterization of XQ-2d. (a) Binding ability of different truncated versions by removing nucleotides at 5' and 3'-terminus (250 nM) on target PL45 cells. (b) Secondary structure of XQ-2d predicted by Nupack. (c) Binding assay of XQ-2d (250 nM) to PL45 cells in the presence of XQ-2 (2.5 µM) or unselected library (2.5 µM). (d) Dissociation constant of truncated XQ-2d for target PL45 cells.
Mentions: To reduce the cost of DNA synthesis, the full-length aptamer XQ-2 (80nt, 1-80) is required truncation, but with minimal loss in binding ability. Six kinds of truncated versions of the XQ-2 aptamer were synthesized by gradually removing the nucleotides at the 5' and 3' termini (Supplementary Table S1) and then testing the binding ability to PL45 cells by flow cytometry. It could be seen that XQ-2a (65nt, 10-74) and XQ-2d (56nt, 15-70) kept strong binding affinity (Figure 6A). However, further truncation resulted in reduction of the binding ability shown by full-length XQ-2. The structure of XQ-2d was predicted by Nupack as a stem-loop structure with two hairpins on the loop (Figure 6B). When the stem of XQ-2d was replaced by other base pairs or random bases, or the loop of XQ-2d was replaced by random bases, respectively (Supplementary Table S2), these substitutions caused the loss of binding ability of XQ-2d (Supplementary Figure S2), indicating that the bases from stem and loop are responsible for the binding function of XQ-2d. When PL45 cells were incubated with XQ-2d in the presence of 15-fold XQ-2 or initial library, it was found that XQ-2, but not library, could inhibit the binding of XQ-2d to PL45 cells (Figure 6C). Since the binding inhibition might be derived from by the fact that the binding site of XQ-2d on the targeted PL45 cell surface were occupied by 10-fold molar excess of XQ-2, this competition assay proved that XQ-2 and XQ-2d bound to the same protein target on the surface of PL45 cells. Thus, XQ-2d was suggested as the most suitable truncated form of XQ-2 still able to maintain strong binding affinity based on their respective Kds (55.02 nM, Figure 6D vs. 82.5 nM, Supplementary Figure S1), while still retaining the selectivity of full-length XQ-2, which had little, to no, binding to hTERT-HPNE cells (Supplementary Figure S3).

Bottom Line: In this work, we have developed a truncated DNA aptamer, termed XQ-2d, with high affinity and specificity for pancreatic ductal adenocarcinoma (PDAC).Moreover, XQ-2d shows better recognition ratio for 40 tissue sections of clinical PDAC samples (82.5%) compared to the initial cell-SELEX selection library (5%).Therefore, XQ-2d can be considered a promising candidate as a tool for PDAC diagnosis and treatment.

View Article: PubMed Central - PubMed

Affiliation: 1. Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China.

ABSTRACT
In this work, we have developed a truncated DNA aptamer, termed XQ-2d, with high affinity and specificity for pancreatic ductal adenocarcinoma (PDAC). Aptamer XQ-2d selectively binds to PL45 cells with a dissociation constant in the nanomolar range, as determined by its recognition of PL45 tumor cells in mice. Moreover, XQ-2d shows better recognition ratio for 40 tissue sections of clinical PDAC samples (82.5%) compared to the initial cell-SELEX selection library (5%). Therefore, XQ-2d can be considered a promising candidate as a tool for PDAC diagnosis and treatment.

No MeSH data available.


Related in: MedlinePlus