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Nonnatural deoxyribonucleoside D_3 incorporated in an intramolecular DNA triplex binds sequence-specifically by intercalation

Koshlap, Karl M. and Gillespie, Paul and Dervan, Peter B. and Feigon, Juli (1993) Nonnatural deoxyribonucleoside D_3 incorporated in an intramolecular DNA triplex binds sequence-specifically by intercalation. Journal of the American Chemical Society, 115 (17). pp. 7908-7909. ISSN 0002-7863. https://resolver.caltech.edu/CaltechAUTHORS:20160510-134706248

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Abstract

Oligonucleotide-directed triple helix formation is one of the most powerful methods for the sequence-specific recognition of double-helical DNA. Pyrimidine oligonucleotides bind purine tracts in the major groove of DNA parallel to the purine Watson-Crick strand through the formation of specific Hoogsteen-type hydrogen bonds. Specificity is derived from thymine (T) recognition of adenine·thymine (A·T) base pairs (T·A·T triplet) and N3-protonated cytosine (C+) recognition of guanine-cytosine (G·C) base pairs (C + G·C triplets). The sequence-specific recognition of double-helical DNA by a third strand to form a triple helix is limited to mostly purine tracts. Although G in the third strand has been found to specifically bind to T·A, the lower stability of the G·T·A triplet and its dependence on the sequence of the neigh boring triplets reveals that this will have limitations. In an attempt to extend the recognition code to all four Watson-Crick base pairs, the nonnatural deoxyribonucleoside 1-(2-deoxy/ β-D-ribofuranosyl)-4-(3-benzamido)phenylimidazole [D_3] was synthesized and incorporated into pyrimidine DNA oligonucleotides (Figure 1a). It was found that D_3 selectively recognizes both T·A and C·G Watson-Crick base pairs within the pyrimidine·purine·pyrimidine triple-helix motif. This was also found to have a nearest neighbor dependence.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1021/ja00070a059DOIArticle
http://pubs.acs.org/doi/abs/10.1021/ja00070a059PublisherArticle
ORCID:
AuthorORCID
Dervan, Peter B.0000-0001-8852-7306
Additional Information:© 1993 American Chemical Society. Received May 26, 1993. This work was supported by grants from NIH (R01 GM 37254-01) and NSF Presidential Young Investigator Award (DMB 89-58280), with matching funds from AmGem Inc., DuPont/Merck Pharmaceuticals, Monsanto Co., and Sterling Drug Inc. to J.F., and Office of Naval Research grant to P.B.D.
Funders:
Funding AgencyGrant Number
NIHR01 GM 37254-01
NSFDMB 89-58280
AmgenUNSPECIFIED
DuPont/Merck PharmaceuticalsUNSPECIFIED
Monsanto Co.UNSPECIFIED
Sterling Drug Inc.UNSPECIFIED
Office of Naval Research (ONR)UNSPECIFIED
Issue or Number:17
Record Number:CaltechAUTHORS:20160510-134706248
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20160510-134706248
Official Citation:Nonnatural deoxyribonucleoside D3 incorporated in an intramolecular DNA triplex binds sequence-specifically by intercalation Karl M. Koshlap, Paul Gillespie, Peter B. Dervan, and Juli Feigon Journal of the American Chemical Society 1993 115 (17), 7908-7909 DOI: 10.1021/ja00070a059
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:66923
Collection:CaltechAUTHORS
Deposited By: Victoria Brennan
Deposited On:19 May 2016 16:57
Last Modified:26 Nov 2019 11:15

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