Endcaps for Stabilizing Short DNA Duplexes

Ng, Pei-Sze; Pingle, Maneesh; Balasundarum, Ganesan; Friedman, Alan M.; Zu, Xiaolin; Bergstrom, Donald E.

doi:10.1081/ncn-120023088

Cited by 5 publications

(5 citation statements)

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“…It is evident from the study of the C12 hydrocarbon end-cap that the nature and length of the end-cap are important considerations in the design. This observation is supported by previous work conducted in the Bergstrom lab on the evaluation of spacers for use as dsDNA end-caps. − The end-capped duplex stem in the capture modules confers high affinity and specificity for hybridization to overhanging sequences at the termini of pRNA overhybridization to the same sequence within the RNA. This specificity is due to the “preorganization” of the duplex stem region by the end-cap.…”

supporting

confidence: 64%

“…We believe that there is a way to rapidly and reversibly add modules to the 3′/5′-pRNA overhang that are small, have high affinity and specificity for the pRNA overhang, are simple to synthesize, and can link virtually any kind of molecule (including small ligands, peptides, lipids, carbohydrates, and fluorophores). Bergstrom and co-workers have utilized a method for stabilizing short segments of double-stranded oligonucleotides by covalently linking the 3′ and 5′ ends of the nucleic acid with a simple spacer. − The simplest spacer is the C12 hydrocarbon ( S2 ) shown in Figure D. Nucleic acid duplexes containing just four base pairs and linked by a spacer at one end have melting temperatures ( T m values) in the range 41–62 °C (the same duplexes without the spacers are unstable at room temperature, i.e., T m < 25 °C).…”

mentioning

confidence: 99%

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Evaluation of End-Capped DNA Modules for pRNA Capture and Functionalization

Laing

Bergstrom

2012

Bioconjugate Chem.

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The ability of packaging RNA (pRNA) from the phi29 DNA packaging motor to form nanoassemblies and nanostructures has been exploited for the development of the nascent field of RNA nanotechnology and subsequent applications in nanomedicine. For applications in nanomedicine, it is necessary to modify the pRNA structure for the conjugation of active molecules. We have investigated endcapped double-stranded DNA segments as reversible capture reagents for pRNA. These capture agents can be designed to allow the conjugation of any desired molecule for pRNA functionalization. The results of model studies presented in this report show that 5- to 7-nucleotide overhangs on a target RNA can provide efficient handles for the high affinity association to capped double-stranded DNA.

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supporting

confidence: 64%

mentioning

confidence: 99%

Evaluation of End-Capped DNA Modules for pRNA Capture and Functionalization

Laing

Bergstrom

2012

Bioconjugate Chem.

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“…In addition, we prepared the terthiophene spacer 2 , which provided an opportunity to study and compare an exceptionally hydrophobic end-cap. Several research groups had reported that hydrophobic, aromatic molecules such as naphthalene diimides 32 − 34 ,, , N , N -dimethylstilbene dicarboxamide , trimethoxystilbenes, and stilbene ether stabilized DNA duplexes through stacking interactions with the DNA bases. We expected that end-cap 2 , with a terthiophene core, would also have significant stacking interactions with the base pairs in a DNA duplex.…”

Section: Resultsmentioning

confidence: 99%

Synthesis and Evaluation of New Spacers for Use as dsDNA End-Caps

Laing

Balasundarum

et al. 2010

Bioconjugate Chem.

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A series of aliphatic and aromatic spacer molecules designed to cap the ends of DNA duplexes have been synthesized. The spacers were converted into dimethoxytrityl protected phosphoramidites as synthons for oligonucleotides synthesis. The effect of the spacers on the stability of short DNA duplexes was assessed by melting temperature studies. Endcaps containing amide groups were found to be less stabilizing than the hexaethylene glycol spacer. Endcaps containing either a terthiophene or a naphthalene tetracarboxylic acid dimide were found to be significantly more stabilizing. The former showed a preference for stacking above an A•T base pair. Spacers containing only methylene (-CH 2 -) and amide (-CONH-) groups interact weakly with DNA and consequently may be optimal for applications that require minimal influence on DNA structure but require a way to hold the ends of double-stranded DNA together.

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“…[11,14] In summary, we have demonstrated the efficient templatedirected synthesis of hairpin metallosalen ± DNA conjugates (Ni-3 and Mn-3) and a metal-free salen ± DNA (EN-3). Templatedirected synthesis of hairpin structures, a demonstrated approach for the synthesis of DNA ± organic molecular conjugates, [15] has been extended to metal ± DNA hybrids.…”

Section: Template-directed Assembly Of Metallosalen ± Dna Hairpin Conmentioning

confidence: 98%

Template‐Directed Assembly of Metallosalen–DNA Hairpin Conjugates

Czlapinski

Sheppard

2003

ChemBioChem

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Nucleic acid template-directed synthesis offers a novel method for the encoded assembly of DNA conjugates.[1] DNA templatedirected reactions have been developed for chemical ligation of DNA oligonucleotides [2±3] and extended to ligation-based detection systems for point mutations.[4] More generally, templated reactions have successfully directed the synthesis of a remarkable range of chemical structures and reaction classes [1±5] and shown potential for multiplexed synthesis of complex organic molecule ± DNA conjugates. [6] Our laboratory previously demonstrated the template-directed synthesis of a new metal ± DNA hybrid, metallosalen ± DNA, by diamine cross-linking of salicylaldehyde-modified DNA on an external template.[5] Herein we report the formation and characterization of nickel, manganese, and metal-free salen ± DNA conjugates that adopt a hairpin-loop motif (Scheme 1). Metallosalen ± DNA hairpin conjugates were designed to determine the three-dimensional structure of metallosalen ± DNA hybrids and to evaluate the effect of metallosalen ± base pair stacking interactions on DNA duplex stability. Our approach to hairpin metallosalen ± DNA conjugates (Scheme 1 A) utilizes two complementary DNA oligonucleotides modified with a salicylaldehyde moiety at either the 3'-or 5'-end (1 and 2, respectively). Strands 1 and 2 were aligned by complementary base pairing, which placed the salicylaldehyde groups at the proximal end of a DNA duplex. The aromatic salicylaldehyde moieties were expected to stack with the adjacent base pairs in the duplex, [7] further organizing the salen ± DNA reaction. Addition of an appropriate diamine in the presence or absence of a divalent metal ion was expected to produce a hairpin-DNA structure capped by a metallosalen or salen moiety.Nickel metallosalen ± DNA hairpin conjugate (Ni-3) formation was assayed by polyacrylamide gel electrophoresis (PAGE) with radiolabeled 1 as a tracer (Figure 1). When strands 1 and 2 were annealed and incubated with 300 mM Ni(OAc) 2 and 150 mM ethylenediamine (EN), Ni-3 was formed in 66 % yield after 24 h (lane 1). Extension of the reaction time to 48 h did not enhance the yield of Ni-3 (lanes 3 and 5). Assembly reactions with strand 2 omitted were performed to assess the rate of unspecific reaction between salicylaldehyde-modified strands (nontemplated, NT). Notably, NT products (lanes 2, 4, and 6) were detected only after 48 h and at very low levels (1 %). Thus, Ni-3 assembly occurred in a template-directed fashion in 24 h. Similar results were obtained with Mn(OAc) 2 in place of Ni(OAc) 2 . However, as observed in our previous work, [5] manganese metallosalen ± DNA hairpin (Mn-3) formed more rapidly: 55 % yield in 1 h, with NT products becoming visible within 24 h (9 %).Previously, we demonstrated that metallosalen ± DNA assembly on an external template required the presence of a metal ion, a diamine, and pH conditions that provided appropriate metal speciation.[5] Interestingly, templated salen ± DNA hairpin (3)[a] Dr.

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Endcaps for Stabilizing Short DNA Duplexes

Cited by 5 publications

References 2 publications

Evaluation of End-Capped DNA Modules for pRNA Capture and Functionalization

Evaluation of End-Capped DNA Modules for pRNA Capture and Functionalization

Synthesis and Evaluation of New Spacers for Use as dsDNA End-Caps

Template‐Directed Assembly of Metallosalen–DNA Hairpin Conjugates

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