Measurement of Nucleobase p<i>K</i><sub>a</sub>Values in Model Mononucleotides Shows RNA−RNA Duplexes To Be More Stable than DNA−DNA Duplexes

Acharya, Parag; Cheruku, Pradeep; Chatterjee, Subhrangsu; Acharya, Sandipta; Chattopadhyaya, J.

doi:10.1021/ja0386546

Cited by 73 publications

(89 citation statements)

References 23 publications

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“…The increased resistance in the n-type SiNW implies an increased negative charge on the wire surface. This is consistent with the fact that DNA molecules with an isoelectric point 31,32 of about 5.0 should possess negative charges in a pH 8 electrolyte. Figure 5b shows resistance of two p-type wires measured simultaneously as a function of gate voltage before and after introduction of 15A ssDNA.…”

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confidence: 85%

Control and Detection of Organosilane Polarization on Nanowire Field-Effect Transistors

et al. 2007

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We demonstrated control and detection of UV-induced 3-aminopropyltriethoxysilane (APTES) polarization using silicon nanowire field-effect transistors made by top-down lithograph technology. The electric dipole moment in APTES films induced by UV-illumination was shown to produce negative effective charges. When individual dipoles were aligned with an externally applied electric field, the collective polarization can prevail over the UV-induced charges in the wires and give rise to an abnormal resistance enhancement in n-type wires. Real-time detection of hybridization of 15-mer poly-T/poly-A DNA molecules was performed, and the amount of hybridization-induced charges in the silicon wire was estimated. Based on these results, detection sensitivity of the wire sensors was discussed.Hetero-interfaces between organic and semiconductor oxides have attracted extensive attentions 1-4 due to the critical role of molecule assembly in the sensing electronics involving hybrid structures. APTES 5 (3-aminopropyltriethoxysilane) and other compounds such as PTS 6 (n-propyltrichlorosilane), OTS 7 (n-octadecyltrichlorosilane), TCTS 8 (n-triacontyltrichlorosilane), OTMS 9 (n-octadecyltrimethoxysilane), and AHT-MS 9 (n-aminoheptadecyltrimethoxysilane) with head-andtail functional groups are widely used interfacing molecules, and assembly of these molecules is essential in surfacemodification technologies. Silanization of oxidized semiconductor surfaces is a commonly employed scheme for functionalization of sensors. The functional groups would then provide binding sites for attachment of probe molecules, such as single-strand DNA (ssDNA), on the semiconductor sensing devices. The nanowire-based sensors have been demonstrated 10-14 as an ultra sensitive detector for probing molecular charges at the wire surface. However, surface modification of the functional groups on the nanowire surface is not a trivial task. Extensive studies in the surfacemodification were reported in the past years, 5-9 but issues concerning monolayer molecule ordering in terms of the electric dipole moment remain unexplored. Taking APTES as an example, in this study, we proposed a simple method to align the molecule dipoles, and the degree of alignment was examined by underneath Si-nanowire (SiNW) field effect transistors. This method provides a sensitive way for structure investigation of few molecules at the nanometer scale, which is otherwise unfeasible by the present-day examination tools. † These authors contributed equally to this work.

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confidence: 85%

Control and Detection of Organosilane Polarization on Nanowire Field-Effect Transistors

et al. 2007

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“…1). Because, in general, 2Ј-deoxyribonucleosides are somewhat more basic than their ribonucleoside counterparts (11,24), ខ ⌬pK a ϭ 0. Under our conditions, the experimental data of the potentiometric pH titrations can be explained fully by considering equilibria 1 and 3, the latter defining complex formation,…”

Section: Resultsmentioning

confidence: 99%

Metal ion-binding properties of (N3)-deprotonated uridine, thymidine, and related pyrimidine nucleosides in aqueous solution

Knobloch

Linert

Sigel

2005

Proc. Natl. Acad. Sci. U.S.A.

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The acidity constants for (N3)H of the uridine-type ligands (U) 5-fluorouridine, 5-chloro-2-deoxyuridine, uridine, and thymidine (2-deoxy-5-methyluridine) and the stability constants of the M(U-H) ؉ complexes for M 2؉ chelate formation ͉ equilibrium constants ͉ metal ion complexes ͉ nucleic acids ͉ nucleobase properties T he importance of metal ion-nucleic acid interactions in the metabolic machinery is well recognized and applied, e.g., in medicinal chemistry (1). Crystal-structure analyses of nucleic acids (2), especially RNAs (3), show that metal ions coordinate to the phosphate-diester bridges as well as to nucleobase residues, and they are important for folding and catalysis of ribozymes (3-5).The N7 sites of purine residues are exposed in the major groove of DNA (2) and accessible for metal ion binding (6). Maybe this is one reason why their metal ion-coordinating properties are relatively well studied (6-11) in contrast to those of pyrimidine-nucleobase residues (8-10). In fact, the stabilities and solution structures of cytidine (Cyd) complexes of biologically relevant metal ions were quantified only recently (12). Knowledge on uridine complexes is scarce: The carbonyl oxygens (C2)O and (C4)O of uracil residues in low (2, 13) and high (2, 3, 14, 15) molecular weight derivatives may interact in the solid state with metal ions, but in aqueous (aq) solution monodentate carbonyl-oxygen ligands bind only if correctly positioned by primary sites (16).In a recent study (17) with Mg 2ϩ

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“…44, No. 14, 2005 5395 strength of hydrogen bonding in DNA and RNA duplexes (70). The stability of the stacked over the destacked conformation is finally determined by the net free-energy of multiple interactions including the electrostatic effects (charges), van der Waals (dipoles and dispersion interactions), and hydrophobic effects between the dangling base and any of the nucleobases in the closing basepair.…”

Section: Dangling-end Stabilization and Stacking Geometrymentioning

confidence: 99%

A Uniform Mechanism Correlating Dangling-End Stabilization and Stacking Geometry

Isaksson

Chattopadhyaya

2005

Biochemistry

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The geometry of the dangling base in 105 published structures (from X-ray/NMR) containing single-stranded overhangs has been analyzed and correlated to the thermodynamic stabilization found (UV) for the corresponding dangling base/closing basepair combination in short oligonucleotides. The study considers most combinations of closing basepairs, sequence and dangling base residue type, attached in both the 3′-and 5′-ends of both DNA and RNA. Linear regression analysis showed a straightforward correlation (R ) 0.873) between the degree of screening for the hydrogen bonds of the closing basepair provided by the dangling base and the resulting thermodynamic stabilization in both DNA and RNA series with dangling ends either at the 3′-or at the 5′-terminus. Regression analysis of only the datasets from RNA gives an improved correlation, R ) 0.934, showing that dangling ends on RNA are more ordered than the dangling ends on DNA, R ) 0.376. This study highlights the gain in the free energy of stabilization owing to the favorable stacking between the dangling nucleobase and the neighboring basepair and the resulting strengthening of the hydrogen bond of the closing basepair. By acting as a hydrophobic cap on the terminal of the DNA or RNA duplex, the dangling-end residue restricts the bulk water access to the terminal basepair, thereby providing it with a microenvironment devoid of water, which consequently enhances its thermodynamic stability, making it energetically comparable to the corresponding internal basepair. Thus, one single structural model consisting of the interplay of the above electrostatic interactions can be used to explain the molecular basis of the observed thermodynamic effects for dangling-end attachment to the 3′-and 5′-ends of both DNA and RNA duplexes, which is a key step toward accurate dangling-end effect prediction.Unpaired terminal nucleotides naturally occur in various biologically important RNA structures: The acceptor stem in tRNA (1-3) has a characteristic 3′-NCCA nucleobase overhang that determines its structure, stability, and function. The dangling ends neighboring the codon-anticodon pair have also been found to stabilize the interaction between tRNA and mRNA (4, 5) for protein synthesis in the ribosomal machinery. The efficiency of down regulation of gene expression by RNA interference (RNAi) has been shown to be dependent on a two to three nucleotide overhang (6-9). Similarly, the structures of pseudoknots (10) are stabilized by a complicated interplay between single-stranded and double-stranded motifs. A multitude of literature on the stabilizing interactions of native single-stranded oligonucleotides is available (9,(11)(12)(13)(14).Accurate prediction of nucleic acid secondary structure and stability from its primary sequence is a key interest for probe binding optimization in biotechnological applications such as microarrays (15) and molecular beacons (16). To develop an accurate algorithm (14,(17)(18)(19)(20)(21)(22)(23)(24) for predicting the thermodynamics of hybridi...

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Measurement of Nucleobase pK_aValues in Model Mononucleotides Shows RNA−RNA Duplexes To Be More Stable than DNA−DNA Duplexes

Cited by 73 publications

References 23 publications

Control and Detection of Organosilane Polarization on Nanowire Field-Effect Transistors

Control and Detection of Organosilane Polarization on Nanowire Field-Effect Transistors

Metal ion-binding properties of (N3)-deprotonated uridine, thymidine, and related pyrimidine nucleosides in aqueous solution

A Uniform Mechanism Correlating Dangling-End Stabilization and Stacking Geometry

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Measurement of Nucleobase pKaValues in Model Mononucleotides Shows RNA−RNA Duplexes To Be More Stable than DNA−DNA Duplexes

Cited by 73 publications

References 23 publications

Control and Detection of Organosilane Polarization on Nanowire Field-Effect Transistors

Control and Detection of Organosilane Polarization on Nanowire Field-Effect Transistors

Metal ion-binding properties of (N3)-deprotonated uridine, thymidine, and related pyrimidine nucleosides in aqueous solution

A Uniform Mechanism Correlating Dangling-End Stabilization and Stacking Geometry

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Measurement of Nucleobase pK_aValues in Model Mononucleotides Shows RNA−RNA Duplexes To Be More Stable than DNA−DNA Duplexes