Nucleobase Orientation and Ordering in Films of Single-Stranded DNA on Gold

Petrovykh, Dmitri Y.; Pérez-Dieste, Virgínia; Opdahl, Aric; Kimura-Suda, Hiromi; Sullivan, J. M.; Tarlov, Michael J.; Himpsel, F. J.; Whitman, L. J.

doi:10.1021/ja052443e

Cited by 131 publications

(230 citation statements)

References 13 publications

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“…At high grafting densities, randomly coiled ssDNA probes were predominantly anchored via thiols and possibly one or two other bases. Further studies using near-edge X-ray absorption fine structure spectroscopy 28 suggested that DNA bases in short probes tended to orient parallel to the surface. In contrast, long DNA probes formed disordered films similar to polyelectrolyte brushes.…”

Section: D Dna Probesmentioning

confidence: 99%

Scaffolded biosensors with designed DNA nanostructures

et al. 2013

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In addition to its fundamental function as a genetic code carrier, the utilization of DNA in various material applications has been actively explored over the past several decades. DNA is intrinsically an excellent type of self-assembly nanomaterial owing to its predictable base-pairing, high chemical stability and the convenience it possesses for synthesis and modification. Because of these unparalleled properties, DNA is widely used as excellent recognition elements in biosensors and as unique building blocks in nanodevices. A critical challenge in surface-based DNA biosensors lies in the reduced accessibility of target molecules to the DNA probes arranged on heterogeneous surfaces, especially when compared to probe-target recognition in homogeneous solutions. To improve the recognition abilities of these heterogeneous surface-confined DNA probes, much effort has been devoted to controlling the surface chemistry, conformation and packing density of the probe molecules, as well as the size and geometry of the surface. In this review, we aim to summarize the recent progress on the improvement of the probetarget recognition properties by introducing DNA nanostructure scaffolds. A range of new strategies have proven to provide a significantly enhanced range in the spatial positioning and the accessibility of the probes to the surface over previously reported linear structures. We will also describe the applications of DNA nanostructure scaffold-based biosensors. INTRODUCTIONDetection of nucleic acids (DNA or RNA) is an integral step in many applications, including in clinical diagnosis, environmental monitoring and antibioterrorism. 1 With these applications in mind, significant efforts have been made to develop sensitive, selective, rapid and cost-effective DNA (or RNA) biosensors. In parallel, DNAbased devices have also attracted a significant, recent interest owing to their promising applications in nanoelectronics, 2,3 biomolecular computations, 4-8 cellular imaging 9 and drug delivery. [10][11][12] In a typical design of DNA biosensors and nanodevices, oligonucleotides are often used as the molecular recognition layer. Because DNA is comprised of only four bases with A-T and G-C pairing, DNA hybridization processes are highly predictable and can be finely tuned with a rational design of the sequence. In addition, DNA oligonucleotides are usually easy to design, chemically stable and cost-effective.Understanding the physical structure of a DNA probe immobilized on a surface is critical in applications using DNA as a molecular recognition element. The properties of the DNA molecular recognition layer (such as selectivity, sensitivity and reproducibility) highly depend on the structure of the self-assembled DNA film. Modeling studies with thiolated DNA have demonstrated that efficient hybridization occurs in the well-controlled condition of surface-attached probes with large interprobe distances and upright conformations. [13][14][15][16][17][18][19][20][21][22][23][24]

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Section: D Dna Probesmentioning

confidence: 99%

Scaffolded biosensors with designed DNA nanostructures

et al. 2013

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“…17,18 The final strand density in self-assembled monolayers plays a critical role in nanomechanical sensing 9 and it is indeed far from being fully controllable. 19,[20][21][22][23] One singularly limiting difficulty has been to accomplish the anchoring of the ssDNA probes with a well-defined uniform density and a standing up conformation. 19,24 For such purpose, sophisticated nanografting methods need to be applied.…”

Section: Introductionmentioning

confidence: 99%

Hydration Induced Stress on DNA Monolayers Grafted on Microcantilevers

et al. 2014

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Surface tethered single-stranded DNA films are relevant biorecognition layers for oligonucleotide sequence identification. Also, hydration induced effects on these films have proven useful for the nanomechanical detection of DNA hybridization. Here, we apply nanomechanical sensors and atomic force microscopy to characterize in air and upon varying relative humidity conditions the swelling and deswelling of grafted single stranded and double stranded DNA films. The combination of these techniques validates a two-step hybridization process, where complementary strands first bind to the surface tethered single stranded DNA probes and then slowly proceed to a fully zipped configuration. Our results also demonstrate that, despite the slow hybridization kinetics observed for grafted DNA onto microcantilever surfaces, ex-situ sequence identification does not require hybridization times typically longer than 1 hour, while quantification is a major challenge.. 2

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“…[1][2][3] A promising alternative strategy is using model peptides to reduce the complexity of the problem. [4][5][6][7][8] For spectral data to be interpretable and informative in the broader context of protein structures, however, peptide model systems must be chosen carefully to embody both the level of structure ͑pri-mary, secondary, tertiary, etc.͒ and type of structure ͑helix, sheet, turn, etc.͒ that one wishes to investigate. A model system that we analyzed in this study, for example, is ␤ helices-helices composed of alternating D-and L-␣-amino acids that are stabilized by ␤-sheet hydrogen bonding.…”

Section: Introductionmentioning

confidence: 99%

Vibrational circular-dichroism spectroscopy of homologous cyclic peptides designed to fold into β helices of opposite chirality

et al. 2011

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Cyclic ␤-helical peptides have been developed as model structured biomolecules for examining peptide adsorption and conformation on surfaces. As a key prerequisite to circular-dichroism ͑CD͒ analysis of these model peptides on surfaces, their conformations and the corresponding vibrational spectra in the 1400-1800 cm −1 range were analyzed by vibrational circular-dichroism ͑VCD͒ spectroscopy in solution. The two model peptides ͑"␤ Leu and ␤ Val"͒ were examined in chloroform, where they each fold into a homogeneous well-defined antiparallel double-stranded ␤-helical species, as determined previously by NMR and electronic CD spectroscopy. Because the ␤-helical conformations of ␤ Leu and ␤ Val are well characterized, the VCD spectra of these peptides can be unambiguously correlated with their structures. In addition, these two ␤-helical peptides differ from one another in two key respects that make them uniquely advantageous for CD analysis-first, while their backbone conformations are topologically similar, ␤ Leu and ␤ Val form helices of opposite chiralities; second, the two peptides differ in their sequences, i.e., composition of the side chains attached to the backbone. The observed VCD spectra for ␤ Leu and ␤ Val are roughly mirror images of each other, indicating that the VCD features are dominated by the chirality and conformation of the peptide backbone rather than by the peptide sequence. Accordingly, spectra similarly characteristic of peptide secondary structure can be expected for peptides designed to be structural analogs of ␤ Leu and ␤ Val while incorporating a variety of side chains for studies of surface adsorption from organic and aqueous solvents.

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Nucleobase Orientation and Ordering in Films of Single-Stranded DNA on Gold

Cited by 131 publications

References 13 publications

Scaffolded biosensors with designed DNA nanostructures

Scaffolded biosensors with designed DNA nanostructures

Hydration Induced Stress on DNA Monolayers Grafted on Microcantilevers

Vibrational circular-dichroism spectroscopy of homologous cyclic peptides designed to fold into β helices of opposite chirality

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