Regulating the on-surface LNA probe density for the highest target recognition efficiency.

The recent emergence of on-surface LNA-based assays as potentially better alternatives over DNA-based approaches, due to enhanced sensitivity and target specificity, raises the need for the precise identification of the factors that control the performance of these assays. In this work, we investigated whether the probe density of fully modified ssLNA probes on the gold(111) surface could influence the target recognition capacity of the LNA sensing layer and illustrated simple means to control it, primarily by adjusting the salt concentration, nature of the cation, and pH of the immobilization buffer. It was observed that monovalent Na(+) could more effectively control the sensor probe density compared to bivalent Mg(2+), leading to better target recognition. Interestingly, unlike in the case of ssDNA sensor probes, the target recognition efficiency of the LNA layer at the optimum probe density was found to be almost spacer-independent, probably due to the rigidity of the LNA backbone. The optimized LNA sensor layer could discriminate single base mismatches, detect a minimum target DNA concentration of 5 nM, and sense a significant level of hybridization within a time scale of a few minutes. To our knowledge, for the first time, we identify the factors that control the on-surface LNA probe density for maximizing the performance of the LNA sensing layer.

Maximizing mismatch discrimination by surface-tethered locked nucleic acid probes via ionic tuning.

Several investigations on DNA-based nucleic acid sensors performed in the past few years point toward the requirement of an alternative nucleic acid that can detect target DNA strands more efficiently, i.e., with higher sensitivity and selectivity, and can be more robust compared to the DNA sensor probes. Locked nucleic acid (LNA), a conformationally restricted DNA analogue, is potentially a better alternative than DNA, since it is nuclease-resistant, it can form a more stable duplex with DNA in a sequence-specific manner, and it interacts less with substrate surface due to presence of a rigid backbone. In this work, we probed solid-phase dehybridization of ssDNA targets from densely packed fully modified ssLNA probes immobilized onto a gold(111) surface by fluorescence-based measurement of the "on-surface" melting temperatures. We find that mismatch discrimination can be clearly improved by applying the surface-tethered LNA probes, in comparison to the corresponding DNA probes. We show that concentration as well as type of cation (monovalent and polyvalent) can significantly influence thermal stability of the surface-confined LNA-DNA duplexes, the nature of concentration dependence contradicting the solution phase behavior. Since the ionic setting influenced the fully matched duplexes more strongly than the singly mismatched duplexes, the mismatch discrimination ability of the surface-confined LNA probes could be controlled by ionic modulations. To our knowledge, this is the first report on ionic regulation of melting behavior of surface-confined LNA-DNA duplexes.

Enhancing on-surface mismatch discrimination capability of PNA probes by AuNP modification of gold(111) surface.

Unambiguous identification of single base mismatches in nucleic acid sequences is of great importance in nucleic acid detection assays. However, ambiguities are often encountered with, and therefore, a strategy for attaining substantially large enhancement of mismatch discrimination has been worked upon in this study. Short single-stranded peptide nucleic acid (PNA) and deoxyribonucleic acid (DNA) sensor probes that are immobilized onto gold nanoparticle (AuNP) modified Au(111) surface have been applied for target DNA detection. It will be shown that while both PNA and the analogous DNA probes exhibit generally better target detection abilities on the AuNP-modified Au(111) surface (elicited from fluorescence-based measurement of on-surface Tm values), compared to the bare Au(111) surface, PNA supersedes DNA, for all sizes of AuNPs (10, 50, and 90 nm) applied, with the difference being quite drastic in the case of the smallest 10 nm AuNP. It is found that while the AuNP curvature plays a pivotal role in target detection abilities of the PNA probes, the changes in the surface roughness caused by AuNP treatment do not exert any significant influence. This study also presents a means for preparing PNA-AuNP hybrids without altering PNA functionality and without AuNP aggregation by working with the surface-affixed AuNPs.

Facilitating mismatch discrimination by surface-affixed PNA probes via ionic regulation.

There has been a search for alternative nucleic acids that can be more effectively used in nucleic acid detection technologies compared to the DNA probes. Peptide nucleic acid (PNA), which contains a non-ionic peptidic backbone, offers such possibilities since it is nuclease-resistant, it binds to DNA with high affinity, and it can be readily self-assembled onto solid substrates, e.g., gold(111), with a molecular backbone orientation away from the substrate. Although application of PNA as a sensor probe has been exemplified, so far there is little or no account of the ionic modulation of single base mismatch discrimination capacity of surface-tethered PNA probes. Herein, we report "on-surface" melting temperatures of PNA-DNA duplexes formed on gold(111) surface, as obtained from fluorescence measurements. We show that surface-tethered PNA forms a stabler duplex than DNA, and is more effective in single base mismatch discrimination than DNA. Importantly, although PNA backbone is non-ionic, variation in the ionic components in hybridization buffer, i.e., varying concentration of monovalent sodium ion, and the nature of anion and the cation, exhibits clear effects on the mismatch discrimination capacity of PNA probes. In general, with decreasing cation concentration, PNA-DNA duplexes are stabilized and mismatch discrimination capacity of the PNA probes is enhanced. The stabilizing/destabilizing effects of anions are found to follow the Hofmeister series, emphasizing the importance of hydrophobic interaction between nucleobases for stability of the PNA-DNA duplexes. Interestingly, the nature of ionic dependence of "on-surface" mismatch detection ability of PNA probes differs significantly from the "solution" behavior of these probes.

Ordered self-assembled locked nucleic acid (LNA) structures on gold(111) surface with enhanced single base mismatch recognition capability.

Locked nucleic acid (LNA) is a conformationally restricted nucleic acid analogue, which is potentially a better alternative than DNA for application in the nucleic acid based biosensor technologies, due to its efficient and sequence-specific DNA/RNA detection capability and lack of molecule-surface interaction on solid surfaces, compared to DNA. We report, for the first time, a straightforward way (based on simple immersion method) of generating an ordered self-assembled LNA monolayer, which is bioactive, onto a gold(111) surface. This layer is capable of giving rise to a stronger DNA recognition signal (4-4.5 times) than its DNA counterpart, and importantly, it can differentiate between a fully complementary DNA target and that having a single base mismatch, where the mismatch discrimination ratio is almost two times compared to the ratio relevant in case of DNA-based detection. We have presented high-resolution atomic force microscopy (AFM) topographs of the well-defined one-dimensional LNA molecular ordering (few hundred nanometers long) and of the two-dimensional ordered assembly formed over a large area (7 µm × 7 µm) due to parallel positioning of the one-dimensional ordered arrangements. The effects of different parameters such as LNA concentration and incubation time on LNA self-assembly have been investigated. Further, reflection absorption infrared (RAIR) spectroscopy has been applied to obtain information about the orientation of the surface-immobilized LNA molecules for the first time. It has been found that the LNA molecules undergo an orientational transition from the "lying down" to the "upright" configuration in a time scale of few hours.

Parotid swelling due to external carotid artery thrombus-a rare manifestation in antiphospholipid syndrome.

Vascular complications in forms of venous and arterial thrombi are common scenario in antiphospholipid syndrome with raised titer of antibodies. Here we describe an 18 years old female who was admitted with right parotid swelling due to external carotid artery thrombi within gland parenchyma in antiphospholipid syndrome, with past history of right lower leg arterial occlusion and digital gangrene.

Enhancing sensitivity in a piezoresistive cantilever-based label-free DNA detection assay using ssPNA sensor probes.

In this work, a strategy for enhancing sensitivity in a label-free DNA detection assay, where the basic operational principle involves detection of the net surface stress induced bending motion of a piezoresistive microcantilever, upon target-binding, has been presented. A microcantilever array that allows experiments using sensor-reference configuration has been employed, where the cantilevers have been functionalized by inkjet printing technology, using short nucleic acid sequences of similar length (here, 12-mer), on both the sensor and the reference cantilevers. It is shown that application of the single stranded peptide nucleic acids (PNA), having non-ionic peptidic backbone, as the sensor probes improves the assay sensitivity about twenty times, even to the level of single base mismatch discrimination, compared to the DNA counterparts. We propose that the significantly improved performance of the PNA-based assay could be due to the orientational advantage of PNA probes as offered when a self-assembled ordered PNA structure is formed. Since the piezoresistive cantilever based method offers a practical means for target detection by rapid monitoring of the recognition events in fluid in real time, and importantly, since PNA is nuclease-resistant, this step of advancement may motivate future endeavours for detection of nucleic acid sequences in complex body fluid mimics.

Study of platelet aggregation in acute coronary syndrome with special reference to metabolic syndrome.

BACKGROUND/CONTEXT: Antiplatelet drug resistance increases the risk of adverse events like stent thrombosis in acute coronary syndrome (ACS). Metabolic syndrome (MS) is a prothrombotic state and presence of MS further increases the risk of antiplatelet drug resistance. AIMS AND OBJECTIVES: We studied platelet aggregation characteristics in patients of ACS for aspirin or clopidogrel resistance. We studied the relation of drug resistance with blood markers like high sensitivity C-reactive protein (hsCRP). We also studied for any relation of drug resistance with presence of MS. MATERIALS AND METHODS: We studied platelet aggregation characteristics by optical aggregometry using platelet-rich plasma (PRP) of patients. Collagen (2 µg/mL) and adenosine diphosphate (ADP; 10 µmol) were used. Greater than 50% aggregation in PRP of patients was taken as an evidence of drug resistance. Suitable blood tests were done including newer risk markers like hsCRP, apolipoprotein B, and fibrinogen. STATISTICAL TEST: Statistical tests included Student's t-test and Kendall's rank correlation coefficient. RESULTS: We had a total of 94 patients of ACS with 47 (50%) having MS. MS patients showed higher blood levels of hsCRP and fibrinogen. Twenty-eight (59.5%) patients with MS showed antiplatelet drug resistance compared to 12 patients without MS. Serum fibrinogen showed strongest correlation with drug resistance. HsCRP levels showed correlation with aspirin resistance (r = 0.53) only in the MS group. DISCUSSION AND CONCLUSION: We found significantly high prevalence of antiplatelet drug resistance. Aspirin and clopidogrel resistance was comparable. MS was a significant risk factor for drug resistance. The prothrombotic and proinflammatory markers showed strong correlation with drug resistance. A larger randomized trial is needed to better characterize this clinical problem.