Structural Variation Detection and Analysis Using Bionano Optical Mapping.

The need to accurately identify the complete structural variation profile of genomes is becoming increasingly evident. In contrast to reference-based methods like sequencing or comparative methods like aCGH, optical mapping is a de novo assembly-based method that enables better realization of true genomic structure. It allows for independently detecting balanced and unbalanced structural variants (SVs) from separate alleles and for discovering de novo events.

Using bifunctional polymers presenting vancomycin and fluorescein groups to direct anti-fluorescein antibodies to self-assembled monolayers presenting d-alanine-d-alanine groups.

This paper describes the synthesis of bifunctional polyacrylamides containing pendant vancomycin (Van) and fluorescein groups, and the use of these polymers to direct antibodies against fluorescein to self-assembled monolayers (SAMs) presenting d-alanine-d-alanine (dAdA) groups. These polymers bind biospecifically to these SAMs via interactions between the dAdA and Van groups and serve as a molecular bridge between the anti-fluorescein antibodies and the SAM. The binding events were characterized using surface plasmon resonance spectroscopy and fluorescence microscopy.

Molecular rectification in a metal-insulator-metal junction based on self-assembled monolayers.

An electrical junction formed by mechanical contact between two self-assembled monolayers (SAMs)--a SAM formed from an dialkyl disulfide with a covalently linked tetracyanoquinodimethane group that is supported by silver (or gold) and a SAM formed from an alkanethiolate SAM that is supported by mercury-rectifies current. The precursor to the SAM on silver (or gold) was bis(20-(2-((2,5-cyclohexadiene-1,4-diylidene)dimalonitrile))decyl)) disulfide and that for the SAM on mercury was HS(CH(2))(n-1)CH(3) (n = 14, 16, 18). The electrical properties of the junctions were characterized by current-voltage measurements.

Ru(phen)(2)dppz(2+) Luminescence: Dependence on DNA Sequences and Groove-Binding Agents.

Emission of Delta-Ru(phen)(2)dppz(2+) bound to nucleic acid polymers of different sequence has been investigated by time-resolved luminescence spectroscopy and the effect of major and minor groove DNA binding agents on the luminescence profile of the complex evaluated. In the presence of a 1:1 mixture of poly d(AT) and poly d(GC), the excited-state decay of Delta-Ru(phen)(2)dppz(2+) can be described by a linear combination of the decay profiles in the presence of poly d(AT) and poly d(GC) independently. This analysis indicates that approximately 85% of the complexes are bound to poly d(AT) and that the metallointercalator preferentially occupies AT sites in mixed-sequence polymers such as calf thymus or T4 DNA.

Correlating Electron Transport and Molecular Structure in Organic Thin Films.

A convenient experimental system is described, with which electron transport through structurally well-defined, 2-5 nm-thick, organic films can be examined. Two types of junction J have been studied in which self-assembled monolayers (SAMs, for example, SAM(1) formed on Ag from aliphatic and aromatic thiols, and SAM(2), formed on Hg from hexadecanethiol) are in contact through either van der Waals interactions or through covalent, hydrogen, or ionic bonds.

Zwitterionic SAMs that Resist Nonspecific Adsorption of Protein from Aqueous Buffer.

This paper describes the use of surface plasmon resonance spectroscopy and self-assembled monolayers (SAMs) of alkanethiols on gold to evaluate the ability of surfaces terminating in different combinations of charged groups to resist the nonspecific adsorption of proteins from aqueous buffer. Mixed SAMs formed from a 1:1 combination of a thiol terminated in a trimethylammonium group and a thiol terminated in a sulfonate group adsorbed less than 1% of a monolayer of two proteins with different characteristics:  fibrinogen and lysozyme. Single-component SAMs formed from thiols terminating in groups combining a positively charged moiety and a negatively charged moiety were also capable of resisting the adsorption of proteins.