Abstract: This invention provides dye phosphoramidites, particularly phosphoramidites of substituted cyclic bridged cyanine and related dyes, of the general formula: In this formula, each dotted line represents carbon atoms necessary to form a fused substituted or unsubstituted aromatic ring; m is an integer from 1 to 18; Y and Z are independently selected from the group consisting of S, O, N, CH2 and C(CH3)2; R1 is an alkyl; (PAM) is a phosphoramidite group; X{circle around (?)} is a negative ion; and Q is L-W, wherein L is a conjugated cyclic moiety and W is OR2, wherein R2 is a second alkyl. Methods of making and using the dye phosphoramidites are also provided.

Abstract: Hybrid multi-threaded access to data structures is provided in which hazard pointers are used for reads and locks are used for updates. Where a reader is attempting to read a data structure, the reader maintains a hazard pointer to the data structure before reading it, without globally acquiring a lock on the data structure. Upon the reader being finished reading the data structure, it removes the hazard pointer from the data structure. Where an updater is attempting to update the data structure, the updater globally acquires a lock on the data structure before updating it. Upon the updater being finished updating the data structure, it releases the lock from the data structure. To delete the data structure, first it is determined whether any hazard pointers point to the data structure, and where no hazard pointers do, the data structure is deleted.

Abstract: A method for accessing a protocol table includes providing a content addressable protocol table comprising a plurality of entries, wherein each entry includes a key field and an output field, constructing a key value from a protocol input, associatively searching the table for an entry whose key field matches the key value constructed from the input, and returning the output field of an entry whose key field matches that of the key value. The table optionally includes a mask field, and searching the table includes seeking the entry whose key field matches a bitwise AND of its mask field with the key value. An error is generated if no matching entry is found on the table.

Abstract: This invention provides dye phosphoramidites, particularly phosphoramidites of substituted cyclic bridged cyanine and related dyes, of the general formula: In this formula, each dotted line represents carbon atoms necessary to form a fused substituted or unsubstituted aromatic ring; m is an integer from 1 to 18; Y and Z are independently selected from the group consisting of S, O, N, CH2 and C(CH3)2; R1 is an alkyl; (PAM) is a phosphoramidite group; X is a n{circle around (?)}egative ion; and Q is L-W, wherein L is a conjugated cyclic moiety and W is OR2, wherein R2 is a second alkyl. Methods of making and using the dye phosphoramidites are also provided.

Abstract: The present invention relates to a method, computer program product and system for a general purpose dynamic memory allocator that is completely lock-free, and immune to deadlock, even when presented with the possibility of arbitrary thread failures and regardless of thread scheduling. Further the invention does not require special hardware or scheduler support and does not require the initialization of substantial portions of the address space.

Abstract: A method of queuing of received transactions that have a resource conflict is disclosed. A first node receives a first transaction from a second node, where the first transaction relates to a resource of the first node. The transaction may be a request relating to a memory line of the first node, for instance. It is determined that a second transaction that relates to this resource of the first node is already being processed by the first node. Therefore, the first transaction is enqueued in a conflict queue within the first node. The queuing may be a linked list, a priority queue, or another type of queue. Once the second transaction has been processed, the first transaction is restarted for processing by the first node. The first transaction is then processed by the first node.

Abstract: The temporary storage of a memory line to be stored in a cache while waiting for another memory line to be evicted from the cache is disclosed. A method includes evicting a first memory line currently stored in the cache and storing a second memory line not currently stored in the cache in its place. While the first memory line is being evicted, such as by first being inserted into an eviction queue, the second memory line is temporarily stored in a buffer. The buffer may be a data transfer buffer (DTB). Upon eviction of the first memory line, the second memory line is moved from the buffer into the cache.

Abstract: This invention provides cyclic-bridged dyes, particularly cyclic-bridged cyanine dyes, of the general formula: In this formula, each dotted line represents carbon atoms necessary to form a fused substituted or unsubstituted aromatic ring; n=1-18; m=1-18, selected independently from n. X and Y are selected independently from the group consisting of S, O, N, CH2 and C(CH3)2; at least one of said R1 and R2 comprises a sulfonic acid or sulfonate group attached to the aromatic ring; and R3 and R4 are independently selected from the group consisting of carboxyl, activated carboxyl and methyl, wherein at least one of said R3 and R4 groups is carboxylate or activated carboxylate. Methods of making and using the cyclic-bridged dyes are also provided.

Abstract: This invention provides dye phosphoramidites, particularly phosphoramidites of cyanine and related dyes, of the general formula: In this formula, each dotted line represents carbon atoms necessary to form a fused substituted or unsubstituted aromatic ring; m is an integer from 1 to 18; Y and Z are independently selected from the group consisting of S, O, N, CH2 and C(CH3)2; R1 is an alkyl; (PAM) is a phosphoramidite group; X⊖ is a negative ion; and Q is or wherein n is 1, 2 or 3. Methods of making and using the dye phosphoramidites are also provided.

Abstract: Activating groups based on N-hydroxynaphthalimide, are disclosed herein. The activating groups can mediate the coupling of labeling moieties, such as biotin or cyanine dyes, to a variety of components, including chain terminators, nucleoside triphosphates, and oligonucleotides, which are used in nucleotide sequencing. From these activating groups, activated esters of the labeling moieties can be prepared. The activated esters react with a component, for example a derivatized nucleotide chain terminator, to give a labeled component. In additions, methods of the present invention provide for labeling a nucleoside triphosphate in organic media. The activating groups and methods of the present invention allow the activation and coupling reactions to occur at a much higher yield, compared with the prior art.

Abstract: Universal solid support oligonucleotide synthesis reagents, oligonucleotide synthesis processes, and reagents for cleaving oligonucleotides from solid supports are disclosed. Oligonucleotide synthesis reagents have the following general formula:SS--R.sup.6 --O--R.sup.3 Iwherein SS is a solid support; R.sup.6 is ##STR1## where R.sup.5 is hydrogen or alkyl and R.sup.4 is a phosphate protecting group; and R.sup.3 is a ring moiety having vicinal groups --XR.sup.1 and --YR.sup.2 wherein each of X and Y is independently selected from the group consisting of O, S and NH and one of R.sup.1 and R.sup.2 is a blocking moiety and the other is hydrogen or a hydroxy protecting group. Oligonucleotide cleaving reagents include methylamine and/or ammonium hydroxide and trimethylamine.

Abstract: Oxidizing compositions particularly for use in automated oligonucleotide synthesis containing a mixture of KI and I.sub.2 in solution, in equilibrium with KI.sub.3. One preferred composition contains 1.75% KI.sub.3 (providing 0.69% KI and 1.06% I.sub.2) in tetrahydrofuran/pyridine/water (93/5/2, v/v). These formulations enable synthesis of oligonucleotides of significantly higher quality than the currently employed formulation comprising 3% I.sub.2 in tetrahydrofuran/pyridine/water (74/21/2, v/v).