Some new constructions of orthogonal designs

In this paper we construct OD(4pqr(q+1); pqr, pqr, pqr, pqr, pqr+1, pqr+1, pqr+1, pqr+1) for each core order q ≡ 3(mod 4), r ≥ 0 or q = 1, p odd, p ≤ 21 and p ∈ {25, 49}, and COD(2qr(q + 1); qr, qr, qr+1, qr+1) for any prime power q ≡ 1 (mod 4) (including q = 1), r ≥ 0

Site- and sequence-selective ultrafast hydration of DNA

Water molecules in the DNA grooves are critical for maintaining structural integrity, conformational changes, and molecular recognition. Here we report studies of site- and sequence-specific hydration dynamics, using 2-aminopurine (Ap) as the intrinsic fluorescence probe and with femtosecond resolution. The dodecamer d[CGCA(Ap)ATTTGCG]2 was investigated, and we also examined the effect of a specific minor groove-binding drug, pentamidine, on hydration dynamics. Two time scales were observed: {approx}1 ps (bulk-like) and 10–12 ps (weakly bound type), consistent with layer hydration observed in proteins and DNA. However, for denatured DNA, the cosolvent condition of 40% formamide hydration is very different: it becomes that of bulk (in the presence of formamide). Well known electron transfer between Ap and nearby bases in stacked assemblies becomes inefficient in the single-stranded state. The rigidity of Ap in the single strands is significantly higher than that in bulk water and that attached to deoxyribose, suggesting a unique role for the dynamics of the phosphate-sugar-base in helix formation. The disparity in minor and major groove hydration is evident because of the site selection of Ap and in the time scale observed here (in the presence and absence of the drug), which is different by a factor of 2 from that observed in the minor groove–drug recognition

Construction of cubic homogeneous boolean bent functions

We prove that cubic homogeneous bent functions f : V2n → GF(2) exist for all n ≥ 3 except for n = 4

Designed Arginine-Rich RNA-Binding Peptides with Picomolar Affinity

Arginine-rich peptide motifs (ARMs) capable of binding unique RNA structures play critical roles in transcription, translation, RNA trafficking, and RNA packaging. Bacteriophage ARMs necessary for transcription antitermination bind to distinct boxB RNA hairpin sequences with a characteristic induced α-helical structure. Characterization of ARMs from lambdoid phages reveals that the dissociation constant of the P22 bacteriophage model−antitermination complex (P22_(N21)−P22boxB) is 200 ± 56 pM in free solution at physiologic concentrations of monovalent cation, significantly stronger than previously determined by gel mobility shift and polyacrylamide gel coelectophoresis, and 2 orders of magnitude stronger than the tightest known native ARM−RNA interaction at physiological salt. Here, we use a reciprocal design approach to enhance the binding affinity of two separate α-helical ARM−RNA interactions; one derived from the native λ phage antitermination complex and a second isolated using mRNA display selection experiments targeting boxB RNA

Thermodynamics of RNA Internal Loops with a Guanosine-Guanosine Pair Adjacent to Another Noncanonical Pair

Thermodynamic parameters measured by optical melting are reported for formation of RNA duplexes containing tandem noncanonical pairs with at least one guanosine-guanosine (GG) pair. For selected sequences, imino proton NMR provides evidence that the desired duplex forms and that the structure of a GG pair adjacent to a noncanonical pair depends on context. A GG pair next to a different noncanonical pair is more stable than expected from measurements of adjacent GG pairs. This is likely due to an unfavorable stacking interaction between adjacent GG pairs, where areas of high negative charge probably overlap. The results suggest a model where tandem noncanonical pairs closed by two GC pairs are assigned the following free energy increments at 37 °C:  0.8 kcal/mol for adjacent GG pairs, 1.0 kcal/mol for GG next to UU, and −0.3 kcal/mol for all others. These values are adjusted by 0.65 kcal/mol for each closing AU pair

Thermodynamics of RNA Internal Loops with a Guanosine-Guanosine Pair Adjacent to Another Noncanonical Pair

Thermodynamic parameters measured by optical melting are reported for formation of RNA duplexes containing tandem noncanonical pairs with at least one guanosine-guanosine (GG) pair. For selected sequences, imino proton NMR provides evidence that the desired duplex forms and that the structure of a GG pair adjacent to a noncanonical pair depends on context. A GG pair next to a different noncanonical pair is more stable than expected from measurements of adjacent GG pairs. This is likely due to an unfavorable stacking interaction between adjacent GG pairs, where areas of high negative charge probably overlap. The results suggest a model where tandem noncanonical pairs closed by two GC pairs are assigned the following free energy increments at 37 °C:  0.8 kcal/mol for adjacent GG pairs, 1.0 kcal/mol for GG next to UU, and −0.3 kcal/mol for all others. These values are adjusted by 0.65 kcal/mol for each closing AU pair

Amicable Orthogonal Designs of Order 8 for Complex Space-Time Block Codes

New amicable orthogonal designs AODs(8; 1; 1; 1; 2; 2; 2), AODs(8; 1; 1; 4; 1; 2; 2), AODs(8; 1; 2;2; 2; 2; 4), AODs(8; 1; 2; 2; 1; 2; 4), AODs(8; 1; 1; 2; 1; 2; 4), AODs(8; 1; 2; 4; 2; 2; 2), AODs(8; 1; 1; 4; 1; 1; 2; 2), AODs(8; 2; 2; 2; 2; 2; 2; 2; 2) and AODs(8; 1; 1; 1; 2; 1; 2; 2; 2) are found by applying a new theorem or by an exhaustive search. Also some previously undecided cases of amicable pairs are demonstrated to be non-existent after a complete search of the equivalence classes for orthogonal designs

Two complex orthogonal space-time codes for eight transmit antennas

Two new constructions of complex orthogonal space-time block codes of order 8 based on the theory of amicable orthogonal designs are presented and their performance compared with that of the standard code of order 8. These new codes are suitable for multi-modulation schemes where the performance can be sacrificed for a higher throughput