POSoligo software for in vitro gene synthesis.

Oligonucleotide synthesis is vital for molecular experiments. Bioinformatics has been employed to create various algorithmic tools for the in vitro synthesis of nucleotides. The main approach to synthesizing long-chain DNA molecules involves linking short-chain oligonucleotides through ligase chain reaction (LCR) and polymerase chain reaction (PCR). Short-chain DNA molecules have low mutation rates, while LCR requires complementary interfaces at both ends of the two nucleic acid molecules or may alter the conformation of the nucleotide chain, leading to termination of amplification. Therefore, molecular melting temperature, length, and specificity must be considered during experimental design. POSoligo is a specialized offline tool for nucleotide fragment synthesis. It optimizes the oligonucleotide length and specificity based on input single-stranded DNA, producing multiple contiguous long strands (COS) and short patch strands (POS) with complementary ends. This process ensures free 5'- and 3'-ends during oligonucleotide synthesis, preventing secondary structure formation and ensuring specific binding between COS and POS without relying on stabilizing the complementary strands based on Tm values. POSoligo was used to synthesize the linear RBD sequence of SARS-CoV-2 using only one DNA strand, several POSs for LCR ligation, and two pairs of primers for PCR amplification in a time- and cost-effective manner.

[Clinical analysis of lymphoblastic lymphoma/leukemia treated with Hyper-CVAD/MA regimen chemotherapy combined with haploidentical hematopoietic stem cell infusion].

This study was aimed to investigate the efficacy of Hyper-CVAD/MA regimen chemotherapy combined with haploidentical hematopoietic stem cell infusion for the treatment of lymphoblastic lymphoma/leukemia (LBL/ALL). Seven patients with LBL/ALL were treated in Second Artillery General Hospital from August 2009 to September 2012. All patients received programmed infusions of granulocyte-colony stimulating factor (G-CSF)-mobilized family related HLA-haploidentical donor peripheral blood hematopoietic stem cell (G-PBHSC) after each of cycle of Hyper-CVAD/MA regimen chemotherapy without graft-versus-host disease (GVHD) prophylaxis. A total of four cycles of therapy were planned. The interval between each cycle of treatment was 8 to 12 weeks. By April 2014, the median follow-up time was 41 (20-57) months. The results showed that the 7 patients totally received 30 cycles of treatment, and all patients achieved complete remission (CR). The patients were generally well-tolerated to therapy, and the most significant toxicities of grade 3 to 4 neutropenia and thrombocytopenia developed in nearly all of the patients after each course of the Hyper-CVAD/MA regimen. No GVHD was observed in any of the patients during treatment. Up to now, 5 patients were still alive, 2 patients were died of relapse. It is concluded that the combination of chemotherapy and programmed haploidentical G-PBHSC infusion is a promising approach to the treatment of LBL/ALL.

[Clinical investigation of refractory lymphoma with HLA-mismatched stem-cell microtransplantation].

OBJECTIVE: To explore the efficacy and safety of HLA-mismatched stem-cell microtransplantation in patients with refractory lymphoma. METHODS: This study included 10 patients with relapsing or refractory lymphoma at Department of Hematology, Second Artillery General Hospital from October 2009 to February 2012. All patients received programmed infusions of G-CSF-mobilized HLA-mismatched donor peripheral blood stem cell (G-PBSC) after each cycle of Hyper-CVAD/MA conditioning without graft-versus-host disease (GVHD) prophylaxis. RESULTS: A total of 31 cycles of microtransplantation were performed. Among them, 6 patients achieved a complete remission (CR) and 2 got partial remission (PR). And the overall response was 8/10. The occurrence of grades III-IV neutrocytopenia and thrombocytopenia was almost 100% after Hyper-CVAD/MA conditioning, but the median recovery times of neutrophils and platelets were 9 days and 14 days respectively because of programmed infusions of G-PBSCs. And 18 bouts of G-PBSC infusion related fever were observed. No GVHD was observed in any of them during treatment. Up to March 2013, 6 patients survived while another 4 died. The 1- and 3-year overall survival and disease-free survival rates were the same (60%). CONCLUSION: The novel therapy of microtransplantation may improve outcome and avoid GVHD in patients with relapsing or refractory lymphoma.